{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import sys\n", "import time\n", "\n", "import hbp_knowledge\n", "import pybel\n", "import pybel_jupyter\n", "from pybel.struct import remove_pathologies" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "3.7.2 (default, Jan 13 2019, 12:50:15) \n", "[Clang 10.0.0 (clang-1000.11.45.5)]\n" ] } ], "source": [ "print(sys.version)" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Thu Feb 21 16:33:08 2019\n" ] } ], "source": [ "print(time.asctime())" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "PyBEL Version: 0.13.2-dev\n", "PyBEL-Jupyter Version: 0.2.1-dev\n", "HBP Knowledge Version: 0.0.3\n" ] } ], "source": [ "print(f'PyBEL Version: {pybel.get_version()}')\n", "print(f'PyBEL-Jupyter Version: {pybel_jupyter.get_version()}')\n", "print(f'HBP Knowledge Version: {hbp_knowledge.VERSION}')" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [], "source": [ "graphs = hbp_knowledge.repository.get_graphs()" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [], "source": [ "proteostasis_graphs = {\n", " path: graph\n", " for path, graph in graphs.items()\n", " if 'proteostasis/' in path\n", "} " ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Proteostasis Subgraph v1.0.0\n", "Number of Nodes: 652\n", "Number of Edges: 1312\n", "Number of Citations: 5\n", "Number of Authors: 27\n", "Network Density: 3.09E-03\n", "Number of Components: 10\n", "Number of Warnings: 0\n" ] } ], "source": [ "proteostasis_graph = pybel.union(proteostasis_graphs.values())\n", "proteostasis_graph.name = 'Proteostasis Subgraph'\n", "proteostasis_graph.summarize()" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [], "source": [ "remove_pathologies(proteostasis_graph)" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "data": { "application/javascript": [ "function init_d3_force(d3, graph, chart, width, height, function_colors) {\n", " var focus_node = null;\n", " var highlight_node = null;\n", "\n", " // Highlight color variables\n", "\n", " // Highlight color of the node boundering\n", " const highlight_node_boundering = \"#4EB2D4\";\n", "\n", " // Highlight color of the edge\n", " const highlighted_link_color = \"#4EB2D4\";\n", "\n", " // Text highlight color\n", " const highlight_text = \"#4EB2D4\";\n", "\n", " // Size when zooming scale\n", " var size = d3.scalePow().exponent(1)\n", " .domain([1, 100])\n", " .range([8, 24]);\n", "\n", " // Simulation parameters\n", " const linkDistance = 100;\n", " const fCharge = -1000;\n", " const linkStrength = 0.7;\n", " const collideStrength = 1;\n", "\n", " // Simulation defined with variables\n", " var simulation = d3.forceSimulation()\n", " .force(\"link\", d3.forceLink()\n", " .distance(linkDistance)\n", " .strength(linkStrength)\n", " )\n", " .force(\"collide\", d3.forceCollide()\n", " .radius(function (d) {\n", " return d.r + 10\n", " })\n", " .strength(collideStrength)\n", " )\n", " .force(\"charge\", d3.forceManyBody()\n", " .strength(fCharge)\n", " )\n", " .force(\"center\", d3.forceCenter(width / 2, height / 2))\n", " .force(\"y\", d3.forceY(0))\n", " .force(\"x\", d3.forceX(0));\n", "\n", " // Pin down functionality\n", " var node_drag = d3.drag()\n", " .on(\"start\", dragstarted)\n", " .on(\"drag\", dragged)\n", " .on(\"end\", dragended);\n", "\n", " function dragstarted(d) {\n", " if (!d3.event.active) simulation.alphaTarget(0.3).restart();\n", " d.fx = d.x;\n", " d.fy = d.y;\n", " }\n", "\n", " function dragged(d) {\n", " d.fx = d3.event.x;\n", " d.fy = d3.event.y;\n", " }\n", "\n", " function dragended(d) {\n", " if (!d3.event.active) simulation.alphaTarget(0);\n", " }\n", "\n", " function releasenode(d) {\n", " d.fx = null;\n", " d.fy = null;\n", " }\n", "\n", " //END Pin down functionality\n", "\n", "\n", " /**\n", " * Gets the best name for a node object\n", " * @param {object} d object\n", " * @returns {str} canonical name of the node\n", " */\n", " function getCanonicalName(d) {\n", " if (d.name && !(d.variants || d.reactants || d.products || d.members)) {\n", " return d.name\n", " } else if (d.bel) {\n", " return d.bel\n", " } else {\n", " console.log('Undefined node: ' + d);\n", " return 'UNDEFINED'\n", " }\n", " }\n", "\n", " const color_circunferencia = \"black\";\n", " const default_link_color = \"#AAAAAA\";\n", " const nominal_base_node_size = 8;\n", "\n", " // Normal and highlighted stroke of the links (double the width of the link when highlighted)\n", " const nominal_stroke = 1.5;\n", "\n", " // Zoom variables\n", " const min_zoom = 0.1;\n", " const max_zoom = 10;\n", "\n", " var svg = d3.select(chart).append(\"svg\")\n", " .attr(\"width\", width)\n", " .attr(\"height\", height);\n", "\n", " // // Create definition for arrowhead.\n", " svg.append(\"defs\").append(\"marker\")\n", " .attr(\"id\", \"arrowhead\")\n", " .attr(\"viewBox\", \"0 -5 10 10\")\n", " .attr(\"refX\", 20)\n", " .attr(\"refY\", 0)\n", " .attr(\"markerUnits\", \"strokeWidth\")\n", " .attr(\"markerWidth\", 6)\n", " .attr(\"markerHeight\", 6)\n", " .attr(\"orient\", \"auto\")\n", " .append(\"path\")\n", " .attr(\"d\", \"M0,-5L10,0L0,5\");\n", "\n", " // // Create definition for stub.\n", " svg.append(\"defs\").append(\"marker\")\n", " .attr(\"id\", \"stub\")\n", " .attr(\"viewBox\", \"-1 -5 2 10\")\n", " .attr(\"refX\", 15)\n", " .attr(\"refY\", 0)\n", " .attr(\"markerUnits\", \"strokeWidth\")\n", " .attr(\"markerWidth\", 6)\n", " .attr(\"markerHeight\", 6)\n", " .attr(\"orient\", \"auto\")\n", " .append(\"path\")\n", " .attr(\"d\", \"M 0,0 m -1,-5 L 1,-5 L 1,5 L -1,5 Z\");\n", "\n", " // Background\n", " svg.append(\"rect\")\n", " .attr(\"width\", \"100%\")\n", " .attr(\"height\", \"100%\")\n", " .attr(\"fill\", \"#ffffff\")\n", " .style(\"pointer-events\", \"all\")\n", " // Zoom + panning functionality\n", " .call(d3.zoom()\n", " .scaleExtent([min_zoom, max_zoom])\n", " .on(\"zoom\", zoomed))\n", " .on(\"dblclick.zoom\", null);\n", "\n", "\n", " function zoomed() {\n", " g.attr(\"transform\", d3.event.transform);\n", " }\n", "\n", " // g = svg object where the graph will be appended\n", " var g = svg.append(\"g\");\n", "\n", " var linkedByIndex = {};\n", " graph.links.forEach(function (d) {\n", " linkedByIndex[d.source + \",\" + d.target] = true;\n", " });\n", "\n", " function isConnected(a, b) {\n", " return linkedByIndex[a.index + \",\" + b.index] || linkedByIndex[b.index + \",\" + a.index] || a.index == b.index;\n", " }\n", "\n", " function ticked() {\n", " link.attr(\"x1\", function (d) {\n", " return d.source.x;\n", " })\n", " .attr(\"y1\", function (d) {\n", " return d.source.y;\n", " })\n", " .attr(\"x2\", function (d) {\n", " return d.target.x;\n", " })\n", " .attr(\"y2\", function (d) {\n", " return d.target.y;\n", " });\n", "\n", " node\n", " .attr(\"transform\", function (d) {\n", " return \"translate(\" + d.x + \", \" + d.y + \")\";\n", " });\n", " }\n", "\n", "\n", " simulation\n", " .nodes(graph.nodes)\n", " .on(\"tick\", ticked);\n", "\n", " simulation.force(\"link\")\n", " .links(graph.links);\n", "\n", " // Definition of links nodes text...\n", "\n", " var link = g.selectAll(\".link\")\n", " .data(graph.links)\n", " .enter().append(\"line\")\n", " .style(\"stroke-width\", nominal_stroke)\n", " .style(\"stroke\", default_link_color)\n", " .style(\"stroke-dasharray\", function (d) {\n", " if (['decreases', 'directlyDecreases', 'increases', 'directlyIncreases', 'negativeCorrelation',\n", " 'positiveCorrelation'].indexOf(d.relation) >= 0) {\n", " return \"none\"\n", " } else {\n", " return \"4, 4\"\n", " }\n", " })\n", " .attr(\"marker-start\", function (d) {\n", " if ('positiveCorrelation' == d.relation) {\n", " return \"url(#arrowhead)\"\n", " }\n", " else if ('negativeCorrelation' == d.relation) {\n", " return \"url(#stub)\"\n", " }\n", " else {\n", " return \"\"\n", " }\n", " })\n", " .attr(\"marker-end\", function (d) {\n", " if (['increases', 'directlyIncreases', 'positiveCorrelation', 'isA', 'partOf'].indexOf(d.relation) >= 0) {\n", " return \"url(#arrowhead)\"\n", " } else if (['decreases', 'directlyDecreases', 'negativeCorrelation'].indexOf(d.relation) >= 0) {\n", " return \"url(#stub)\"\n", " } else {\n", " return \"\"\n", " }\n", " });\n", "\n", " var node = g.selectAll(\".nodes\")\n", " .data(graph.nodes)\n", " .enter().append(\"g\")\n", " .attr(\"class\", \"node\")\n", " // Next two lines -> Pin down functionality\n", " .on('dblclick', releasenode)\n", " .call(node_drag);\n", "\n", " var circle = node.append(\"path\")\n", " .attr(\"d\", d3.symbol()\n", " .size(function (d) {\n", " return Math.PI * Math.pow(size(d.size) || nominal_base_node_size, 2);\n", " })\n", " )\n", " .attr(\"class\", function (d) {\n", " return d.function\n", " })\n", " .style('fill', function (d) {\n", " return function_colors[d.function]\n", " })\n", " .style(\"stroke-width\", nominal_stroke)\n", " .style(\"stroke\", color_circunferencia);\n", "\n", " var text = node.append(\"text\")\n", " .attr(\"class\", \"node-name\")\n", " // .attr(\"id\", nodehashes[d])\n", " .attr(\"fill\", \"black\")\n", " .attr(\"dx\", 12)\n", " .attr(\"dy\", \".35em\")\n", " .text(function (d) {\n", " return getCanonicalName(d)\n", " });\n", "\n", " // Highlight on mouseenter and back to normal on mouseout\n", " node.on(\"mouseenter\", function (d) {\n", " set_highlight(d);\n", " })\n", " .on(\"mousedown\", function () {\n", " d3.event.stopPropagation();\n", " }).on(\"mouseout\", function () {\n", " exit_highlight();\n", " });\n", "\n", " function exit_highlight() {\n", " highlight_node = null;\n", " if (focus_node === null) {\n", " if (highlight_node_boundering != color_circunferencia) {\n", " circle.style(\"stroke\", color_circunferencia);\n", " text.style(\"fill\", \"black\");\n", " link.style(\"stroke\", default_link_color);\n", " }\n", " }\n", " }\n", "\n", " function set_highlight(d) {\n", " if (focus_node !== null) d = focus_node;\n", " highlight_node = d;\n", "\n", " if (highlight_node_boundering != color_circunferencia) {\n", " circle.style(\"stroke\", function (o) {\n", " return isConnected(d, o) ? highlight_node_boundering : color_circunferencia;\n", " });\n", " text.style(\"fill\", function (o) {\n", " return isConnected(d, o) ? highlight_text : \"black\";\n", " });\n", " link.style(\"stroke\", function (o) {\n", " return o.source.index == d.index || o.target.index == d.index ? highlighted_link_color : default_link_color;\n", " });\n", " }\n", " }\n", "\n", "\n", " // Freeze the graph when space is pressed\n", " function freezeGraph() {\n", " // Space button Triggers STOP\n", " if (d3.event.keyCode == 32) {\n", " simulation.stop();\n", " }\n", " }\n", "\n", " // Call freezeGraph when a key is pressed, freezeGraph checks whether this key is \"Space\" that triggers the freeze\n", " d3.select(window).on(\"keydown\", freezeGraph);\n", "}\n", "\n", "require.config({\n", " paths: {\n", " d3: '//cdnjs.cloudflare.com/ajax/libs/d3/4.5.0/d3.min'\n", " }\n", "});\n", "\n", "var elementInnerHTML = \"
\";\n", "\n", "element.append(elementInnerHTML);\n", "\n", "require(['d3'], function (d3) {\n", " return init_d3_force(d3, {\"directed\": true, \"graph\": {\"annotation_list\": {}, \"annotation_pattern\": {\"Species\": \"^\\\\d+$\"}, \"annotation_url\": {\"Anatomy\": \"https://arty.scai.fraunhofer.de/artifactory/bel/annotation/anatomy/anatomy-20170511.belanno\", \"Cell\": \"https://arty.scai.fraunhofer.de/artifactory/bel/annotation/cell/cell-20170511.belanno\", \"CellLine\": \"https://arty.scai.fraunhofer.de/artifactory/bel/annotation/cell-line/cell-line-20170511.belanno\", \"CellStructure\": \"https://arty.scai.fraunhofer.de/artifactory/bel/annotation/cell-structure/cell-structure-20170511.belanno\", \"Confidence\": \"https://arty.scai.fraunhofer.de/artifactory/bel/annotation/confidence/confidence-1.0.0.belanno\", \"Disease\": \"https://arty.scai.fraunhofer.de/artifactory/bel/annotation/disease/disease-20170511.belanno\", \"MeSHAnatomy\": \"https://arty.scai.fraunhofer.de/artifactory/bel/annotation/mesh-anatomy/mesh-anatomy-20170511.belanno\", \"MeSHDisease\": \"https://arty.scai.fraunhofer.de/artifactory/bel/annotation/mesh-diseases/mesh-diseases-20170511.belanno\", \"Subgraph\": \"https://arty.scai.fraunhofer.de/artifactory/bel/annotation/neurommsig/neurommsig-1.0.3.belanno\", \"TextLocation\": \"https://arty.scai.fraunhofer.de/artifactory/bel/annotation/text-location/text-location-1.0.1.belanno\"}, \"document_metadata\": {\"authors\": \"Esther Wollert\", \"contact\": \"charles.hoyt@scai.fraunhofer.de\", \"copyright\": \"Copyright © 2018 Fraunhofer Institute SCAI, All rights reserved.\", \"description\": \"\", \"licenses\": \"CC BY 4.0\", \"name\": \"Proteostasis Subgraph\", \"version\": \"1.0.0\"}, \"namespace_pattern\": {\"DBSNP\": \"rs[0-9]+\", \"PUBCHEM\": \"^\\\\d+$\", \"TAXONOMY\": \"^\\\\d+$\", \"UNIPROT\": \"^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\\\.\\\\d+)?$\"}, \"namespace_url\": {\"CHEBI\": \"https://raw.githubusercontent.com/pharmacome/terminology/b46b65c3da259b6e86026514dfececab7c22a11b/external/chebi-names.belns\", \"CTO\": \"https://arty.scai.fraunhofer.de/artifactory/bel/namespace/clinical-trial-ontology/clinical-trial-ontology-1.0.0.belns\", \"DO\": \"https://arty.scai.fraunhofer.de/artifactory/bel/namespace/disease-ontology/disease-ontology-20170725.belns\", \"DRUGBANK\": \"https://raw.githubusercontent.com/pharmacome/terminology/b46b65c3da259b6e86026514dfececab7c22a11b/external/drugbank-names.belns\", \"ECCODE\": \"https://raw.githubusercontent.com/pharmacome/terminology/b46b65c3da259b6e86026514dfececab7c22a11b/external/ec-code.belns\", \"FPLX\": \"https://raw.githubusercontent.com/sorgerlab/famplex/e8ae9926ff95266032cb74f77973c84939bffbeb/export/famplex.belns\", \"GO\": \"https://raw.githubusercontent.com/pharmacome/terminology/a5b84013a08880975ca84f40999e4404b14a97e2/external/go-names.belns\", \"HBP\": \"https://raw.githubusercontent.com/pharmacome/terminology/cf4d8bb88754f036b943b4d94ad96e103dcb7149/export/hbp-names.belns\", \"HGNC\": \"https://raw.githubusercontent.com/pharmacome/terminology/b46b65c3da259b6e86026514dfececab7c22a11b/external/hgnc-names.belns\", \"HGNCGENEFAMILY\": \"https://raw.githubusercontent.com/pharmacome/terminology/3074b85b858455d8eeb76cfcdef685ced19bbe11/external/hgnc.genefamily-names.belns\", \"HP\": \"https://arty.scai.fraunhofer.de/artifactory/bel/namespace/hp/hp-20171108.belns\", \"INTERPRO\": \"https://raw.githubusercontent.com/pharmacome/terminology/f2f993e599694ab5ce989cc39d789a499f75db99/external/interpro-names.belns\", \"MESH\": \"https://raw.githubusercontent.com/pharmacome/terminology/01c9daa61012b37dd0a1bc962521ba51a15b38f1/external/mesh-names.belns\", \"MGI\": \"https://raw.githubusercontent.com/pharmacome/terminology/f2f993e599694ab5ce989cc39d789a499f75db99/external/mgi-names.belns\", \"MIRBASE\": \"https://raw.githubusercontent.com/pharmacome/terminology/b46b65c3da259b6e86026514dfececab7c22a11b/external/mirbase-names.belns\", \"NCBIGENE\": \"https://raw.githubusercontent.com/pharmacome/terminology/b46b65c3da259b6e86026514dfececab7c22a11b/external/entrez.belns\", \"PFAM\": \"https://raw.githubusercontent.com/pharmacome/terminology/8ccfed235e418e4c8aa576f9a5ef0f838e794c7f/external/pfam-names.belns\", \"RGD\": \"https://raw.githubusercontent.com/pharmacome/terminology/f2f993e599694ab5ce989cc39d789a499f75db99/external/rgd-names.belns\"}, \"namespaces_uncached\": [], \"path\": \"proteostasis/brehme2014.bel\", \"pybel_version\": \"0.13.2-dev\"}, \"links\": [{\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Concomitant cleavage of APP by beta and gamma secretase at specific sites can result in fragments (Abeta1-40 or Abeta1-42) that can misfold and form extracellular fibrils.\", \"key\": \"4f2326c5ee18a22527873786a64d2e80a4226644d9a9665e5374d10ddb1567e94cffd680e20b4660291498dc47e789c7337e45ffc326ac9600382982bd62e752\", \"line\": 666, \"relation\": \"increases\", \"source\": 4, \"target\": 34}, {\"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"The ATP-dependent chaperones are comprised of the 5 HSP90s, 17 HSP70s, 14 HSP60s, 6 ER-specific, and 8 MITO-specific Hsp100/AAA+ ATPases, respectively.\", \"key\": \"e16a4ad53ea0a6726cc9c0d9c456acd748dcc4ca052b6f5d927e5ee0bb826240ba80768d2dc21ffd00d0ce4cb0e5de070cd42f58afbb0e36d0c2b693a91d392e\", \"line\": 87, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"association\", \"source\": 10, \"target\": 360}, {\"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"The ATP-dependent chaperones are comprised of the 5 HSP90s, 17 HSP70s, 14 HSP60s, 6 ER-specific, and 8 MITO-specific Hsp100/AAA+ ATPases, respectively.\", \"key\": \"86bfeeece2bca97bf63b174d41e49c57bb9fe8e6a456960c12cd4ba149dff34f09114b638b90facb19b52e2e00bbd1fed91b75e009e236c3bcd5794bb7f349ba\", \"line\": 88, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"association\", \"source\": 10, \"target\": 361}, {\"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"The ATP-dependent chaperones are comprised of the 5 HSP90s, 17 HSP70s, 14 HSP60s, 6 ER-specific, and 8 MITO-specific Hsp100/AAA+ ATPases, respectively.\", \"key\": \"abd0c930b954363134e575e69bf251fda8449b3ba653a2e700e2fac83db0e7d964533ea0c6179329b777a27ada8303610346e64702757e70f03a55fa5af8a24b\", \"line\": 89, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"association\", \"source\": 10, \"target\": 458}, {\"citation\": {\"authors\": [\"Kleiger G\", \"Mayor T\"], \"date\": \"2014-06-01\", \"first\": \"Kleiger G\", \"last\": \"Mayor T\", \"name\": \"Trends in cell biology\", \"pages\": \"352-9\", \"reference\": \"24457024\", \"title\": \"Perilous journey: a tour of the ubiquitin-proteasome system.\", \"type\": \"PubMed\", \"volume\": \"24\"}, \"evidence\": \"Another key early finding was that the cleavage of the ubiquitin chain from the substrate was ATP-dependent and was coupled to the translocation of the protein substrate into the 20S core\", \"key\": \"5ef77aaebbf96e346bd843643f9d2da4bd6ee8231b1059c2d6888bd054b93830da26ed6f9129d7bc804698eb019f7128dd1886f0bb93385777b41a2fc709aefc\", \"line\": 282, \"relation\": \"decreases\", \"source\": 10, \"target\": 178}, {\"citation\": {\"authors\": [\"Kleiger G\", \"Mayor T\"], \"date\": \"2014-06-01\", \"first\": \"Kleiger G\", \"last\": \"Mayor T\", \"name\": \"Trends in cell biology\", \"pages\": \"352-9\", \"reference\": \"24457024\", \"title\": \"Perilous journey: a tour of the ubiquitin-proteasome system.\", \"type\": \"PubMed\", \"volume\": \"24\"}, \"evidence\": \"Another key early finding was that the cleavage of the ubiquitin chain from the substrate was ATP-dependent and was coupled to the translocation of the protein substrate into the 20S core\", \"key\": \"db4ac17a482200bd98637e96c0c4439a5028d80ab73beb44ba225abd4b0772d3ecf070bc2ce8d5fab628e1f5a69e8f9ecc27157feb8432f10ec9c71ad7b0410f\", \"line\": 283, \"object\": {\"effect\": {\"fromLoc\": {\"name\": \"cytosol\", \"namespace\": \"GO\"}, \"toLoc\": {\"name\": \"20 S Proteasome\", \"namespace\": \"HBP\"}}, \"modifier\": \"Translocation\"}, \"relation\": \"increases\", \"source\": 10, \"target\": 61}, {\"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \"Proteome fidelity is maintained by the protein homeostasis (proteostasis) network (PN), a multi-compartmental system that coordinatesprotein synthesis, folding, disaggregation, and degradation (1).\", \"key\": \"06ca84e0c9005f672d726671ac51908c9363099d804795cd2235244e005b9abf3949dcf9ff1c9f10fa8cb5a0ff83092999cb502bc27e1e3fe9b065e1db7888e6\", \"line\": 82, \"relation\": \"association\", \"source\": 106, \"target\": 133}, {\"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi 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\"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"Ranked by decreasing median aging correlation, the induction of sHSPs and TPR genes consistently ranked high and the HSP60s, HSP40s, and HSP70s were consistently repressed.\", \"key\": \"d7a2e03dc4920d68b2f3a1f31679198abe16c6d874a50707853e3059ef0e8aadabd0089ee20e247afcf51f86193643fca341e83235b470671ca9d012b0309a10\", \"line\": 110, \"relation\": \"increases\", \"source\": 147, \"target\": 566}, {\"annotations\": {\"MeSHDisease\": {\"Alzheimer Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome 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Furthermore, 62 chaperone genes, including several small HSPs, were found to be significantly induced, likely as a result of the cellular response to accumulating protein damage with age (113).\", \"key\": \"ad38cfb43a22b54516bde3c30925ee281181b426202aec6a7fa0bf0825e479d420e827b1dba46c65ed563840cff15c56b34f1b6a2dc42c6e44c812d5835cdc21\", \"line\": 315, \"relation\": \"increases\", \"source\": 147, \"target\": 362}, {\"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"Ranked by decreasing median aging correlation, the induction of sHSPs and TPR genes consistently ranked high and the HSP60s, HSP40s, and HSP70s were consistently repressed.\", \"key\": \"0d6de566a28638f93d6a206aee7e47432749432b0dbda0f73dc559f21a6476c14a43b8e5762897c532572507cc6b2f2dfd7d66ea8645f87838fa33a6bfc44753\", \"line\": 111, \"relation\": \"decreases\", \"source\": 147, \"target\": 458}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"For example, concordantly aggravated expression pat- terns for the aging-induced genes HSPA2 (HSP70) and DNAJB2 (HSP40) and the aging-repressed HSPA12A (HSP70) and TOMM70A (TPR) were observed in brain biopsies from AD, HD, and PD patients (Figure 2C).\", \"key\": \"a9952d574beae00db14141ea019a018baa88e0180a5479ccb227c48e168d2e8ba92f90834680728186b14d388f0f571d010b2f15a46aa84a4481deb16f7512e5\", \"line\": 138, \"relation\": \"increases\", \"source\": 147, \"target\": 451}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"For example, concordantly aggravated expression pat- terns for the aging-induced genes HSPA2 (HSP70) and DNAJB2 (HSP40) and the aging-repressed HSPA12A (HSP70) and TOMM70A (TPR) were observed in brain biopsies from AD, HD, and PD patients (Figure 2C).\", \"key\": \"b8621f342fbcf40bf9449d09ccd6c0d5d3fd3642f3b5510094fba59ac6c349915c05e43a1717186f9a02ef508fddfa0f968552f57ef89a24ed251eb5b90c2dc5\", \"line\": 139, \"relation\": \"increases\", \"source\": 147, \"target\": 423}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"For example, concordantly aggravated expression pat- terns for the aging-induced genes HSPA2 (HSP70) and DNAJB2 (HSP40) and the aging-repressed HSPA12A (HSP70) and TOMM70A (TPR) were observed in brain biopsies from AD, HD, and PD patients (Figure 2C).\", \"key\": \"0840c533cd69b0ed395e3affc6e0dd059ab60b84bd1e43821c8f5134d513e08e6a668bf2c6be737b7c61db78d13d55043cf72365df9012a0ead025cb7c187f84\", \"line\": 140, \"relation\": \"decreases\", \"source\": 147, \"target\": 447}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"For example, concordantly aggravated expression pat- terns for the aging-induced genes HSPA2 (HSP70) and DNAJB2 (HSP40) and the aging-repressed HSPA12A (HSP70) and TOMM70A (TPR) were observed in brain biopsies from AD, HD, and PD patients (Figure 2C).\", \"key\": \"cee4264242a512bbca30494cd8c3b232b3c729ac09c150d390450fc18602e63d3c7e9c40f0bbe2599502d66c9549326fe31267267f5dfc9a3dc58a6810cc6d6d\", \"line\": 141, \"relation\": \"decreases\", \"source\": 147, \"target\": 564}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"Four genes that are significantly repressed both in AD and HD (HSP90AB1, HSPA8, HSPA14, and TCP1) are also repressed in aging (Figure 6B).\", \"key\": \"c94d54ff2dfe89f47529d5a0c614f4e4157226110007f636dbc038cacd3c8a9f48e25881e00ebe6fd1e681d0bab29c576272fad6c1006926e51b2bf8a5f5737e\", \"line\": 192, \"relation\": \"decreases\", \"source\": 147, \"target\": 446}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"Four genes that are significantly repressed both in AD and HD (HSP90AB1, HSPA8, HSPA14, and TCP1) are also repressed in aging (Figure 6B).\", \"key\": \"ef79f937f80c044832e7612a1e7c22dd9936d5c875c1440b5a6e568658aecaee766d146bc24f7cec4d6e698f4d576bccf94a88719986daa311b076d383d87404\", \"line\": 193, \"relation\": \"decreases\", \"source\": 147, \"target\": 454}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"Four genes that are significantly repressed both in AD and HD (HSP90AB1, HSPA8, HSPA14, and TCP1) are also repressed in aging (Figure 6B).\", \"key\": \"1ce0c1c4c78432cac72871381447dc6d9dee276009069181af7e85767fa6af3aa32e3121a50c2787c0f1b6dd62735878a61b0b4cddbd316a2d5b353ed1d24010\", \"line\": 194, \"relation\": \"decreases\", \"source\": 147, \"target\": 448}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"Four genes that are significantly repressed both in AD and HD (HSP90AB1, HSPA8, HSPA14, and TCP1) are also repressed in aging (Figure 6B).\", \"key\": \"41be69ccb70f0032928f350e2f63ad466cec4198a26880fbdbba40029354e4bc91c42a1fe548e3f7c5c3c13e342be4873798370297e0ee86ed9937757071a027\", \"line\": 195, \"relation\": \"decreases\", \"source\": 147, \"target\": 561}, {\"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \" Furthermore, the activity of the PN can be altered permanently or transiently by development and aging, alterations in physiology, or exposure to environmental stress (1).\", \"key\": \"467da8ad5e7a27aa808bb09249e830a29060df4e751a9d868b542e5755a9a8124cce770facc10e85c384769bb181923c7768ed75de1b67b3b129902991425608\", \"line\": 90, \"relation\": \"regulates\", \"source\": 147, \"target\": 133}, {\"annotations\": {\"Cell\": {\"motor neuron\": true}}, \"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \"Additionally, an investigation of chaperone and cochaperone gene expression in young (36±4 years of age) and aged (73 ±4 years of age) human brain tissue revealed that of 332 genes examined, 101 are significantly repressed with age, including HSP70, HSP40, HSP90, and TRiC genes (113). Furthermore, 62 chaperone genes, including several small HSPs, were found to be significantly induced, likely as a result of the cellular response to accumulating protein damage with age (113).\", \"key\": \"d478cb7b2c9a695b62d7f610bc9489d7c05dc4f9ddab6073993bc20e80f22fa69f97df9e55c9e940ecd76340ff8f8cbdf7eceb71034768a98d2f57294f2f7ad9\", \"line\": 313, \"relation\": \"decreases\", \"source\": 147, \"target\": 360}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"This functional screen identified 18 genes (Figure 3D), corresponding to ten ATP-dependent chaperones, HSC70 (hsp-1), HSP90 (daf-21), and eight subunits of the CCT/TRiC chaperonin complex; the co-chaperones, HSP40 (dnj-12) and CDC37 (cdc-37); and the TPR-domain pro- tein STI1 that upon knockdown significantly enhanced A b 42 pro- teotoxicity (Figure 3D).\", \"key\": \"e2900e7a7712c7cfeb757049b10e890c572762aec764cbbc9e7e8c7a40ab45b1b333318808d68a1dca3ac79c3447d6878aa2a0619ed68c87d69235f32eb191f6\", \"line\": 152, \"relation\": \"decreases\", \"source\": 357, \"target\": 4}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"These included all subunits of the CCT/TRiC complex (except CCT5); HSP40 and HSP70 family members DNAJA1 (HDJ-2), DNAJA4, HSPA8 (HSC70), and HSPA14 (Figures 5B and 5C); and the TPR-domain APC/C subunits CDC23 and CDC27 that, upon knockdown, led to significantly elevated aggregation (Figure S5B).\", \"key\": \"08b814872bf8157eb5680402205108d550925158409ebe4c6566c18e8dd90c274ba986bc1550352b887a3eecfff673a68e9df8245bc64469c8b2dfa9a4692d1f\", \"line\": 172, \"relation\": \"increases\", \"source\": 357, \"target\": 35}, {\"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \" TRiC is essential for proper posttranslational folding of the cytoskeletal components actin and tubulin and is therefore essential for cell structure, division, and cargo delivery (11).\", \"key\": \"c7c81abb3f5513941e4b1aa48950a8a48028f40cc8444e2eb7dbff6c6f9c3962c5bc4e56435990652c44ce7c91df3aa9c9904a21549efa55400d5c2a24fdc904\", \"line\": 130, \"relation\": \"association\", \"source\": 357, \"target\": 43}, {\"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \" TRiC is essential for proper posttranslational folding of the cytoskeletal components actin and tubulin and is therefore essential for cell structure, division, and cargo delivery (11).\", \"key\": \"fcfd568bcacefbf0591a9fa1794c5c5fd5c6501ae3cbbd4d4e4d6a7654833f8d2a28c4dc99baa3baa68540dd7b458ac5351ccd1bdd414ea41d6554b1bc6833a9\", \"line\": 131, \"relation\": \"association\", \"source\": 357, \"target\": 82}, {\"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \" TRiC is essential for proper posttranslational folding of the cytoskeletal components actin and tubulin and is therefore essential for cell structure, division, and cargo delivery (11).\", \"key\": \"c00060f815267532b7bf811b7a55f2d45f30318e81cc173faca0777fd20c453dc107b1fa95ee08c6278e37d93ed564202eccf0829f301d29cdece149297fc0fb\", \"line\": 132, \"relation\": \"association\", \"source\": 357, \"target\": 94}, {\"annotations\": {\"Cell\": {\"motor neuron\": true}}, \"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \"HSF1A suppresses toxicity in cell and tissue culture models of HD and SCA-3/MJD and appears to activate HSF1 by impairing the activity of TRiC, a recently discovered negative regulator of HSF1.\", \"key\": \"a9a44cf30b4b3e911a50c9f697cb391a96be66b59589c3750beb27fac2a117819996eb8daf10b9915c748d9fcfca6ab60772e0bd850ba214947b792b962d9abd\", \"line\": 347, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 357, \"target\": 444}, {\"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"The ATP-dependent chaperones are comprised of the 5 HSP90s, 17 HSP70s, 14 HSP60s, 6 ER-specific, and 8 MITO-specific Hsp100/AAA+ ATPases, respectively.\", \"key\": \"7e02a3d6056c35aa855e52fb6c96c3d0a19144fecdece19e4738cf2e4c3b8c9f1bac6b74bb595719e5d1ab2339b4a1ed6262c45d7b40a3e24f062b7eecd8ea1d\", \"line\": 87, \"relation\": \"association\", \"source\": 360, \"subject\": {\"modifier\": \"Activity\"}, \"target\": 10}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"This functional screen identified 18 genes (Figure 3D), corresponding to ten ATP-dependent chaperones, HSC70 (hsp-1), HSP90 (daf-21), and eight subunits of the CCT/TRiC chaperonin complex; the co-chaperones, HSP40 (dnj-12) and CDC37 (cdc-37); and the TPR-domain pro- tein STI1 that upon knockdown significantly enhanced A b 42 pro- teotoxicity (Figure 3D).\", \"key\": \"3026c41bfc95808bd2a1319c8c19b7f32dbb4bd6e6645bfd31ea9f0334a6ccf162b251134a18f1f161610963e518efe2538dc4acc10190fb49e4b89e9d2f705c\", \"line\": 151, \"relation\": \"decreases\", \"source\": 360, \"target\": 4}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \" Knockdown of daf-21 (HSP90) or hsp-1 (HSC70) led to increased paralysis in 45% and 44% of day 6 animals, respectively, and knockdown of TPR co-chaper- ones tpr-1 and dnj-12 resulted in 70% impairment (Figure S4D).\", \"key\": \"ced04efdb335c62b8415ace3144e8fa06c0a92428ce947060baf3fb04f78963f92a3676abd944c3c466ed4cbcfe749b62912d27d760c80ca11037994f6ecc0df\", \"line\": 161, \"relation\": \"increases\", \"source\": 360, \"target\": 106}, {\"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \" As such, HSP70 and HSP90 are central to the process of triaging proteins for refolding or elimination.\", \"key\": \"9d0448cbcbece6dd98fb1a93cac966e9f34ee799f934a6360620dbd181320b140dfb8f9619059ab6f85bfac1dc79e7b31007828974400b8307c97bfceec9debe\", \"line\": 111, \"relation\": \"regulates\", \"source\": 360, \"target\": 106}, {\"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \"Molecular chaperones are central to the function of the PN and can be broadly grouped into the HSP70, HSP90, DNAJ/HSP40, chaperonin/HSP60, and small HSP (sHSP) families (10, 11).\", \"key\": \"0568fe2ff61c8accd758891078ea2bdeb5214cbd049eeb932bb0198224f48caf34b8407c9324b6c1e8677152b080ea08e45c66abb6ef2c33f83e329d86d6f7b3\", \"line\": 97, \"relation\": \"isA\", \"source\": 360, \"target\": 49}, {\"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \" As such, HSP70 and HSP90 are central to the process of triaging proteins for refolding or elimination.\", \"key\": \"1daeeea7ec8f3b23fa8814014af5233408556a60e097e461ea5e66b5c59a3faa27f17d49c422fb05a2153988bb6fec639765abda2d8eb57353b42677352393e7\", \"line\": 112, \"relation\": \"regulates\", \"source\": 360, \"target\": 148}, {\"annotations\": {\"Cell\": {\"motor neuron\": true}}, \"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \"One strategy is to directly activate HSF1, thereby increasing the expression of multiple molecular chaperones simultaneously. This approach has been traditionally achieved by inhibition of HSP90 with compounds that bind the N-terminal ATP-binding pocket, such as radicicol, geldanamycin, or 17-AAG (64, 132–134). \", \"key\": \"d038c69f6e6fc34e178e553cdbb4a01973b7dc4dfa10d3b9d1ac8502ff5221e446852c96b9087e6abfb92796be9ae1f80800c99d87b071bfee163a5d35ea5091\", \"line\": 333, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 360, \"subject\": {\"modifier\": \"Activity\"}, \"target\": 444}, {\"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"The ATP-dependent chaperones are comprised of the 5 HSP90s, 17 HSP70s, 14 HSP60s, 6 ER-specific, and 8 MITO-specific Hsp100/AAA+ ATPases, respectively.\", \"key\": \"f5fd78850c54f760afadca0bb1bf49d16beab03c51203ce124e64351e7061f8e739246dad57882eb95cacae14001242d7008aa2260d5cb86ac3a98f94a36ec5e\", \"line\": 88, \"relation\": \"association\", \"source\": 361, \"subject\": {\"modifier\": \"Activity\"}, \"target\": 10}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"The affinity of the polyglutamine fragment to Parkin was increased by Hsp70, in agreement with the hypothesis that molecular chaperones may play a role in the recruitment of misfolded proteins to the conjugation machinery (see, for example, Bercovich et al., 1997).\", \"key\": \"50c27270a4817c689e3d0b0ebcf27cf3f52ed213e3924defc9198d36b7ec3d27b2ab749902ffd2cd5d977d5eac902678a8d958a7b6579aab73009074064412c1\", \"line\": 450, \"relation\": \"increases\", \"source\": 361, \"target\": 215}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Overexpression of the chaperone HSP70 has been found to reduce aggregate formation and death in nonneuronal cultured cells expressing mutant SOD1 (Bruening et al.,1999).\", \"key\": 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80}, {\"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \"Molecular chaperones are central to the function of the PN and can be broadly grouped into the HSP70, HSP90, DNAJ/HSP40, chaperonin/HSP60, and small HSP (sHSP) families (10, 11).\", \"key\": \"851c8774c01ed2831e3b8655c5c4de286606cf349178beed0db574d9235b9c0f6f90197bc07eae042471c7596a178eef09ffd2085d1d0a3c2c2138825fed06a3\", \"line\": 96, \"relation\": \"isA\", \"source\": 361, \"target\": 49}, {\"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \" As such, HSP70 and HSP90 are central to the process of triaging proteins for refolding or elimination.\", \"key\": \"3e8efd73e8b6ef94f564e0d554217689bad28e08953a1ec0e3e7c46b6ef177023b4494f34698e87a85916e4cba1e0e9cb0424b9a4d4f360b769fcd1417ba5cee\", \"line\": 109, \"relation\": \"regulates\", \"source\": 361, \"target\": 106}, {\"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \" As such, HSP70 and HSP90 are central to the process of triaging proteins for refolding or elimination.\", \"key\": 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{\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"These included all subunits of the CCT/TRiC complex (except CCT5); HSP40 and HSP70 family members DNAJA1 (HDJ-2), DNAJA4, HSPA8 (HSC70), and HSPA14 (Figures 5B and 5C); and the TPR-domain APC/C subunits CDC23 and CDC27 that, upon knockdown, led to significantly elevated aggregation (Figure S5B).\", \"key\": \"6d5b0510b3c31a4b14b6620b209a285cb1e8f7bccb428cf9a00451fcf50dc8782627c6710235bced5996c39e977dcbf3e164f0e7d52f8fdc95e7e44c16ed7c60\", \"line\": 173, \"relation\": \"causesNoChange\", \"source\": 400, \"target\": 35}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"These included all subunits of the CCT/TRiC complex (except CCT5); HSP40 and HSP70 family members DNAJA1 (HDJ-2), DNAJA4, HSPA8 (HSC70), and HSPA14 (Figures 5B and 5C); and the TPR-domain APC/C subunits CDC23 and CDC27 that, upon knockdown, led to significantly elevated aggregation (Figure S5B).\", \"key\": \"1e08086ebf57b46f9f4e7ba6b4f68f681ba0fe89fc05d920dba29f068dc50302f0addf89f7f2a1010b43ff30a7f973800dd195e60272c4237134a4430bcb152f\", \"line\": 178, \"relation\": \"increases\", \"source\": 401, \"target\": 35}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"These included all subunits of the CCT/TRiC complex (except CCT5); HSP40 and HSP70 family members DNAJA1 (HDJ-2), DNAJA4, HSPA8 (HSC70), and HSPA14 (Figures 5B and 5C); and the TPR-domain APC/C subunits CDC23 and CDC27 that, upon knockdown, led to significantly elevated aggregation (Figure S5B).\", \"key\": \"b9cbcfd3730f1828baba14c70955d44a58a6e87456964ea63d07585e8884fcf2cddd1539f9bb2acaf25642029f286420dd201d3e20420c87bc87205661895d89\", \"line\": 179, \"relation\": \"increases\", \"source\": 402, \"target\": 35}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"This functional screen identified 18 genes (Figure 3D), corresponding to ten ATP-dependent chaperones, HSC70 (hsp-1), HSP90 (daf-21), and eight subunits of the CCT/TRiC chaperonin complex; the co-chaperones, HSP40 (dnj-12) and CDC37 (cdc-37); and the TPR-domain pro- tein STI1 that upon knockdown significantly enhanced A b 42 pro- teotoxicity (Figure 3D).\", \"key\": \"3cfd4fa8c1e2f93c362c932d6d7bc84f566928ec55ab6389efb650d0b57a8f8160c5e4af82cef2bbc221b309284b3ebdb86d76ca7fd38ae8db9b8b3acfc68650\", \"line\": 153, \"relation\": \"decreases\", \"source\": 420, \"target\": 4}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \" Knockdown of daf-21 (HSP90) or hsp-1 (HSC70) led to increased paralysis in 45% and 44% of day 6 animals, respectively, and knockdown of TPR co-chaper- ones tpr-1 and dnj-12 resulted in 70% impairment (Figure S4D).\", \"key\": \"1ccaba662ec7eba564233f33fb915e30320e2f704b3358327f41b30c17638342c70f0303cc2e17a661b09cb578cb7f903fbd458e0e787e88410b4cc6bd7b76b9\", \"line\": 163, \"relation\": \"increases\", \"source\": 420, \"target\": 106}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"These included all subunits of the CCT/TRiC complex (except CCT5); HSP40 and HSP70 family members DNAJA1 (HDJ-2), DNAJA4, HSPA8 (HSC70), and HSPA14 (Figures 5B and 5C); and the TPR-domain APC/C subunits CDC23 and CDC27 that, upon knockdown, led to significantly elevated aggregation (Figure S5B).\", \"key\": \"271092916f87bbf6a6fcf272ca3c669bff4c7afd4e9d8326bbb2e57315b36cf87652c6bc13e18fc5cfc13ea1d75cb692cae2c6a59f72d551dc18c9bf48796293\", \"line\": 174, \"relation\": \"increases\", \"source\": 420, \"target\": 35}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"These included all subunits of the CCT/TRiC complex (except CCT5); HSP40 and HSP70 family members DNAJA1 (HDJ-2), DNAJA4, HSPA8 (HSC70), and HSPA14 (Figures 5B and 5C); and the TPR-domain APC/C subunits CDC23 and CDC27 that, upon knockdown, led to significantly elevated aggregation (Figure S5B).\", \"key\": \"ba25840e8490594e6f63b26be7bcc137947b3ac3b10fc34bbdd0e3574d40aab19bda6c000e32274ad298a44fe6adb784e7ce92eb991389cae6fd3bfa9e3720e6\", \"line\": 175, \"relation\": \"increases\", \"source\": 421, \"target\": 35}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": \"Lindquist S\", \"name\": \"Cell\", \"pages\": \"434-448\", \"reference\": \"25036637\", \"title\": \"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.\", \"type\": \"PubMed\", \"volume\": \"158\"}, \"evidence\": \"Hsp90beta interacted particularly strongly with kinases (Figure 5B, filled blue circles), whereas the transcription factors p53 and HSF1 were among the most Hsp70-biased interactors (Figure 5B,green circles)\", \"key\": \"d71bb5c83877d6cb86b64119612995d0fad09ca56a79c6ff30c0f18ecb25ae9a562727590a6acf5357e188a2f52231ff120c2eaae51a98944aff3e816db552ce\", \"line\": 327, \"relation\": \"directlyIncreases\", \"source\": 446, \"target\": 176}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"These included all subunits of the CCT/TRiC complex (except CCT5); HSP40 and HSP70 family members DNAJA1 (HDJ-2), DNAJA4, HSPA8 (HSC70), and HSPA14 (Figures 5B and 5C); and the TPR-domain APC/C subunits CDC23 and CDC27 that, upon knockdown, led to significantly elevated aggregation (Figure S5B).\", \"key\": \"d868b0807f7f5dfb7ef53846db3bbb0cebaff0539235e1378c01997585cde4c3cb6508cf688aa735c99aaed9a842f774ff9be194a8cf3b4c0d49e6795e8ffe1f\", \"line\": 177, \"relation\": \"increases\", \"source\": 448, \"target\": 35}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"This functional screen identified 18 genes (Figure 3D), corresponding to ten ATP-dependent chaperones, HSC70 (hsp-1), HSP90 (daf-21), and eight subunits of the CCT/TRiC chaperonin complex; the co-chaperones, HSP40 (dnj-12) and CDC37 (cdc-37); and the TPR-domain pro- tein STI1 that upon knockdown significantly enhanced A b 42 pro- teotoxicity (Figure 3D).\", \"key\": \"fe81059f40ebd01f914958ff5bfe8d58154a42c99a902912a59729bf027b3a8db6524ed65a255f76da3444f99481a2dca62ab6b9ab5fd4446e0cb6d7611dd2d1\", \"line\": 150, \"relation\": \"decreases\", \"source\": 454, \"target\": 4}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \" Knockdown of daf-21 (HSP90) or hsp-1 (HSC70) led to increased paralysis in 45% and 44% of day 6 animals, respectively, and knockdown of TPR co-chaper- ones tpr-1 and dnj-12 resulted in 70% impairment (Figure S4D).\", \"key\": \"fba43b75c4e915e13e24b02879cc75831d20effb878a9ca8f845ca4eafd61f4182bf29c330d8af2f48500d2fd2a827b088d8e9c81eb4fc506060352d204d09e5\", \"line\": 162, \"relation\": \"increases\", \"source\": 454, \"target\": 106}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"These included all subunits of the CCT/TRiC complex (except CCT5); HSP40 and HSP70 family members DNAJA1 (HDJ-2), DNAJA4, HSPA8 (HSC70), and HSPA14 (Figures 5B and 5C); and the TPR-domain APC/C subunits CDC23 and CDC27 that, upon knockdown, led to significantly elevated aggregation (Figure S5B).\", \"key\": \"e2e72c755986ed5d85f9f0601fd25ab1038e8cfdba8be8d9ced3aaa39e4096f2734583617756aaca8bd237d6479d968da5be1841b1e336c072643db399e83385\", \"line\": 176, \"relation\": \"increases\", \"source\": 454, \"target\": 35}, {\"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"The ATP-dependent chaperones are comprised of the 5 HSP90s, 17 HSP70s, 14 HSP60s, 6 ER-specific, and 8 MITO-specific Hsp100/AAA+ ATPases, respectively.\", \"key\": \"64229570a5cc58d069d4c681074b93d7efe2e560c65b0d7e9f0bd29211e158a8e106bebb1bd3e6dc17f67374c9502855c6d025eea38aea177896f1cc1ff6ce31\", \"line\": 89, \"relation\": \"association\", \"source\": 458, \"subject\": {\"modifier\": \"Activity\"}, \"target\": 10}, {\"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \"Molecular chaperones are central to the function of the PN and can be broadly grouped into the HSP70, HSP90, DNAJ/HSP40, chaperonin/HSP60, and small HSP (sHSP) families (10, 11).\", \"key\": \"d0a6f0180426b905549946a303324277c36d142714851547b7b7c52a6d8b2277e8b7f6a72df4baeddfaee63be33cedf6c6ebc70d90520080a6f02d609cece147\", \"line\": 99, \"relation\": \"isA\", \"source\": 458, \"target\": 49}, {\"annotations\": {\"MeSHAnatomy\": {\"Mitochondria\": true}}, \"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \" HSP60 is essential for maturation and maintenance of the mitochondrial proteome and is therefore intimately linked to energy production.\", \"key\": \"c2603fa4245c9166d1e077bd79cb680dba594a62572f055c4eced76e5c4da7c77dd730ab5b3278fa1d61abfcd109135276600b9711af645a78473ba853778812\", \"line\": 123, \"relation\": \"increases\", \"source\": 458, \"target\": 133}, {\"annotations\": {\"MeSHAnatomy\": {\"Mitochondria\": true}}, \"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \" HSP60 is essential for maturation and maintenance of the mitochondrial proteome and is therefore intimately linked to energy production.\", \"key\": \"013a36db042a1285aa8758480491d47992fe53e36cd84bd790c5583011549f54273c881e0820a5a594086643bdb51941c86d2fc5bfcd4eb470c5ad9d8808d635\", \"line\": 124, \"relation\": \"association\", \"source\": 458, \"target\": 137}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \"This functional screen identified 18 genes (Figure 3D), corresponding to ten ATP-dependent chaperones, HSC70 (hsp-1), HSP90 (daf-21), and eight subunits of the CCT/TRiC chaperonin complex; the co-chaperones, HSP40 (dnj-12) and CDC37 (cdc-37); and the TPR-domain pro- tein STI1 that upon knockdown significantly enhanced A b 42 pro- teotoxicity (Figure 3D).\", \"key\": \"057ec4293be21ca030b0adb942e755d62d75a49b25f9020c78645a97fc0d473e984ee7af70b8d259195770873993cb005a08ac92a0f95f7149c5e4aea0bd1eac\", \"line\": 154, \"relation\": \"decreases\", \"source\": 553, \"target\": 4}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": \"Lindquist S\", \"name\": \"Cell\", \"pages\": \"434-448\", \"reference\": \"25036637\", \"title\": \"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.\", \"type\": \"PubMed\", \"volume\": \"158\"}, \"evidence\": \"Two subnetworks emerged within this central network, corresponding to known Hsp90 and Hsp70 chaperone complexes (Figure 2, blue and orange squares, respectively). These two subnetworks were bridged by a unique set of cochaperones (Figure 2, tan squares). Among these were the wellknown bridging factors HOP/STIP1, TPR2/DNAJC7, and CHIP/ STUB1, validating our approach (Brychzy et al., 2003; Schmid et al., 2012; Xu et al., 2002). Other bridging factors in this first tier of organization included members of the Hsp40 chaperone family (DNAJB1 and DNAJB6), HSP70-binding protein 1 (HSPBP1), the TPR domain protein EDRF1, and the E3 ligase NRDP1/RNF41\", \"key\": \"7155bf2b6f6e41511dc6cf90fc3a0202cb1843920fb1603a2ab2d96e8e979bbfadea1472e6686f3e87071f60df86bcbd0b27716d79782c88fa15a579e90c3884\", \"line\": 89, \"relation\": \"increases\", \"source\": 553, \"target\": 336}, {\"annotations\": {\"MeSHAnatomy\": {\"Brain\": true}, \"MeSHDisease\": {\"Alzheimer Disease\": true, \"Huntington Disease\": true, \"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brehme M\", \"Garza D\", \"Ge H\", \"Morimoto RI\", \"Orton K\", \"Rolland T\", \"Soper JH\", \"Vidal M\", \"Villella A\", \"Voisine C\", \"Wachi S\", \"Zhu Y\"], \"date\": \"2014-11-06\", \"first\": \"Brehme M\", \"last\": \"Morimoto RI\", \"name\": \"Cell reports\", \"pages\": \"1135-50\", \"reference\": \"25437566\", \"title\": \"A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease.\", \"type\": \"PubMed\", \"volume\": \"9\"}, \"evidence\": \" Knockdown of daf-21 (HSP90) or hsp-1 (HSC70) led to increased paralysis in 45% and 44% of day 6 animals, respectively, and knockdown of TPR co-chaper- ones tpr-1 and dnj-12 resulted in 70% impairment (Figure S4D).\", \"key\": \"70cd5279c623a609b889dfe4509021ffd844a2dd0395a09283069fb2090c42951804b6cb48304273d3c730bff5eb55c869ebf693feac786329160306e93d34cb\", \"line\": 164, \"relation\": \"increases\", \"source\": 567, \"target\": 106}, {\"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \"Molecular chaperones are central to the function of the PN and can be broadly grouped into the HSP70, HSP90, DNAJ/HSP40, chaperonin/HSP60, and small HSP (sHSP) families (10, 11).\", \"key\": \"9c1c1a35e9ed2731f45c4034f548db3fe2f49164fbf1bca19a9842e87ff7530e864bb4565dc4e632bf5b33a139e99b2aae992a6f10633cf973a38c2abd79ecc7\", \"line\": 98, \"relation\": \"isA\", \"source\": 590, \"target\": 49}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"If oligomerization of mutant Huntingtin is inhibited by administration of Congo red starting at this age, no aggregates can be detected in the brain 5weeks later (Sanchez et al., 2003).\", \"key\": \"549a03f7815c5332e45e3eb3a8e971ad913392d17c959d8224390d53881a84eb126ceb341fb9d27f57576ecb2f93b52612749d5e59adfc7bf3c39c4d84a207d0\", \"line\": 961, \"relation\": \"decreases\", \"source\": 0, \"target\": 35}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"In a parallel experiment using a cell culture model, Congo red was found to increase proteasomal activity in cells expressing a polyglutamine protein but not in cells expressing a control protein (Sanchez et al., 2003).\", \"key\": \"96ea9841f44a5523817a3b31ea0ad9bd9a36db5adb396625ac8686cb22fe2808312ff17838e1f95628543b3b9c63199c67e68c7a6fb17da6b576a88ff9b2b0e9\", \"line\": 967, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"increases\", \"source\": 0, \"target\": 155}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Overexpression of Parkin can rescue cells from the UPR elicited by a variety of stresses, such as exposure to H2O2, DNA alkylating agents, short-wavelength UV light, high osmolarity, and heat shock (Imai et al., 2000)\", \"key\": \"ab01161721f6f7797592aba6e2f0d4a542daab849d8b1662fc95082d311b86b288daee24e3c2b04da9fc6a17137926aa4136f4ef88493e46961aef196c1beae6\", \"line\": 401, \"relation\": \"increases\", \"source\": 2, \"target\": 116}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Concomitant cleavage of APP by beta and gamma secretase at specific sites can result in fragments (Abeta1-40 or Abeta1-42) that can misfold and form extracellular fibrils.\", \"key\": \"6cc125a8aa458f04db1a62ded4e36bc6147dd4bfeb399443321293cf82e219630ffe3f72a0fd8f0ab57a1ebab22cd64f354fe7f37d2cf60690c68e2a3d456548\", \"line\": 665, \"relation\": \"increases\", \"source\": 3, \"target\": 34}, {\"annotations\": {\"MeSHAnatomy\": {\"Reticulocytes\": true}}, \"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"However, Abeta has been demonstrated to reduce proteasome activity in reticulocyte lysates (Gregori et al., 1995), suggesting that increased levels of the peptide could underlie the reduction in UPS function observed in the AD brain.\", \"key\": \"15850b74f0ea3804dc9a0d2c940fc1063c27331561e8507b65df9a543579bdadd65cbca083357f7b0275140011d463df97c30ee2de0d4f9e69bf1689024ecfed\", \"line\": 748, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 5, \"target\": 155}, {\"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \"Experiments examining the effects of Aβ on proteasomal activity in vitro revealed an inhibitory effect on the chymotrypsin-like properties of the 20S core (73), consistent with observations of impaired proteasome function in AD patient brains (74). \", \"key\": \"d34b0ac8e667876b55a4f33f61236d9f7239d336ed1bc2cd85b5eaa789d5278be638e403d4d4068bdc604d818e7cee62d12bb1a96be8ccc4681fca6db6f64874\", \"line\": 249, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 5, \"target\": 363}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Overexpression of Parkin can rescue cells from the UPR elicited by a variety of stresses, such as exposure to H2O2, DNA alkylating agents, short-wavelength UV light, high osmolarity, and heat shock (Imai et al., 2000)\", \"key\": \"ffe5b479502012200c08704bc4697395812377e46c3ee83d09df59714d96cc0c6f82b8acd023ae050b00dc676cae41b02e02a2299c2b17925a9b77b32fb8cb5c\", \"line\": 400, \"relation\": \"increases\", \"source\": 9, \"target\": 116}, {\"annotations\": {\"Cell\": {\"astrocyte\": true, \"neuron\": true}}, \"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"It has been shown that Abeta can be degraded by the proteasome in cultured neurons and astrocytes, and reatment with the proteasome inhibitor lactacystin decreased viability of cells exposed to Abeta (Lopez Salon et al., 2003).\", \"key\": \"c9f4722fae323c847e0b17209ddcb1e64c6347fda418d2930388a77cbd6278225c4fa075a06d1abb17fe986a833c34920568197a9dcf57516b64569d5c855c74\", \"line\": 714, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 15, \"target\": 155}, {\"annotations\": {\"Cell\": {\"astrocyte\": true, \"neuron\": true}}, \"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"It has been shown that Abeta can be degraded by the proteasome in cultured neurons and astrocytes, and reatment with the proteasome inhibitor lactacystin decreased viability of cells exposed to Abeta (Lopez Salon et al., 2003).\", \"key\": \"09ecfb2235993ae6d9df32dd4964fc69779dc9c2082ae09f7124540491c926bba9f82de9394a4991434e97d29e86db0d88b5452ae359fe035f9d32673f601df5\", \"line\": 715, \"relation\": \"increases\", \"source\": 15, \"target\": 80}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Finally, Synaptotagmin XI has also recently been reported to be a substrate of Parkin (Huynh et al., 2003). It is possible that ubiquitination of this substrate affects synaptic vesicle transport and/or transmitter release.\", \"key\": \"7585e471b81e948ad992111b8301731e5198135cd59f2914dbc1b036ac1a6421da57edcaa8d004058301af2bf5bef7fbed0ac90c3abaef3f5690d875324ed502\", \"line\": 489, \"relation\": \"association\", \"source\": 17, \"subject\": {\"effect\": {\"fromLoc\": {\"name\": \"intracellular\", \"namespace\": \"bel\"}, \"toLoc\": {\"name\": \"extracellular space\", \"namespace\": \"bel\"}}, \"modifier\": \"Translocation\"}, \"target\": 559}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Accumulation of ubiquitin conjugates and/or inclusion bodies associated with ubiquitin, proteasome, and certain disease-characteristic proteins have been reported in a broad array of chronic neurodegenerative diseases, such as the neurofibrillary tangles of Alzheimer’s disease (AD), brainstem Lewy bodies (LBs) (the neuropathological hallmark in Parkinson’s disease [PD]), Bunina bodies in Amyotrophic Lateral Sclerosis (ALS), and nuclear inclusions in CAG repeat expansion (polyglutamine/Q extension) disorders such as Huntington’s disease, Spinocerebellar Ataxias (SCAs), and Spinal and Bulbar Muscular Atrophy (SBMA; Kennedy’s disease) (reviewed recently by Alves-Rodrigues et al., 1998; Sherman and Goldberg, 2001) (Figure 2)\", \"key\": \"7cf27f75941c79317a440c760f64f450479106c36a70a618edd990e1d1e60b927d044e0a9d3b09022c5cd9819aaa419253a4fe35890e93651c62d37a87f0aa95\", \"line\": 249, \"relation\": \"positiveCorrelation\", \"source\": 22, \"target\": 172}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Accumulation of ubiquitin conjugates and/or inclusion bodies associated with ubiquitin, proteasome, and certain disease-characteristic proteins have been reported in a broad array of chronic neurodegenerative diseases, such as the neurofibrillary tangles of Alzheimer’s disease (AD), brainstem Lewy bodies (LBs) (the neuropathological hallmark in Parkinson’s disease [PD]), Bunina bodies in Amyotrophic Lateral Sclerosis (ALS), and nuclear inclusions in CAG repeat expansion (polyglutamine/Q extension) disorders such as Huntington’s disease, Spinocerebellar Ataxias (SCAs), and Spinal and Bulbar Muscular Atrophy (SBMA; Kennedy’s disease) (reviewed recently by Alves-Rodrigues et al., 1998; Sherman and Goldberg, 2001) (Figure 2)\", \"key\": \"4d940bf686868acd7ec658ccab1905a70078aeeae6d4a8eab96786fced4831fdbb12c5e7b331de19a1af3e9ee57ac907badb7e1174f6be664f83039442ed029a\", \"line\": 250, \"relation\": \"positiveCorrelation\", \"source\": 22, \"target\": 161}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Parkin has been reported also to associate with actin filaments but not with microtubules (Huynh et al., 2000).\", \"key\": \"3fe6d90ea57da2b75d186d80975873dc56dcceecbeb0bff2995cc2477ab03fa8d8060a9633e722d70f904e10a562db023271469f8b6d2a5cfb1f2dbca375d87d\", \"line\": 493, \"relation\": \"association\", \"source\": 25, \"target\": 503}, {\"annotations\": {\"MeSHAnatomy\": {\"Pars Compacta\": true}, \"MeSHDisease\": {\"Parkinson Disease\": true}}, \"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"In the vast majority of patients, some of the remaining nigral dopaminergic neurons exhibit aggregated proteins in the form of cytoplasmic LB inclusions\", \"key\": \"cdaaffe58019967b126f51967a3ae98655a7a1818c1e0f8f6888be05acd37001b1a3d4f7f4acabfbf2312c7392b554c8fa671a2f01c0393fcf1516c5f8766fe3\", \"line\": 278, \"relation\": \"association\", \"source\": 26, \"target\": 48}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"In contrast, the neurofibrillary tangles are intracellular and are rich in tau, a structural protein that is normally associated with microtubuli\", \"key\": \"7ccd10bb44db7fc81420c424f9f51a3ce0330353af97d7a99af080b91b0dc6fba886b2ad5bd32a8c665e21790e61fd54ff3bdf0cd48b6b951705df1d17022adf\", \"line\": 671, \"relation\": \"association\", \"source\": 29, \"target\": 471}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"The protofibrils can further aggregate and precipitate as amyloid fibrils that are present in Lewy bodies, the hallmark of sporadic, late-onset PD\", \"key\": \"c81dc3b3f1d666a36a3211e984450e8e71fa47efea4c1a743aaa61896f60b0721fe87fea4176e783744f728b31b7621540dd76f8e15b15bb75efa8c7ef00e863\", \"line\": 555, \"relation\": \"association\", \"source\": 31, \"target\": 48}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Thus, aggregation, which is the primary event, may lead to secondary damage by inhibiting the UPS (Bence et al., 2001).\", \"key\": \"5b78ea70f41538ca03211f484536a30e6a0a87435d82655212ae32dbc71f052f6e6896555b606efefbadb95483872346f7b87d58cb31f2c3b6f93d5efd591fe7\", \"line\": 598, \"relation\": \"decreases\", \"source\": 31, \"target\": 101}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"The protofibrils can further aggregate and precipitate as amyloid fibrils that are present in Lewy bodies, the hallmark of sporadic, late-onset PD\", \"key\": \"9bd347733fa9cc862985cbd2c920f02da97d656ea445e43f5381f128f0ae13150d0d07d93ce77fd58b3a64615f00ef9cd1a6ea0dc9676351be3bc3708ee8379e\", \"line\": 554, \"relation\": \"increases\", \"source\": 32, \"target\": 31}, {\"annotations\": {\"MeSHDisease\": {\"Alzheimer Disease\": true}}, \"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"They present evidence that paired helical filaments obtained from AD brain or generated in vitro can inhibit proteasome function and that in AD brain tissue these filaments coimmunoprecipitate with the proteasome (Keck et al., 2003).\", \"key\": \"882e645c30f22d0f64d498b66e04883d800edc0a12852fffbc33bea284c93fdd88e25aea7b46a628403c72db4c5c6b7a6252bec98a2f5253dfb615bdc9e7b100\", \"line\": 722, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 36, \"target\": 155}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Recent findings demonstrate that soluble aggregated proteins can inhibit the ubiquitin system (Bence et al., 2001)\", \"key\": \"4ea3ae388a3cf9602632c7bf2f86a3b8e4e963ad73cc2c42c8256062feea533feef34359931aa265209b81a03b95ac6058ac38348fe79e93136ccbc6439e7b44\", \"line\": 264, \"relation\": \"decreases\", \"source\": 37, \"target\": 101}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Three different proteases, called alpha, beta, and gamma secretases, can cleave APP at specific sites and generate products that are well characterized.\", \"key\": \"c1a6d846260f37a0afc10fcd55ed1ccc8f8df350cf795431fde4d25b724301054913338b23a10044e801e3e55498cd172af7252ec2ee07b95d9803a640b0baf1\", \"line\": 659, \"relation\": \"increases\", \"source\": 38, \"target\": 623}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"However, mice homozygous for both UCH-L1 and UCH-L3 deletions die early due to dysphagia and display degeneration of the nucleus tractus solitarius and area postrema in addition to the degeneration of the gracile tract that is observed in GAD mice that only have a UCH-L1 deletion\", \"key\": \"7f10c0005e5ee03c8351a5786f9f74260f161bcfab71396e5e8e628ef8c8313561449119ac48561666eb805881b380a328a64c7202f93bec09ec26a25adc4d34\", \"line\": 538, \"relation\": \"positiveCorrelation\", \"source\": 40, \"target\": 577}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"However, mice homozygous for both UCH-L1 and UCH-L3 deletions die early due to dysphagia and display degeneration of the nucleus tractus solitarius and area postrema in addition to the 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disease-characteristic proteins have been reported in a broad array of chronic neurodegenerative diseases, such as the neurofibrillary tangles of Alzheimer’s disease (AD), brainstem Lewy bodies (LBs) (the neuropathological hallmark in Parkinson’s disease [PD]), Bunina bodies in Amyotrophic Lateral Sclerosis (ALS), and nuclear inclusions in CAG repeat expansion (polyglutamine/Q extension) disorders such as Huntington’s disease, Spinocerebellar Ataxias (SCAs), and Spinal and Bulbar Muscular Atrophy (SBMA; Kennedy’s disease) (reviewed recently by Alves-Rodrigues et al., 1998; Sherman and Goldberg, 2001) (Figure 2)\", \"key\": \"0054450cb6d9236745b09be36dacc28f82710f6ff9e9e1ea57a57fe707083a10a50d91ceca3dfc1eb7cdde7610d732dad87c691db6fda2d17f7a205c4297547d\", \"line\": 248, \"relation\": \"positiveCorrelation\", \"source\": 161, \"target\": 50}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", 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\"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Indeed, it has been reported that Parkin associates with the RPN10 (S5a) subunit of the 26S proteasome (Sakata et al., 2003)\", \"key\": \"5b0ca0bf4b65edb5a56c2b41a479d136854175d6255795cd4ac6cc5c4492027653957027d9f7b4737cc5a1b711648967fbec01e693c1f918dc8b2cdf120f4484\", \"line\": 299, \"relation\": \"association\", \"source\": 503, \"target\": 524}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"On the other hand, Parkin appears to have a role in synaptic transmission that has not been described previously and that was not possible to observe in patients.\", \"key\": \"be8828f14883f4b1bb43848a93e4d0a91e9772826f2fc37fe0f3bf425a86d92e26988ca0d8c56de1ea88bfcad48bf5d3884fac6a4a10d673b849b37eb9e39114\", \"line\": 331, \"relation\": \"association\", \"source\": 503, \"target\": 145}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"The overriding hypothesis is that a defect in Parkin will result in accumulation of this protein(s), which is toxic to the dopaminergic neurons\", \"key\": 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\"increases\", \"source\": 503, \"target\": 534}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"A second important substrate of Parkin is the Parkin-associated endothelial-like (Pael) receptor, a putative G protein-coupled transmembrane polypeptide (Imai et al., 2001). When overexpressed in cells, the receptor becomes misfolded\", \"key\": \"81cd8d0e0329956b1207415075179598fc342fa904a0f75d618c0f5bdefcfe5c248c18e73fc4f6542e1eb528aa2dc84139b2b4d1719f0edc240672e5593a706b\", \"line\": 364, \"relation\": \"association\", \"source\": 503, \"target\": 442}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Overexpression of Parkin can rescue cells from the UPR elicited by a variety of stresses, such as exposure to H2O2, DNA alkylating agents, short-wavelength UV light, high osmolarity, and heat shock (Imai et al., 2000)\", \"key\": 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\"relation\": \"decreases\", \"source\": 503, \"target\": 536}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Of note is that overexpression of Parkin also suppresses alpha-synuclein (alphSYN) toxicity, suggesting that Parkin may play a role in regulating this protein as well (see below)\", \"key\": \"553aa2538c6963c811ef5019700dbcd16aa8264087af9b5a83cf3686c6ffd7281fd85342fc8e6f37c8511ffefe358b803eb2aea19be1cb3fd18339dc77b9f386\", \"line\": 409, \"relation\": \"regulates\", \"source\": 503, \"target\": 536}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Another substrate of Parkin is a novel 22 kDa form of O-glycosylated \\u0001SYN (\\u0001Sp22) (Shimura et al., 2001)\", \"key\": \"2c5cff47e9af55ce4a171eac9e2070e279aea9c45f927efdb6e0bb446f239f09e390796cf0d20c2f043e1f833dcc0499b48f0c2b2c7d638c706ea3f7aeed53c7\", \"line\": 412, \"relation\": \"association\", \"source\": 503, \"target\": 538}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Parkin also ubiquitinates Synphilin-1, a protein of hitherto unknown function that contains a coiled-coiled domain and an ATP/GTP binding motif and that associates with alphaSYN (Chung et al., 2001).\", \"key\": \"9800e6740dfb7b565cd729830eb851a7cfbc6dbc3fcb149a42e63c525419d611ffb0ce41f007bb941a97bea5be4782d7584db6c93eca12bb4b678959f15ddc41\", \"line\": 423, \"relation\": \"increases\", \"source\": 503, \"target\": 544}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Since inclusion bodies are lacking in most cases of AR-JP, it is possible that the ubiquitination of Synphilin by wildtype Parkin plays a role in their formation, by targeting ubiquitinated Synphilin to these bodies and removing it from the cytosol where it can be toxic\", \"key\": \"5834ee1379a032fae25c99f61cbf6804a4cd4c9c65d3fbc80a25abf0a3acf7ff71b5bbc01bc219afaf2e6989e5c0f3c738bb805ef284bc5130623702bbb35bfd\", \"line\": 435, \"relation\": \"increases\", \"source\": 503, \"target\": 544}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Since inclusion bodies are lacking in most cases of AR-JP, it is possible that the ubiquitination of Synphilin by wildtype Parkin plays a role in their formation, by targeting ubiquitinated Synphilin to these bodies and removing it from the cytosol where it can be toxic\", \"key\": \"20fce5684548c7fbe1fb8eb46d93739926ddea697da5e1edea0888352bd78bd12e5c97297d399bf75504f6189d4a8de383d3313d51087403067de9339d4d5b19\", \"line\": 436, \"object\": {\"effect\": {\"fromLoc\": {\"name\": \"cytosol\", \"namespace\": \"GO\"}, \"toLoc\": {\"name\": \"Inclusion Bodies\", \"namespace\": \"MESH\"}}, \"modifier\": \"Translocation\"}, \"relation\": \"increases\", \"source\": 503, \"target\": 544}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Concomitantly, it reduced the inhibition of the proteasome and the activation of caspase 12 that are induced by accumulation of the polyglutamine-containing fragment\", \"key\": \"937fb00fa8cc03d06ae1cbe846b011ccb675d2b694bd67577e5f806262d74f98bc181f7719615b4be378c2375e058c12db66099b1c76e88f36b6a4eff13e6884\", \"line\": 442, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"increases\", \"source\": 503, \"target\": 155}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Concomitantly, it reduced the inhibition of the proteasome and the activation of caspase 12 that are induced by accumulation of the polyglutamine-containing fragment\", \"key\": \"86d1119d1f88c70eb8bb5bf9d55720f76bb2cab576b527a1d216c94fd468bf801309dfa2a53eea32ac68995376ecf58c78de26bd6db0b465437eb8510c6baf5a\", \"line\": 443, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 503, \"target\": 397}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"A rather surprising, recently discovered substrate of Parkin is cyclin E (Staropoli et al., 2003) that is ubiquitinated by the SCF complex that contains Parkin.\", \"key\": \"b34f018601cd9a450e08e66cec8be6ff6318c3225be7503b4d177244277c800b45437bec6244f4d8f98b0b1aa93451c717c339606708177d9db0ec8e9549660c\", \"line\": 456, \"relation\": \"association\", \"source\": 503, \"target\": 398}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Overexpression of Parkin is reported to attenuate cyclin E accumulation and rescue the cells from apoptosis\", \"key\": \"ef3ebfb379a45d1b2b8ad05fa03cb063c8c782ae0b1dd6490196f15129d07dfeb989f6a7ca670c7aeb34d01126f3facb404e6eecca3d1a44b9b4c0d3e20fcd3e\", \"line\": 468, \"relation\": \"decreases\", \"source\": 503, \"target\": 398}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Overexpression of Parkin is reported to attenuate cyclin E accumulation and rescue the cells from apoptosis\", \"key\": \"fce42292675ace4fdbcd94f722d7f678cd1d7ea68c9bbc6ecfed186a5c9476d17532b79f3422be07c969ed536a12e178592bfb0021475eea4d5964dad50de05d\", \"line\": 469, \"relation\": \"decreases\", \"source\": 503, \"target\": 97}, {\"annotations\": {\"CellLine\": {\"SH-SY5Y\": true}}, \"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"In the dopamine-producing neuroblastoma cell line SH-SY5Y, Parkin rescued the cells from p38-induced cell death\", \"key\": 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529, \"target\": 80}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Similarly, overexpression of the putative SOD1 E3 ligase dorfin can inhibit cell death induced by the mutant protein (Niwa et al., 2002), presumably by promoting its removal via the UPS.\", \"key\": \"e45824702c7c8de093889110a9886afbd7661aaa578cea659f98e5a2c70af29212fc2c3cce199723f227bebb097a89c84af331fa7fe8c79839f7cdc09eaf13bf\", \"line\": 850, \"relation\": \"increases\", \"source\": 529, \"target\": 101}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": 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\"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"The suggestion that the glycosylated form of alphaSYN is targeted by Parkin (Shimura et al., 2001) may resolve part of the enigma\", \"key\": \"a9518dc80b8ebd1818d3fd3332409fb88fc71110783fd726066eaebfd5d728fd762b7ee681362871cf3d317629a8e527dfb7403426407f43ebdda19f5da71307\", \"line\": 580, \"relation\": \"association\", \"source\": 537, \"target\": 503}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Another substrate of Parkin is a novel 22 kDa form of O-glycosylated \\u0001SYN (\\u0001Sp22) (Shimura et al., 2001)\", \"key\": \"d769370e5f1e3a094f683daa4572d0c9c7dbb99d1768b93bf3cc9a7c098d8cf1195c0f25f8d807edee41249d697cbb43d66cfecc429f5427f43599ac85680bd6\", \"line\": 412, \"relation\": \"association\", \"source\": 538, \"target\": 503}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Overexpression of wild-type, but in particular mutant alphaSYN in many cell types but not in all, induces apoptosis or sensitizes the cells to toxic agents, including proteasome inhibitors (see, for example, Lee et al.,2001a).\", \"key\": \"d49a38fa64ce48acbe76f0608aafa8b4c5cda6f32d927f518ff532dc2c91c9a9fe8bb1a4ac5799f872ac46c8b1834e16966521bccbd60840ec99f04f7418e1c8\", \"line\": 572, \"relation\": \"increases\", \"source\": 540, \"target\": 76}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"The mutant proteins have a higher tendency to generate protofibrils\", \"key\": \"b784934181a1f3c5b97355ea806f866cbd1ed8d80b4233912e98b868a23fd7d22b190411d950446e9fb304152a55419d802a9902e11111db1b15a909f0deec8d\", \"line\": 566, \"relation\": \"increases\", \"source\": 541, \"target\": 32}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"The mutant proteins have a higher tendency to generate protofibrils\", \"key\": \"6ab89c0669b23dbdbcc19506575be71647729eef0c6f2a47268a31e5029b3031f3fe6a03aae866f6062df8f8ae0f166988bb1ed9c3f77cd153605f57a012f23b\", \"line\": 567, \"relation\": \"increases\", \"source\": 542, \"target\": 32}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Alternatively, the enzyme itself may misfold and generate protein aggregates, thereby implicating a role for the UPS in disease pathogenesis (Cleveland and Liu, 2000; Julien, 2001;Valentine and Hart, 2003).\", \"key\": \"e4e03510306a5ef2213a99c87bc18e1cd1a654c3bea097039b53e6bf4548b486f17cabe8dd6a759dc10fe8cc05c38d472741937a50816d464013a35df141ddb3\", \"line\": 835, \"relation\": \"increases\", \"source\": 547, \"target\": 37}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"For example, in the case of IkBalpha,the inhibitor of the transcriptional regulator NF-kB, modification by SUMO-1 was shown to 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It is possible that ubiquitination of this substrate affects synaptic vesicle transport and/or transmitter release.\", \"key\": \"ae208bdb2b303a4c0dee10f160f6c31a400e02c96f1895383dc2dda1c9afb66af785e2e0d2db59258cbfbc2a92ee3975e12248acb6772e39360b53beacfa9330\", \"line\": 488, \"relation\": \"association\", \"source\": 559, \"target\": 122}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"Finally, Synaptotagmin XI has also recently been reported to be a substrate of Parkin (Huynh et al., 2003). 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recycled from conjugates, which results in general impairment of the function of the UPS.\", \"key\": \"3f1af396df8c63f9c8f35088a33f071290d15dde1687d50c1ad307dae9f8f981c3cbb4bc66f09058e3f637a7813e5d4f1a04480e0f759d26ac1127f569d6dca1\", \"line\": 514, \"relation\": \"decreases\", \"source\": 578, \"target\": 101}, {\"citation\": {\"authors\": [\"Brundin P\", \"Ciechanover A\"], \"date\": \"2003-10-09\", \"first\": \"Ciechanover A\", \"last\": \"Brundin P\", \"name\": \"Neuron\", \"pages\": \"427-46\", \"reference\": \"14556719\", \"title\": \"The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg.\", \"type\": \"PubMed\", \"volume\": \"40\"}, \"evidence\": \"However, mice homozygous for both UCH-L1 and UCH-L3 deletions die early due to dysphagia and display degeneration of the nucleus tractus solitarius and area postrema in addition to the degeneration of the gracile tract that is observed in GAD mice that only have a UCH-L1 deletion\", 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Proteins can be degraded either individually or en masse by proteasomes (20) or lysosomes (21), respectively. \", \"key\": \"917a2a508597dd892389b3acbadb23cdf8098d0b0a9883d699b5466026e2e87de57153a7acea1d8d3ec80477dd5dc873db46398d052c1616d5f64bf987f17603\", \"line\": 137, \"relation\": \"increases\", \"source\": 363, \"target\": 148}, {\"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \"The cytosolic N-terminal fragment of ATF6 that is generated translocates to the nucleus, binds DNA, and drives expression of a complementary set of UPR genes (8).\", \"key\": 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{\"Cell\": {\"motor neuron\": true}, \"Species\": {\"10090\": true}}, \"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \" Reduced levels of lipofuscin, LC3, and p62 have been observed in motor neurons of SOD1(G85R) mice (92). Treatment with the autophagy inhibitor chloroquine restored lipofuscin, LC3, and p62 levels in motor neurons, suggesting that mutant SOD1 causes hyperactive autophagy in mice (92). \", \"key\": \"5d5af5a17ae195d3064d39bef88f80d877074ce7437f3190ed12b56bfe35ef4e01a5bb46ec09dcbcba198184eb1cc442e21cc96b0156bd5d4de35df1128a4be8\", \"line\": 287, \"relation\": \"decreases\", \"source\": 551, \"target\": 1}, {\"annotations\": {\"Cell\": {\"motor neuron\": true}, \"Species\": {\"10090\": true}}, \"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \" Reduced levels of lipofuscin, LC3, and p62 have been observed in motor neurons of SOD1(G85R) mice (92). Treatment with the autophagy inhibitor chloroquine restored lipofuscin, LC3, and p62 levels in motor neurons, suggesting that mutant SOD1 causes hyperactive autophagy in mice (92). \", \"key\": \"149772b460239bca0e6d6b80ac1e4d4304a7b85910e304f0a967d59941fc090ca460e41673bae7e78c2f3e051d5044661aaa863af9766c17ec03411f03e4b5eb\", \"line\": 288, \"relation\": \"decreases\", \"source\": 551, \"target\": 470}, {\"annotations\": {\"Cell\": {\"motor neuron\": true}, \"Species\": {\"10090\": true}}, \"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \" Reduced levels of lipofuscin, LC3, and p62 have been observed in motor neurons of SOD1(G85R) mice (92). Treatment with the autophagy inhibitor chloroquine restored lipofuscin, LC3, and p62 levels in motor neurons, suggesting that mutant SOD1 causes hyperactive autophagy in mice (92). \", \"key\": \"03379113bcc6a4aed345d8b912374bd1085f6c1cee232f791e1819bee40f37df78b1e44cc52e65a0c64e65aaffee86540f11e1950d6f08cb886e600424627ac3\", \"line\": 289, \"relation\": \"decreases\", \"source\": 551, \"target\": 552}, {\"annotations\": {\"Cell\": {\"motor neuron\": true}, \"Species\": {\"10090\": true}}, \"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \" Reduced levels of lipofuscin, LC3, and p62 have been observed in motor neurons of SOD1(G85R) mice (92). Treatment with the autophagy inhibitor chloroquine restored lipofuscin, LC3, and p62 levels in motor neurons, suggesting that mutant SOD1 causes hyperactive autophagy in mice (92). \", \"key\": \"a0a4f7b45b2d99e4ff0c378bbfc04141ccf719fae3824f6b12663d74aaff7abf433c008f2327df2394f02da11b873ad40c4945cb79ca2fe710a68ee514af3919\", \"line\": 294, \"relation\": \"increases\", \"source\": 551, \"target\": 125}, {\"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \"This process allows active IRE1 to cleave XBP1 messenger RNA (mRNA), thereby generating a spliced transcript (XBP1s) that encodes a stable form of XBP1 that binds DNA and induces transcription of UPR target genes (8).\", \"key\": \"a1ead0c9149de76af67b0683d6e5033ea9a4b0fd2f73ad09f1c5610d1d60a9fade6cb37a3969aff062abb44f823d9cb5f8a691bf24cdf4fb538f42b1778a1a0f\", \"line\": 178, \"relation\": \"increases\", \"source\": 589, \"subject\": {\"effect\": {\"name\": \"tscript\", \"namespace\": \"bel\"}, \"modifier\": \"Activity\"}, \"target\": 114}, {\"annotations\": {\"Species\": {\"10090\": true}}, \"citation\": {\"authors\": [\"Labbadia J\", \"Morimoto RI\"], \"date\": \"2015-01-01\", \"first\": \"Labbadia J\", \"last\": \"Morimoto RI\", \"name\": \"Annual review of biochemistry\", \"pages\": \"435-64\", \"reference\": \"25784053\", \"title\": \"The biology of proteostasis in aging and disease.\", \"type\": \"PubMed\", \"volume\": \"84\"}, \"evidence\": \" Mice deficient for the autophagy-related genes Atg5 and Atg7 exhibit severe neurodegeneration (84, 85), and the expression of disease- associated proteins is reported to exert differential inhibitory effects on autophagic pathways.\", \"key\": 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\"source\": 30, \"target\": 275}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": \"Lindquist S\", \"name\": \"Cell\", \"pages\": \"434-448\", \"reference\": \"25036637\", \"title\": \"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.\", \"type\": \"PubMed\", \"volume\": \"158\"}, \"evidence\": \"LRR proteins interacted particularly strongly with the SGT1 cochaperone, whereas Argonaute proteins bound the protein phosphatase PP5 and p23, both of which are well-characterized Hsp90 cochaperones (Figure 6A)\", \"key\": \"6a935affdc02fa0f00a9f20bb952d316efd3574af4bb6e764044a66ae2831f659471c4ec63e81906d0c428ee8d0df7824cff73069ecf98af0d97e8db533da363\", \"line\": 421, \"relation\": \"directlyIncreases\", \"source\": 41, \"target\": 170}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": \"Lindquist S\", \"name\": \"Cell\", \"pages\": \"434-448\", \"reference\": \"25036637\", \"title\": \"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.\", \"type\": \"PubMed\", \"volume\": \"158\"}, \"evidence\": \"LRR proteins interacted particularly strongly with the SGT1 cochaperone, whereas Argonaute proteins bound the protein phosphatase PP5 and p23, both of which are well-characterized Hsp90 cochaperones (Figure 6A)\", \"key\": \"0d4eaddc5670d5465a0e6a5b4ca2a6d56cd8ecb80c301edc4f86597e8955c252ff5ec069ad4e9b66fb6c40565373cd2b030315125c867ab99f4b5387a7298610\", \"line\": 422, \"relation\": \"directlyIncreases\", \"source\": 41, \"target\": 171}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": \"Lindquist S\", \"name\": \"Cell\", \"pages\": \"434-448\", \"reference\": \"25036637\", \"title\": \"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.\", \"type\": \"PubMed\", \"volume\": \"158\"}, \"evidence\": \"Ganetespib treatment had a strong effect on most Hsp90- client interactions. Of the 630 unique proteins that we detected by LUMIER assay, 46% significantly decreased their interaction with Hsp90beta (change in LUMIER score > 1.5, adjusted p value <0.05; Figure 4A)\", \"key\": \"aaf985929750cece53f1ada7765043c5cdaa34f495136b0a54f47d12f641ef0df276e7c4d963e1cbb700a1b45a9495e1458ad6e3ed409c868567a60d01fa5b43\", \"line\": 277, \"object\": {\"modifier\": \"Activity\"}, \"relation\": \"decreases\", \"source\": 66, \"target\": 599}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": \"Lindquist S\", \"name\": \"Cell\", \"pages\": \"434-448\", \"reference\": \"25036637\", \"title\": \"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.\", \"type\": \"PubMed\", \"volume\": \"158\"}, \"evidence\": \"Ganetespib treatment had a strong effect on most Hsp90- client interactions. Of the 630 unique proteins that we detected by LUMIER assay, 46% significantly decreased their interaction with Hsp90beta (change in LUMIER score > 1.5, adjusted p value <0.05; Figure 4A)\", \"key\": \"374371c612e3680f912571f47748ae22f1ad772999959e6608d0bfb2dde82ef1006be1137a6a830bcbeedc8d1c68346cf2232db9999d4a71ec73c220d1153d21\", \"line\": 278, \"relation\": \"decreases\", \"source\": 66, \"target\": 278}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": \"Lindquist S\", \"name\": \"Cell\", \"pages\": \"434-448\", \"reference\": \"25036637\", \"title\": \"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.\", \"type\": \"PubMed\", \"volume\": \"158\"}, \"evidence\": \"Ganetespib treatment had a strong effect on most Hsp90- client interactions. Of the 630 unique proteins that we detected by LUMIER assay, 46% significantly decreased their interaction with Hsp90beta (change in LUMIER score > 1.5, adjusted p value <0.05; Figure 4A)\", \"key\": \"02eab9ce4745f9f4b642261ef34a23e5d2bf4d2678d99405556ee4aa95825fb3495f77dedd75c7b3a0093043170f1374845635c0f446f7b8e7943a752482bf72\", \"line\": 279, \"relation\": \"decreases\", \"source\": 66, \"target\": 280}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": \"Lindquist S\", \"name\": \"Cell\", \"pages\": \"434-448\", \"reference\": \"25036637\", \"title\": \"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.\", \"type\": \"PubMed\", \"volume\": \"158\"}, \"evidence\": \"A few, mostly cochaperones, decreased their interaction with both Hsp90b and Hsc70 (blue circles, Figure 4C).\", \"key\": \"c285f30d1b20ca407a8bd7c7e365701e1b6537db539432d2442dc9c765ab82825ad5ac283ca5aa3fb80ea42b541287a6407dfe33a3e10c21652941c172eab152\", \"line\": 294, \"relation\": \"decreases\", \"source\": 66, \"target\": 280}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": \"Lindquist S\", \"name\": \"Cell\", \"pages\": \"434-448\", \"reference\": \"25036637\", \"title\": \"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.\", \"type\": \"PubMed\", \"volume\": \"158\"}, \"evidence\": \"Ganetespib treatment had a strong effect on most Hsp90- client interactions. Of the 630 unique proteins that we detected by LUMIER assay, 46% significantly decreased their interaction with Hsp90beta (change in LUMIER score > 1.5, adjusted p value <0.05; Figure 4A)\", \"key\": \"2b5288b19ebe3edbd0f7c4f274ad582cc7d767f059f60ae13dfe4327ababc2efb02eb443aae4d3f129b880b3f3bcc06506fcf89aaa2b211147c2cd6fea660e2e\", \"line\": 280, \"relation\": \"decreases\", \"source\": 66, \"target\": 267}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": \"Lindquist S\", \"name\": \"Cell\", \"pages\": \"434-448\", \"reference\": \"25036637\", \"title\": \"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.\", \"type\": \"PubMed\", \"volume\": \"158\"}, \"evidence\": \"A few, mostly cochaperones, decreased their interaction with both Hsp90b and Hsc70 (blue circles, Figure 4C).\", \"key\": \"9ab278098b28229e482a86d765d179afc73593eab7644be91959e493e03f5d604ec4536a376a8bb46d79906001af5b0697951fffccf154b7a65d7f9b53a7e881\", \"line\": 295, \"relation\": \"decreases\", \"source\": 66, \"target\": 267}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": \"Lindquist S\", \"name\": \"Cell\", \"pages\": \"434-448\", \"reference\": \"25036637\", \"title\": \"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.\", \"type\": \"PubMed\", \"volume\": \"158\"}, \"evidence\": \"The effect of ganetespib on Hsc70 interactions was more subtle but still clearly detectable: 16% of the tested proteins increased their interaction with Hsc70 upon ganetespib treatment. This was particularly noticeable for proteins that interacted strongly with Hsc70 (Figure 4B).\", \"key\": \"ce1ba024fbc22bada98110e35c371b0c0fed9f2667ebc2bbd9fdd30a356abd1cb3e6d1a099d2877791ed766424d2f52ac37bfa29ee25c65292155caa82ebed30\", \"line\": 286, \"relation\": \"increases\", \"source\": 66, \"target\": 227}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": \"Lindquist S\", \"name\": \"Cell\", \"pages\": \"434-448\", \"reference\": \"25036637\", \"title\": \"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.\", \"type\": \"PubMed\", \"volume\": \"158\"}, \"evidence\": \"The effect of ganetespib on Hsc70 interactions was more subtle but still clearly detectable: 16% of the tested proteins increased their interaction with Hsc70 upon ganetespib treatment. This was particularly noticeable for proteins that interacted strongly with Hsc70 (Figure 4B).\", \"key\": \"a71600a75dc11ff41b80a4dea0b13696d261f15c750853522d0f07d3a9c720cbcf47fa5b73fddd8d019dcd5034945203412b13d283f0387c468bf8d81167e4b3\", \"line\": 287, \"relation\": \"increases\", \"source\": 66, \"target\": 218}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": \"Lindquist S\", \"name\": \"Cell\", \"pages\": \"434-448\", \"reference\": \"25036637\", \"title\": \"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.\", \"type\": \"PubMed\", \"volume\": \"158\"}, \"evidence\": \"The effect of ganetespib on Hsc70 interactions was more subtle but still clearly detectable: 16% of the tested proteins increased their interaction with Hsc70 upon ganetespib treatment. This was particularly noticeable for proteins that interacted strongly with Hsc70 (Figure 4B).\", \"key\": \"a034a126f8571cb5bd610390216c0347aabdf77a3994250bbc975478fdd80e4f8e21e51c5c142af6c57aa2970ff05e65ef8844488b4cf15ce0861fb64307cf32\", \"line\": 288, \"relation\": \"increases\", \"source\": 66, \"target\": 235}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": \"Lindquist S\", \"name\": \"Cell\", \"pages\": \"434-448\", \"reference\": \"25036637\", \"title\": \"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.\", \"type\": \"PubMed\", \"volume\": \"158\"}, \"evidence\": \"The effect of ganetespib on Hsc70 interactions was more subtle but still clearly detectable: 16% of the tested proteins increased their interaction with Hsc70 upon ganetespib treatment. This was particularly noticeable for proteins that interacted strongly with Hsc70 (Figure 4B).\", \"key\": \"f2075651d6ad21758581db57bc58beea0d11336f38424ce1863c76ba504bf20254f02cb59e4edb3c3dd1cad919590114988af9e292c5f08890f65dd2474069c1\", \"line\": 289, \"relation\": \"increases\", \"source\": 66, \"target\": 238}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": \"Lindquist S\", \"name\": \"Cell\", \"pages\": \"434-448\", \"reference\": \"25036637\", \"title\": \"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.\", \"type\": \"PubMed\", \"volume\": \"158\"}, \"evidence\": \"A few, mostly cochaperones, decreased their interaction with both Hsp90b and Hsc70 (blue circles, Figure 4C).\", \"key\": \"9049da04664835db84e3e169fa34c18ad11b9f4cbdb3f6f4f84404113c878caa49f322e19e36fca75b460a205501cf45c52649578daacb3249751b347d50ec26\", \"line\": 296, \"relation\": \"decreases\", \"source\": 66, \"target\": 269}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": \"Lindquist S\", \"name\": \"Cell\", \"pages\": \"434-448\", \"reference\": \"25036637\", \"title\": \"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.\", \"type\": \"PubMed\", \"volume\": \"158\"}, \"evidence\": \"A few, mostly cochaperones, decreased their interaction with both Hsp90b and Hsc70 (blue circles, Figure 4C).\", \"key\": \"83de256c133db73efd6566347d3bbfbd68352403e188464d17e51c00f4b3b42083940f11b0f20d2b351c0c72e9f1c7216e4db4b30480c9eba76f7fbd7dfa03a7\", \"line\": 297, \"relation\": \"decreases\", \"source\": 66, \"target\": 285}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": \"Lindquist S\", \"name\": \"Cell\", \"pages\": \"434-448\", \"reference\": \"25036637\", \"title\": \"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.\", \"type\": \"PubMed\", \"volume\": \"158\"}, \"evidence\": \"A few, mostly cochaperones, decreased their interaction with both Hsp90b and Hsc70 (blue circles, Figure 4C).\", \"key\": \"f68e2cb29e787b48ba026e4a67fb305172712481079879451b9e18bc4bbd2c76d500756a39e65e612d6d79491a045a1fb057b97af665ea48914e79ded43397ba\", \"line\": 298, \"relation\": \"decreases\", \"source\": 66, \"target\": 268}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": \"Lindquist S\", \"name\": \"Cell\", \"pages\": \"434-448\", \"reference\": \"25036637\", \"title\": \"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.\", \"type\": \"PubMed\", \"volume\": \"158\"}, \"evidence\": \"A few, mostly cochaperones, decreased their interaction with both Hsp90b and Hsc70 (blue circles, Figure 4C).\", \"key\": \"2a8e6eddb1b5fdf3d5a1e9a80084da060fc8f663ee9072e46387b6046d6a2218100df3b54664fbf4d72b1bed567406155fceec75b5b3a4fa13ba77056b292e2b\", \"line\": 299, \"relation\": \"decreases\", \"source\": 66, \"target\": 270}, {\"citation\": {\"authors\": [\"Berger B\", \"Choi H\", \"Gingras AC\", \"Krykbaeva I\", \"Larsen B\", \"Lin ZY\", \"Lindquist S\", \"Peng J\", \"Taipale M\", \"Tucker G\"], \"date\": \"2014-07-17\", \"first\": \"Taipale M\", \"last\": 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beta-Peptides\", \"namespace\": \"MESH\"}], \"reactants\": [{\"bel\": \"p(HGNC:APP)\", \"function\": \"Protein\", \"id\": \"ed1d45f3255226e4210017e6c179950e0e04a300727326d7fea6a9659868e8818ff64fd5e8a2a92a703fb1566b3f48323750ac6c28e7adb40843053d276710bc\", \"name\": \"APP\", \"namespace\": \"HGNC\"}]}]}, \"#qoemztryhdvkqpbg\", 1000, 650, {'Protein': '#1F77B4', 'Pathology': '#FF7F0E', 'BiologicalProcess': '#2CA02C', 'miRNA': '#D62728', 'Complex': '#98DF8A', 'Composite': '#9467BD', 'Reaction': '#000000', 'Gene': '#FFBB78', 'Abundance': '#AEC7E8', 'RNA': '#FF9896'});\n", "});" ], "text/plain": [ "" ] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "pybel_jupyter.to_jupyter(proteostasis_graph)" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", 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