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   "cells": [
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "Searching for info on AMP-activated protein kinase in oysters / qDOD"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "![pw](http://www.cellsignal.com/reference/pathway/images/AMPK.jpg)"
     ]
    },
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "SQLShare"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "```\n",
      "SELECT * \n",
      "  FROM [sr320@washington.edu].[qDOD Cgigas Gene Descriptions (Swiss-prot)]\n",
      "  where Description like '%AMP-activated%'\n",
      "```"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "CGI_ID|SPID|evalue|Description    \n",
      "CGI_10003983|Q28948|0|5'-AMP-activated protein kinase catalytic subunit alpha-2   \n",
      "CGI_10010273|Q91WG5|4E-36|5'-AMP-activated protein kinase subunit gamma-2   \n",
      "CGI_10010275|Q91WG5|1E-128|5'-AMP-activated protein kinase subunit gamma-2   \n",
      "CGI_10016569|Q9QZH4|2E-09|5'-AMP-activated protein kinase subunit beta-2   \n",
      "CGI_10021816|Q5RDH5|5E-15|5'-AMP-activated protein kinase catalytic subunit alpha-1  \n",
      "CGI_10025389|Q6PAM0|3E-84|5'-AMP-activated protein kinase subunit beta-2   \n",
      "  "
     ]
    },
    {
     "cell_type": "heading",
     "level": 4,
     "metadata": {},
     "source": [
      "Emma's Proteomic Data"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "```\n",
      "SELECT * FROM [sr320@washington.edu].[OABS_ETS_S3]\n",
      "Where [Gene Name] like '%AMP-activated protein kinase%'\n",
      "```"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Q6PAM0   \n",
      "3e-84   \n",
      "5'-AMP-activated protein kinase subunit beta-2   "
     ]
    },
    {
     "cell_type": "heading",
     "level": 4,
     "metadata": {},
     "source": [
      "OsHV\n"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "```\n",
      "SELECT * FROM [sr320@washington.edu].[Cgigas Larvae RNA-Seq OsHV]\n",
      "  where ID like 'CGI_10003983'\n",
      "```    "
     ]
    },
    {
     "cell_type": "raw",
     "metadata": {},
     "source": [
      "CGI_10003983\n",
      "165\n",
      "165\n",
      "18.094\n",
      "CGI_10003983\n",
      "Q28948\n",
      "0\n",
      "5'-AMP-activated protein kinase catalytic subunit alpha-2"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "more on CGI_10003983"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "```\n",
      "SELECT * FROM [sr320@washington.edu].[qDOD_v9_gene]\n",
      "  where Column9 like '%CGI_10003983%'\n",
      "```"
     ]
    },
    {
     "cell_type": "raw",
     "metadata": {},
     "source": [
      "scaffold1375\n",
      "GLEAN\n",
      "mRNA\n",
      "40162\n",
      "57556\n",
      "1\n",
      "+\n",
      ".\n",
      "ID=CGI_10003983;\n"
     ]
    },
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "IGV Genome Browser"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Loading session `http://eagle.fish.washington.edu/cnidarian/oyster_v9_igv_session.xml`"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/IGV_-_Session__http__eagle.fish.washington.edu_cnidarian_oyster_v9_igv_session.xml_and_CC_ampk_183269B4.png\" alt=\"IGV_-_Session__http__eagle.fish.washington.edu_cnidarian_oyster_v9_igv_session.xml_and_CC_ampk_183269B4.png\" />"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/IGV_-_Session__http__eagle.fish.washington.edu_trilobite_Crassostrea_gigas_v9_tracks_BiGill_igv_charlie.xml_18326ABC.png\" alt=\"IGV_-_Session__http__eagle.fish.washington.edu_trilobite_Crassostrea_gigas_v9_tracks_BiGill_igv_charlie.xml_18326ABC.png\" />"
     ]
    },
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "Oyster Genome Browser"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<IMAGE src=\"http://www.animalgenome.org/cgi-bin/gbrowse_img/oyster/?name=scaffold1375:34951..60000;type=mRNA+CDS;width=800;id=e4ddd1ba16785b17463c3e7ea44c4e9f;keystyle=between;grid=on\" />\n"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}