{ "metadata": { "name": "", "signature": "sha256:344a9d1506e7cc09be34b0b255ba60ac795e23c147f5f03e922fadb83d6e1411" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Quick Look at Array data" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"CLC_Genomics_Workbench_6.5_17E8EF30.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"CLC_Genomics_Workbench_6.5_17E8EF4F.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"CLC_Genomics_Workbench_6.5_17E8EF74.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"CLC_Genomics_Workbench_6.5_17E8F00A.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"CLC_Genomics_Workbench_6.5_17E8F10C.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"CLC_Genomics_Workbench_6.5_17E8F136.png\"/" ] }, { "cell_type": "heading", "level": 1, "metadata": {}, "source": [ "Characterizing the 42 genes with differential methylation" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/DMRmgavery_mRNA_annotated.csv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "DMR_chr,DMR_source,DMR_type,DMR_start,DMR_stop,gene_chr,gene_source,gene_type,gene_start,gene_stop,gene_score,gene_strand,gene_CGI,gene_SPID,gene_eval,gene_description\r\n", "scaffold1017,MBD_ChIP,HYPO,117844,118366,scaffold1017,GLEAN,mRNA,89381,134984,0.662353,+,CGI_10024982,P45844,0,ATP-binding cassette sub-family G member 1\r\n", "scaffold1017,MBD_ChIP,HYPO,120083,120710,scaffold1017,GLEAN,mRNA,89381,134984,0.662353,+,CGI_10024982,P45844,0,ATP-binding cassette sub-family G member 1\r\n", "scaffold1174,MBD_ChIP,HYPER,585061,585688,scaffold1174,GLEAN,mRNA,584434,586898,1,-,CGI_10026054,P10155,1.00E-113,60 kDa SS-A/Ro ribonucleoprotein\r\n", "scaffold1179,MBD_ChIP,HYPER,1238509,1239014,scaffold1179,GLEAN,mRNA,1232531,1260961,0.415854,-,CGI_10027416,Q8C8U0,4.00E-146,Liprin-beta-1\r\n", "scaffold13,MBD_ChIP,HYPER,106323,106835,scaffold13,GLEAN,mRNA,104907,109173,0.999981,+,CGI_10013201,P02595,1.00E-21,Calmodulin\r\n", "scaffold13,MBD_ChIP,HYPER,107092,107468,scaffold13,GLEAN,mRNA,104907,109173,0.999981,+,CGI_10013201,P02595,1.00E-21,Calmodulin\r\n", "scaffold1301,MBD_ChIP,HYPER,958441,958944,scaffold1301,GLEAN,mRNA,940827,961246,0.536299,+,CGI_10027751,O15027,4.00E-123,Protein transport protein Sec16A\r\n", "scaffold1337,MBD_ChIP,HYPER,331697,331825,scaffold1337,GLEAN,mRNA,330650,341044,0.999409,-,CGI_10012845,Q9JHU4,1.00E-93,Cytoplasmic dynein 1 heavy chain 1\r\n", "scaffold1409,MBD_ChIP,HYPO,145389,145656,scaffold1409,GLEAN,mRNA,123560,153776,0.210676,-,CGI_10013783,Q8TDB6,1.00E-52,E3 ubiquitin-protein ligase DTX3L\r\n" ] } ], "prompt_number": 2 }, { "cell_type": "code", "collapsed": false, "input": [ "#upload to SQLShare" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 3 }, { "cell_type": "code", "collapsed": false, "input": [ "!python /Users/sr320/sqlshare-pythonclient/tools/singleupload.py -d DMRmgavery_mRNA_annotated /Volumes/web/cnidarian/DMRmgavery_mRNA_annotated.csv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "processing chunk line 0 to 47 (0.00136613845825 s elapsed)\r\n", "pushing /Volumes/web/cnidarian/DMRmgavery_mRNA_annotated.csv...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "parsing BB469E48...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "finished DMRmgavery_mRNA_annotated\r\n" ] } ], "prompt_number": 5 }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Joining CCD_domain_concise_Superfamily" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "```\n", "SELECT * FROM [sr320@washington.edu].[DMRmgavery_mRNA_annotated]dmr\n", " left join\n", " [sr320@washington.edu].[TJGR_CCD_domain_concise_Superfamily_def]sf\n", " on dmr.gene_CGI = sf.CGI_ID\n", " ```\n", " \n" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!head -2 /Volumes/web/cnidarian/DMRmgavery_prodom.csv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "DMR_chr,DMR_source,DMR_type,DMR_start,DMR_stop,gene_chr,gene_source,gene_type,gene_start,gene_stop,gene_score,gene_strand,gene_CGI,gene_SPID,gene_eval,gene_description,Query,CGI_ID,Hit type,PSSM-ID,From,To,E-Value,Bitscore,Accession,Short name,Incomplete,Superfamily,Definition\r", "\r\n", "scaffold601,MBD_ChIP,HYPER,1116073,1116588,scaffold601,GLEAN,mRNA,1099885,1117707,0.780387,+,CGI_10026858,P41436,8E-31,Apoptosis inhibitor IAP,Q#10321 -,CGI_10026858,superfamily,241564,281,335,1.01E-21,88.4767,cl00035,BIR superfamily,C,-,\"\"\"Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.\"\"\"\r", "\r\n" ] } ], "prompt_number": 9 }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Joining for GO!" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "```\n", "SELECT distinct * FROM [sr320@washington.edu].[DMRmgavery_mRNA_annotated]dmr\n", " left join\n", " [sr320@washington.edu].[qDOD_Cgigas_GO_GOslim]sf\n", " on dmr.gene_CGI = sf.CGI_ID\n", " ```" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!head -2 /Volumes/web/cnidarian/DMRmgavery_GO.csv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "DMR_chr,DMR_source,DMR_type,DMR_start,DMR_stop,gene_chr,gene_source,gene_type,gene_start,gene_stop,gene_score,gene_strand,gene_CGI,gene_SPID,gene_eval,gene_description,CGI_ID,SPID,evalue,Description,SPID1,GOID,GO_id,term,GOSlim_bin,aspect\r", "\r\n", "scaffold1017,MBD_ChIP,HYPO,117844,118366,scaffold1017,GLEAN,mRNA,89381,134984,0.662353,+,CGI_10024982,P45844,0,ATP-binding cassette sub-family G member 1,CGI_10024982,P45844,0,ATP-binding cassette sub-family G member 1,P45844,GO:0000139,GO:0000139,Golgi membrane,ER/Golgi,C\r", "\r\n" ] } ], "prompt_number": 10 }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"REVIGO_Output_18521FBB.png\"/" ] }, { "cell_type": "heading", "level": 3, "metadata": {}, "source": [ "GOslim Pie" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"Screenshot_12_6_13_7_18_AM_18522243.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"Screenshot_12_6_13_7_19_AM_185222A2.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"Screenshot_12_6_13_7_21_AM_18522312.png\"/\n" ] }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "IGV " ] }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/DMRmgavery_track1.bed" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "scaffold1017\t117844\t118366\tHYPO\r\n", "scaffold1017\t120083\t120710\tHYPO\r\n", "scaffold1174\t585061\t585688\tHYPER\r\n", "scaffold1179\t1238509\t1239014\tHYPER\r\n", "scaffold1301\t958441\t958944\tHYPER\r\n", "scaffold1337\t331697\t331825\tHYPER\r\n", "scaffold1409\t145389\t145656\tHYPO\r\n", "scaffold146\t686526\t687786\tHYPO\r\n", "scaffold1532\t587965\t588458\tHYPO\r\n", "scaffold1562\t130359\t130794\tHYPER\r\n" ] } ], "prompt_number": 12 }, { "cell_type": "code", "collapsed": false, "input": [ "#spot checks" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 14 }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"IGV_and_sr320_\u2014_igv.command_\u2014_java_\u2014_80\u00d724_18522760.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"Liprin-beta-1_-_Homo_sapiens__Human__18522884.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "
" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"IGV_and_sr320_\u2014_igv.command_\u2014_java_\u2014_80\u00d724_18522A8B.png\"/" ] }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] } ], "metadata": {} } ] }