{
 "metadata": {
  "name": "",
  "signature": "sha256:9a51028e32fa02e3d32f7bd408a7594f00dfc8cad5141087a13a7666caaa67ef"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "I have a DEG list, now what?"
     ]
    },
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "Pacific Oyster Tuxedo DEG list"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "All data <http://eagle.fish.washington.edu/whale/index.php?dir=fish546%2Fiplant%2F>"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#DEG List\n",
      "!head /Volumes/web/cnidarian/fish546sort_gene.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "gene_id\tgene_name\tsample1\tsample2\tfold_change\tdirection\ttotal_fpkm\tq-value\tgene_description\r\n",
        "CGI_10006532\t.\tTroco\tUmbo\t8.37\tUP\t55.29\t0.00049485\t\r\n",
        "CGI_10023338\t.\tTroco\tUmbo\t31.68\tDOWN\t152.66\t0.00049485\t\r\n",
        "EKC17242\tCGI_10001446\tTroco\tUmbo\t3.76\tDOWN\t42.09\t0.00049485\t\r\n",
        "EKC17313\tCGI_10001190\tTroco\tUmbo\t7.90\tUP\t16.74\t0.00049485\t\r\n",
        "EKC17492\tCGI_10000706\tTroco\tUmbo\t14.59\tDOWN\t328.69\t0.00049485\t\r\n",
        "EKC17563\tCGI_10000573\tTroco\tUmbo\t3.20\tUP\t3470.43\t0.00049485\t\r\n",
        "EKC17629\tCGI_10000434\tTroco\tUmbo\t97.59\tDOWN\t416.64\t0.00049485\t\r\n",
        "EKC17663\tCGI_10000384\tTroco\tUmbo\t3.91\tUP\t1535.08\t0.00049485\t\r\n",
        "EKC17667\tCGI_10000377\tTroco\tUmbo\t182.69\tDOWN\t1851.02\t0.00049485\t\r\n"
       ]
      }
     ],
     "prompt_number": 1
    },
    {
     "cell_type": "raw",
     "metadata": {},
     "source": [
      "In order to get enrichment you need to rely on SPID or other (here we use SPID as we have it). This means a simple join to get SPID that correspond to table above"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!python /Users/sr320/sqlshare-pythonclient/tools/singleupload.py -d fish546_DEgene_out /Volumes/web/cnidarian/fish546sort_gene.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "processing chunk line 0 to 2988 (0.863645076752 s elapsed)\r\n",
        "pushing /Volumes/web/cnidarian/fish546sort_gene.txt...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "parsing 2D0D0BB8...\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "finished fish546_DEgene_out\r\n"
       ]
      }
     ],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cd /Volumes/web/cnidarian/"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "/Volumes/web/cnidarian\n"
       ]
      }
     ],
     "prompt_number": 8
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!python /Users/sr320/sqlshare-pythonclient/tools/fetchdata.py -s \"SELECT * FROM [sr320@washington.edu].[fish546_DEgene_out]deg left join [sr320@washington.edu].[qDOD Cgigas Gene Descriptions (Swiss-prot)]sp on deg.gene_name = sp.CGI_ID\" -f tsv -o fish546_DEGjoinSP.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!head fish546_DEGjoinSP.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "gene_id\tgene_name\tsample1\tsample2\tfold_change\tdirection\ttotal_fpkm\tq-value\tgene_description\tCGI_ID\tSPID\tevalue\tDescription\r",
        "\r\n",
        "EKC17945\tCGI_10000015\tTroco\tUmbo\t2.13\tDOWN\t450.32\t0.0482194\t\tCGI_10000015\tQ9BYW2\t3E-38\tHistone-lysine N-methyltransferase SETD2\r",
        "\r\n",
        "EKC17931\tCGI_10000033\tTroco\tUmbo\t2.69\tUP\t1266.47\t0.00205159\t\tCGI_10000033\tP47835\t8E-65\t40S ribosomal protein S3-B\r",
        "\r\n",
        "EKC17929\tCGI_10000035\tTroco\tUmbo\t7.55\tDOWN\t14.56\t0.00428566\t\tCGI_10000035\tQ99NE9\t9E-12\tPre-B-cell leukemia transcription factor 4\r",
        "\r\n",
        "EKC17923\tCGI_10000041\tTroco\tUmbo\t3.06\tUP\t766.73\t0.012281\t\tCGI_10000041\tP10817\t4E-08\tCytochrome c oxidase subunit 6A2, mitochondrial\r",
        "\r\n",
        "EKC17914\tCGI_10000051\tTroco\tUmbo\t3.27\tUP\t80.76\t0.0215094\t\tCGI_10000051\tQ5RF33\t1E-49\tDown syndrome critical region protein 3 homolog\r",
        "\r\n",
        "EKC17913\tCGI_10000052\tTroco\tUmbo\t3.67\tUP\t30.54\t0.0182539\t\tCGI_10000052\tA7Y2W8\t1E-39\tSodium- and chloride-dependent glycine transporter 1\r",
        "\r\n",
        "EKC17910\tCGI_10000055\tTroco\tUmbo\t3.14\tDOWN\t1322.16\t0.00205159\t\tCGI_10000055\tP84245\t3E-90\tHistone H3.3\r",
        "\r\n",
        "EKC17900\tCGI_10000066\tTroco\tUmbo\t2.9\tUP\t89.22\t0.0269801\t\tCGI_10000066\tP23038\t6E-08\tMetallothionein\r",
        "\r\n",
        "EKC17893\tCGI_10000073\tTroco\tUmbo\t8.29\tUP\t14.78\t0.00571421\t\tCGI_10000073\tP47727\t5E-105\tCarbonyl reductase [NADPH] 1\r",
        "\r\n"
       ]
      }
     ],
     "prompt_number": 10
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{ print $10 }' fish546_DEGjoinSP.txt > fish546_DEGjoinSPonly.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 11
    },
    {
     "cell_type": "raw",
     "metadata": {},
     "source": [
      "!cat fish546_DEGjoinSPonly.txt"
     ]
    },
    {
     "cell_type": "heading",
     "level": 4,
     "metadata": {},
     "source": [
      "DAVID"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/DAVID__Functional_Annotation_Tools_18A6ABB3.png\" alt=\"DAVID__Functional_Annotation_Tools_18A6ABB3_png\"/>"
     ]
    },
    {
     "cell_type": "raw",
     "metadata": {},
     "source": [
      "Now need to upload Backgroung list (all corresponding IDs in oyster genome)"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!python /Users/sr320/sqlshare-pythonclient/tools/fetchdata.py -s \"SELECT SPID FROM [sr320@washington.edu].[qDOD Cgigas Gene Descriptions (Swiss-prot)]\" -f tsv -o Cgigas_allSP.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 14
    },
    {
     "cell_type": "raw",
     "metadata": {},
     "source": [
      "!cat Cgigas_allSP.txt"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/DAVID__Functional_Annotation_Tools_18A6AD0F.png\" alt=\"DAVID__Functional_Annotation_Tools_18A6AD0F_png\"/>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/pc3_18A6AD70.png\" alt=\"pc3_18A6AD70_png\"/>"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!wget http://david.abcc.ncifcrf.gov/data/download/chart_B89D12125EAE1391883715950.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "--2014-02-08 10:26:32--  http://david.abcc.ncifcrf.gov/data/download/chart_B89D12125EAE1391883715950.txt\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Resolving david.abcc.ncifcrf.gov... "
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "129.43.1.164\r\n",
        "Connecting to david.abcc.ncifcrf.gov|129.43.1.164|:80... "
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "connected.\r\n",
        "HTTP request sent, awaiting response... "
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "200 OK\r\n",
        "Length: 47347 (46K) [text/plain]\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Saving to: `chart_B89D12125EAE1391883715950.txt'\r\n",
        "\r\n",
        "\r",
        " 0% [                                       ] 0           --.-K/s              "
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r",
        "69% [==========================>            ] 33,060       149K/s              \r",
        "100%[======================================>] 47,347       184K/s   in 0.3s    \r\n",
        "\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "2014-02-08 10:26:49 (184 KB/s) - `chart_B89D12125EAE1391883715950.txt' saved [47347/47347]\r\n",
        "\r\n"
       ]
      }
     ],
     "prompt_number": 20
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/exclde_18A6AEF4.png\" alt=\"exclde_18A6AEF4_png\"/>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/adhajfh_18A6AF5F.png\" alt=\"adhajfh_18A6AF5F_png\"/>"
     ]
    },
    {
     "cell_type": "heading",
     "level": 4,
     "metadata": {},
     "source": [
      "Revigo "
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/ref_88_18A6AFBF.png\" alt=\"ref_88_18A6AFBF_png\"/>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/REVIGO_Output_18A6B01E.png\" alt=\"REVIGO_Output_18A6B01E_png\"/>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<http://eagle.fish.washington.edu/cnidarian/f546_bubREVIGO.r>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/REVIGO_Output_18A6B052.png\" alt=\"REVIGO_Output_18A6B052_png\"/>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<http://eagle.fish.washington.edu/cnidarian/f546REViGO.xgmml>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/Session__New_Session_18A6B255.png\" alt=\"Session__New_Session_18A6B255_png\"/>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/REVIGO_Output_18A6B2BA.png\" alt=\"REVIGO_Output_18A6B2BA_png\"/>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<http://eagle.fish.washington.edu/cnidarian/f546REVIGO_treemap.r>"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "Olympia Oyster Example"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#from DESeq \n",
      "!head /Volumes/web/cnidarian/fish546_0lyMF_DElist"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\"id\"\t\"baseMean\"\t\"baseMeanA\"\t\"baseMeanB\"\t\"foldChange\"\t\"log2FoldChange\"\t\"pval\"\t\"padj\"\r\n",
        "\"comp10002_c0_seq1\"\t5.11042261412799\t6.56521445318632\t3.65563077506966\t0.556818181818182\t-0.844721774522088\t0.885218680234281\t1\r\n",
        "\"comp10005_c0_seq1\"\t4.89904260332464\t4.92391083988974\t4.87417436675954\t0.989898989898991\t-0.0146467759644005\t1\t1\r\n",
        "\"comp10007_c0_seq1\"\t11525.6691667085\t17587.3888682795\t5463.94946513745\t0.310674285197173\t-1.68652526171154\t0.147533184864772\t1\r\n",
        "\"comp10008_c0_seq1\"\t6329.84902821593\t6860.6491035797\t5799.04895285216\t0.845262432941859\t-0.242528763050997\t0.833689827988819\t1\r\n",
        "\"comp10009_c0_seq1\"\t11933.5704169675\t13182.9506219981\t10684.1902119369\t0.810455149100568\t-0.303195746233489\t0.792097629317823\t1\r\n",
        "\"comp1000_c0_seq1\"\t24.3833059520802\t42.6738939457111\t6.09271795844943\t0.142773892773893\t-2.80819589849697\t0.159574074144965\t1\r\n",
        "\"comp10010_c0_seq1\"\t11.0290629166217\t12.3097770997243\t9.74834873351908\t0.791919191919192\t-0.336574870851763\t0.936698849449615\t1\r\n",
        "\"comp10012_c0_seq1\"\t2.25057540914152\t3.28260722659316\t1.21854359168989\t0.371212121212121\t-1.42968427524324\t0.920190447196145\t1\r\n",
        "\"comp10013_c0_seq1\"\t3.87944490415555\t4.10325903324145\t3.65563077506966\t0.890909090909092\t-0.16664986940945\t1\t1\r\n"
       ]
      }
     ],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Want pval < .02  \n",
      "\n",
      "HOW in commandline  "
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "raw",
     "metadata": {},
     "source": [
      "comp42267_c0_seq1\n",
      "comp27506_c0_seq1\n",
      "comp31078_c0_seq1\n",
      "comp42994_c1_seq12\n",
      "comp43376_c0_seq11\n",
      "comp43684_c0_seq63\n",
      "comp43850_c0_seq2\n",
      "comp23647_c0_seq1\n",
      "comp37750_c2_seq5\n",
      "comp14218_c0_seq1\n",
      "comp38365_c0_seq23\n",
      "comp42326_c1_seq2\n",
      "comp42897_c0_seq4\n",
      "comp41990_c0_seq3\n",
      "comp39888_c0_seq2\n",
      "comp41088_c0_seq3\n",
      "comp22830_c0_seq1\n",
      "comp33776_c1_seq2\n",
      "comp9895_c0_seq2\n",
      "comp34272_c0_seq1\n",
      "comp43741_c0_seq9\n",
      "comp19578_c0_seq1\n",
      "comp28371_c1_seq1\n",
      "comp44708_c0_seq2\n",
      "comp38094_c0_seq2\n",
      "comp46998_c0_seq1\n",
      "comp7324_c0_seq1\n",
      "comp30573_c0_seq1\n",
      "comp42812_c1_seq2\n",
      "comp40434_c1_seq2\n",
      "comp38128_c0_seq1\n",
      "comp37019_c0_seq1\n",
      "comp29092_c0_seq2\n",
      "comp43755_c0_seq29\n",
      "comp36701_c0_seq7\n",
      "comp39792_c1_seq4\n",
      "comp44757_c0_seq12\n",
      "comp41431_c0_seq1\n",
      "comp42010_c0_seq2\n",
      "comp38830_c0_seq3\n",
      "comp41430_c0_seq1\n",
      "comp19258_c0_seq1\n",
      "comp34994_c0_seq1\n",
      "comp37019_c0_seq9\n",
      "comp35574_c1_seq2\n",
      "comp7357_c0_seq1\n",
      "comp33776_c1_seq3\n",
      "comp9790_c0_seq2\n",
      "comp30947_c0_seq1\n",
      "comp10747_c0_seq1\n",
      "comp28235_c0_seq1\n",
      "comp30920_c0_seq1\n",
      "comp30920_c1_seq1\n",
      "comp33014_c0_seq7\n",
      "comp34795_c4_seq2\n",
      "comp44292_c0_seq1\n",
      "comp43755_c0_seq14\n",
      "comp40760_c0_seq3\n",
      "comp39494_c0_seq7\n",
      "comp40881_c2_seq3\n",
      "comp43800_c0_seq2\n",
      "comp43937_c0_seq7\n",
      "comp44612_c0_seq13\n",
      "comp40727_c0_seq1\n",
      "comp35003_c0_seq2\n",
      "comp38767_c1_seq4\n",
      "comp28714_c1_seq1\n",
      "comp33568_c0_seq2\n",
      "comp36518_c0_seq7\n",
      "comp43171_c0_seq2\n",
      "comp41734_c0_seq1\n",
      "comp38114_c0_seq2\n",
      "comp44603_c0_seq5\n",
      "comp42486_c0_seq1\n",
      "comp35826_c3_seq1\n",
      "comp35864_c0_seq3\n",
      "comp36501_c1_seq2\n",
      "comp9904_c0_seq1\n",
      "comp44992_c0_seq1\n",
      "comp33559_c0_seq2\n",
      "comp39175_c0_seq4\n",
      "comp42186_c0_seq7\n",
      "comp25575_c0_seq1\n",
      "comp36140_c0_seq1\n",
      "comp7810_c0_seq1\n",
      "comp40947_c0_seq2\n",
      "comp44325_c2_seq1\n",
      "comp37915_c0_seq2\n",
      "comp38004_c0_seq1\n",
      "comp16665_c0_seq1\n",
      "comp30134_c0_seq1\n",
      "comp34952_c0_seq1\n",
      "comp37019_c0_seq14\n",
      "comp18651_c1_seq1\n",
      "comp39943_c0_seq3\n",
      "comp39216_c0_seq1\n",
      "comp26913_c0_seq4\n",
      "comp44542_c1_seq2\n",
      "comp42117_c0_seq2\n",
      "comp38371_c0_seq1\n",
      "comp39745_c1_seq10\n",
      "comp42837_c1_seq2\n",
      "comp37098_c0_seq5\n",
      "comp23692_c0_seq2\n",
      "comp40869_c0_seq2\n",
      "comp11822_c0_seq1\n",
      "comp40954_c0_seq1\n",
      "comp30027_c0_seq1\n",
      "comp36832_c0_seq1\n",
      "comp46105_c0_seq1\n",
      "comp41537_c0_seq5\n",
      "comp38489_c0_seq2\n",
      "comp38316_c0_seq1\n",
      "comp39573_c0_seq3\n",
      "comp37098_c0_seq7\n",
      "comp37430_c6_seq1\n",
      "comp44721_c0_seq5\n",
      "comp30821_c0_seq3\n",
      "comp36096_c1_seq2\n",
      "comp41426_c1_seq3\n",
      "comp43937_c0_seq5\n",
      "comp44825_c0_seq2\n",
      "comp38562_c2_seq4\n",
      "comp29985_c0_seq1\n",
      "comp44175_c0_seq9\n",
      "comp28031_c0_seq1\n",
      "comp42897_c0_seq7\n",
      "comp24054_c1_seq1\n",
      "comp39365_c0_seq10\n",
      "comp40252_c2_seq4\n",
      "comp42897_c0_seq5\n",
      "comp37359_c0_seq1\n",
      "comp20796_c1_seq1\n",
      "comp22241_c0_seq1\n",
      "comp22723_c0_seq1\n",
      "comp31492_c0_seq3\n",
      "comp36183_c1_seq1\n",
      "comp36849_c3_seq1\n",
      "comp10314_c0_seq1\n",
      "comp23359_c0_seq2\n",
      "comp38801_c1_seq7\n",
      "comp46088_c0_seq1\n",
      "comp38176_c0_seq1\n",
      "comp39569_c0_seq1\n",
      "comp42004_c0_seq1\n",
      "comp27215_c0_seq1\n",
      "comp26537_c0_seq3\n",
      "comp43766_c3_seq1\n",
      "comp36804_c4_seq9\n",
      "comp34249_c2_seq1\n",
      "comp46035_c0_seq1\n",
      "comp44200_c0_seq12\n",
      "comp31563_c0_seq2\n",
      "comp46089_c0_seq1\n",
      "comp27903_c0_seq1\n",
      "comp42005_c0_seq5\n",
      "comp20379_c0_seq1\n",
      "comp41153_c1_seq2\n",
      "comp41861_c0_seq8\n",
      "comp44076_c0_seq18\n",
      "comp41709_c1_seq5\n",
      "comp40221_c0_seq2\n",
      "comp30876_c0_seq1\n",
      "comp37208_c0_seq5\n",
      "comp42410_c0_seq3\n",
      "comp37788_c0_seq2\n",
      "comp7811_c0_seq1\n",
      "comp44684_c0_seq2\n",
      "comp19258_c3_seq1\n",
      "comp39776_c0_seq4\n",
      "comp32996_c0_seq11\n",
      "comp31314_c0_seq1\n",
      "comp36096_c1_seq1\n",
      "comp41407_c0_seq1\n",
      "comp40252_c1_seq1\n",
      "comp41557_c0_seq5\n",
      "comp38611_c0_seq21\n",
      "comp41352_c1_seq2\n",
      "comp31534_c1_seq1\n",
      "comp42401_c0_seq2\n",
      "comp34365_c0_seq2\n",
      "comp35587_c0_seq1\n",
      "comp33091_c2_seq2\n",
      "comp35782_c0_seq2\n",
      "comp25748_c0_seq1\n",
      "comp38972_c0_seq2\n",
      "comp10314_c0_seq2\n",
      "comp15683_c0_seq1\n",
      "comp41118_c0_seq2\n",
      "comp43196_c0_seq3\n",
      "comp43376_c1_seq1\n",
      "comp44545_c1_seq1\n",
      "comp47715_c0_seq1\n",
      "comp37822_c0_seq1\n",
      "comp39193_c0_seq2\n",
      "comp36859_c0_seq1\n",
      "comp41972_c4_seq8\n",
      "comp7160_c0_seq1\n",
      "comp41218_c1_seq13"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "What we want is SPID list for DEG and SPID list for all proteins"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "<img src=\"http://eagle.fish.washington.edu/cnidarian/skitch/SQLShare_-_View_Query_189AB723.png\" alt=\"SQLShare_-_View_Query_189AB723_png\"/>"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": []
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}