th17_heatmap.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Stand alone heatmap\n",
    "\n",
    "The interaction below loads and initializes a stand alone\n",
    "heatmap widget for exploring gene expression data.  The widget supports\n",
    "selection of genes and conditions using space separated lists of\n",
    "names or \"glob\" patterns.\n",
    "\n",
    "For example to select all `th0` conditions add `th0*` in the conditions\n",
    "text area and click the conditions button.\n",
    "\n",
    "To select `nsf`, `nme4`, and `nudt4` genes add `nsf nme4 nudt4` in the\n",
    "genes text area and click the genes button."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from jp_gene_viz import dExpression\n",
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
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       "\n",
       "// imitating ipywidgets/docs/source/examples/Custom Widget - Hello World.ipynb\n",
       "\n",
       "//require([\"widgets/js/widget\", \"widgets/js/manager\"], function(widget, manager){\n",
       "\n",
       "require.undef(\"SVGCanvas\");\n",
       "\n",
       "define(\"SVGCanvas\", [\"jupyter-js-widgets\"], function(widgets) {\n",
       "    \n",
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       "                if ((ty == \"number\") ||\n",
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       "                    (ty == \"boolean\")) {\n",
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       "                }\n",
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       "            info.svgX = ept.x;\n",
       "            info.svgY = ept.y;\n",
       "            var json = JSON.stringify(info);\n",
       "            that.model.set(\"event\", json);\n",
       "            that.touch();\n",
       "        };\n",
       "        return svgEventHandler;\n",
       "    };\n",
       "\n",
       "    var SVGEventLocation = function(that, e) {\n",
       "        // http://stackoverflow.com/questions/10298658/mouse-position-inside-autoscaled-svg\n",
       "        var pt = that.reference_point;\n",
       "        var svg = that.$svg[0];\n",
       "        pt.x = e.clientX;\n",
       "        pt.y = e.clientY;\n",
       "        return pt.matrixTransform(svg.getScreenCTM().inverse());\n",
       "    }\n",
       "    \n",
       "    var SVGCanvasView = widgets.DOMWidgetView.extend({\n",
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       "        render: function() {\n",
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       "            var svg = that.svg_elt(\"svg\");\n",
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       "            that.eventHandler = eventHandler;\n",
       "            that.named_elements = {};\n",
       "            svg.ipy_name = \"\";\n",
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       "            svg.setAttribute(\"preserveAspectRatio\", \"none\");\n",
       "            that.$el.append(that.$svg);\n",
       "            that.svg_parameters_changed();\n",
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       "            that.model.on(\"change:commands\", that.commands_changed, that);\n",
       "            that.model.on(\"change:viewBox\", that.svg_parameters_changed, that);\n",
       "            that.model.on(\"change:svg_width\", that.svg_parameters_changed, that);\n",
       "            that.model.on(\"change:svg_height\", that.svg_parameters_changed, that);\n",
       "            that.model.on(\"change:style\", that.svg_parameters_changed, that);\n",
       "            that.model.on(\"change:watch_event\", that.start_watch_event, that);\n",
       "            that.model.on(\"change:unwatch_event\", that.stop_watch_event, that);\n",
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       "        \n",
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       "                that.$svg.on(event_types, that.eventHandler);\n",
       "                that.model.set(\"watch_event\", \"\");\n",
       "                that.touch();\n",
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       "        },\n",
       "        \n",
       "        stop_watch_event: function() {\n",
       "            var that = this;\n",
       "            var event_types = that.model.get(\"unwatch_event\");\n",
       "            if (event_types != \"\") {\n",
       "                that.$svg.off(event_types);\n",
       "                that.model.set(\"watch_event\", \"\");\n",
       "                that.touch();\n",
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       "        },\n",
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       "        commands_changed: function() {\n",
       "            var that = this;\n",
       "            var svg = that.$svg[0];\n",
       "            var commands = that.get_JSON(\"commands\")\n",
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       "                var command_dict = commands[i];\n",
       "                var indicator = command_dict[\"command\"];\n",
       "                var method = that[\"do_\"+indicator];\n",
       "                method(that, command_dict);\n",
       "            }\n",
       "        },\n",
       "\n",
       "        do_fit: function(that, info) {\n",
       "            // fit viewport to bounding box.\n",
       "            var svg = that.$svg[0];\n",
       "            var bbox = svg.getBBox();\n",
       "            var D = {\"width\": bbox.width, \"height\": bbox.height, \"x\": bbox.x, \"y\": bbox.y}\n",
       "            var vbox = \"\" + D.x + \" \" + D.y + \" \" + D.width + \" \" + D.height;\n",
       "            if ((D.width > 0) && (D.height > 0)) {\n",
       "                that.model.set(\"boundingBox\", D);\n",
       "                if (info.changeView) {\n",
       "                    that.model.set(\"viewBox\", vbox);\n",
       "                }\n",
       "                // Element viewBox will be updated later by model change.\n",
       "                that.touch();\n",
       "            }\n",
       "        },\n",
       "        \n",
       "        do_add_element: function (that, info) {\n",
       "            var tag = info.tag;\n",
       "            var name = info.name;\n",
       "            var element = that.svg_elt(tag);\n",
       "            element.ipy_name = name;\n",
       "            var $element = $(element);\n",
       "            that.update_element($element, info);\n",
       "            // add event callbacks\n",
       "            that.$svg.append($element);\n",
       "            that.named_elements[name] = $element;\n",
       "        },\n",
       "        \n",
       "        do_change_element: function (that, info) {\n",
       "            var name = info.name;\n",
       "            var $element = that.named_elements[name];\n",
       "            if ($element) {\n",
       "                that.update_element($element, info);\n",
       "            } else {\n",
       "                console.warn(\"couldn't find element for \"+name);\n",
       "            }\n",
       "        },\n",
       "        \n",
       "        do_delete: function (that, info) {\n",
       "            var names = info.names;\n",
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       "        \n",
       "        update_element: function($element, info) {\n",
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       "                    element.setAttribute(att, atts[att]);\n",
       "                }\n",
       "            }\n",
       "            if (style) {\n",
       "                for (var styling in style) {\n",
       "                    element.style[styling] = style[styling];\n",
       "                }\n",
       "            }\n",
       "            if (text) {\n",
       "                $element.empty();\n",
       "                var node = document.createTextNode(text);\n",
       "                element.appendChild(node);\n",
       "            }\n",
       "        },\n",
       "        \n",
       "        do_empty: function (that, info) {\n",
       "            that.named_elements = {};\n",
       "            that.$svg.empty();\n",
       "        },\n",
       "        \n",
       "        svg_parameters_changed: function() {\n",
       "            var that = this;\n",
       "            var style_additions = that.get_JSON(\"style\");\n",
       "            var svg = that.$svg[0];\n",
       "            svg.setAttribute(\"viewBox\", that.model.get(\"viewBox\"));\n",
       "            svg.setAttribute(\"width\", that.model.get(\"svg_width\"));\n",
       "            svg.setAttribute(\"height\", that.model.get(\"svg_height\"));\n",
       "            for (var style_attr in style_additions) {\n",
       "                svg.style[style_attr] = style_additions[style_attr];\n",
       "            }\n",
       "        },\n",
       "        \n",
       "        get_JSON: function(name) {\n",
       "            var json = this.model.get(name);\n",
       "            return $.parseJSON(json);\n",
       "        },\n",
       "        \n",
       "        svg_elt: function(kind) {\n",
       "            return document.createElementNS('http://www.w3.org/2000/svg', kind);\n",
       "        }\n",
       "        \n",
       "    });\n",
       "    \n",
       "    //manager.WidgetManager.register_widget_view('SVGCanvasView', SVGCanvasView);\n",
       "    return {\n",
       "        SVGCanvasView: SVGCanvasView\n",
       "    }\n",
       "});\n"
      ],
      "text/plain": [
       "<IPython.core.display.Javascript object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "dExpression.load_javascript_support()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Widget Javascript not detected.  It may not be installed properly. Did you enable the widgetsnbextension? If not, then run \"jupyter nbextension enable --py --sys-prefix widgetsnbextension\"\n"
     ]
    }
   ],
   "source": [
    "tsv = \"data/pTh17jj_RNAseq_VSDcounts.txt\"\n",
    "E = dExpression.display_heat_map(tsv, show=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "E.match_text.value = \"th17_reg48hr*\"\n",
    "E.match_click()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Th17N 96 hr Analysis"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "fdr_cutoff = .01"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "contrast_file = \"data/pTh17jj_RNAseq_th17N_48h_aKo_v_th17N_48h.txt\"\n",
    "contrast_table = pd.read_table(contrast_file, index_col=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# Get genes whose difference in expression \n",
    "top_aKO_genes =  contrast_table[contrast_table['padj'] < fdr_cutoff].index.tolist()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "ValueError",
     "evalue": "too many draws",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-9-4e90093e7934>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0mE\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgenes_text\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalue\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\" \"\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtop_aKO_genes\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mE\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgenes_click\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m//anaconda/lib/python2.7/site-packages/jp_gene_viz-0.0.1-py2.7.egg/jp_gene_viz/dExpression.pyc\u001b[0m in \u001b[0;36mgenes_click\u001b[0;34m(self, b)\u001b[0m\n\u001b[1;32m    165\u001b[0m             \u001b[0mrows\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msorted\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrow_set\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m200\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    166\u001b[0m             \u001b[0mcolumns\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdisplay_heat_map\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcol_names\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 167\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdisplay_data\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrows\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcolumns\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    168\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    169\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mmatch_click\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mb\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m//anaconda/lib/python2.7/site-packages/jp_gene_viz-0.0.1-py2.7.egg/jp_gene_viz/dExpression.pyc\u001b[0m in \u001b[0;36mdisplay_data\u001b[0;34m(self, rows, cols, side_length)\u001b[0m\n\u001b[1;32m     83\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrow\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcol\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     84\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msvg\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mempty\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 85\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdraw\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     86\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     87\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mselect_rows\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrows\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m//anaconda/lib/python2.7/site-packages/jp_gene_viz-0.0.1-py2.7.egg/jp_gene_viz/dExpression.pyc\u001b[0m in \u001b[0;36mdraw\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    217\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mdraw\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    218\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdrawing\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 219\u001b[0;31m             \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"too many draws\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    220\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply_transform\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    221\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdrawing\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mTrue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mValueError\u001b[0m: too many draws"
     ]
    }
   ],
   "source": [
    "E.genes_text.value = \" \".join(top_aKO_genes)\n",
    "E.genes_click()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "contrast_file = \"data/pTh17jj_RNAseq_th17N_48h_dKo_v_th17N_48h.txt\"\n",
    "contrast_table = pd.read_table(contrast_file, index_col=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# Get genes whose difference in expression \n",
    "top_dKO_genes =  contrast_table[contrast_table['padj'] < fdr_cutoff].index.tolist()\n",
    "E.genes_text.value = \" \".join(top_dKO_genes)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "E.genes_click()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "contrast_file = \"data/pTh17jj_RNAseq_th17N_48h_gKo_v_th17N_48h.txt\"\n",
    "contrast_table = pd.read_table(contrast_file, index_col=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "top_gKO_genes =  contrast_table[contrast_table['padj'] < fdr_cutoff].index.tolist()\n",
    "E.genes_text.value = \" \".join(top_gKO_genes)\n",
    "E.genes_click()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Barplot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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DTASSFkbEziPY7nTgjuL1ncAeEXE5cHmVFZTX1h4YGGBgYGAE4ZiZTUa1/GhvWIlghEkA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\nSUVORK5CYII=\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x10e1f5610>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "ind = np.arange(3)\n",
    "width = .5\n",
    "plt.bar(ind, [len(top_aKO_genes),  len(top_gKO_genes), len(top_dKO_genes)], log=True, width=width)\n",
    "plt.ylabel('# of DE genes (FDR < {}'.format(fdr_cutoff))\n",
    "plt.title('aKO, gKO, and dKO Differential Expression')\n",
    "plt.xticks(ind + width/2., ('G1', 'G2', 'G3'))\n",
    "plt.xticks(ind + width/2., ['aKO', 'gKO', 'dKO'])\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['0610007P14Rik',\n",
       " '0610010F05Rik',\n",
       " '1600014C10Rik',\n",
       " '4632428N05Rik',\n",
       " '4632434I11Rik',\n",
       " '4930573O16Rik',\n",
       " '5830428M24Rik',\n",
       " '9130015A21Rik',\n",
       " 'AA467197',\n",
       " 'Aasdhppt',\n",
       " 'Abcb9',\n",
       " 'Ablim1',\n",
       " 'Ablim2',\n",
       " 'Abtb1',\n",
       " 'Acadl',\n",
       " 'Acvrl1',\n",
       " 'Adam8',\n",
       " 'Adap1',\n",
       " 'Adcy4',\n",
       " 'Adh4',\n",
       " 'Aff3',\n",
       " 'Agpat4',\n",
       " 'Alcam',\n",
       " 'Aldoc',\n",
       " 'Alpk2',\n",
       " 'Ankrd33b',\n",
       " 'Ankrd46',\n",
       " 'Aplp1',\n",
       " 'Arhgef1',\n",
       " 'Arhgef10',\n",
       " 'Arl4c',\n",
       " 'Arntl',\n",
       " 'Atp2a3',\n",
       " 'Atp2b4',\n",
       " 'Atp5sl',\n",
       " 'Atp9a',\n",
       " 'Avpi1',\n",
       " 'B3gnt8',\n",
       " 'B430306N03Rik',\n",
       " 'Bace2',\n",
       " 'Bcl2a1d',\n",
       " 'Bcl2l11',\n",
       " 'Bst1',\n",
       " 'Cacnb2',\n",
       " 'Ccdc43',\n",
       " 'Ccdc50',\n",
       " 'Ccdc63',\n",
       " 'Ccl20',\n",
       " 'Ccny',\n",
       " 'Ccr5',\n",
       " 'Ccr6',\n",
       " 'Cd101',\n",
       " 'Cd24a',\n",
       " 'Cd27',\n",
       " 'Cdkn1b',\n",
       " 'Chchd4',\n",
       " 'Chd7',\n",
       " 'Chit1',\n",
       " 'Chl1',\n",
       " 'Chmp4b',\n",
       " 'Chuk',\n",
       " 'Cldn25',\n",
       " 'Cndp2',\n",
       " 'Cnp',\n",
       " 'Col5a3',\n",
       " 'Cpd',\n",
       " 'Cry1',\n",
       " 'Csf1',\n",
       " 'Csf2',\n",
       " 'Ctbp2',\n",
       " 'Ctdsp2',\n",
       " 'Ctsa',\n",
       " 'Ctsw',\n",
       " 'Cul2',\n",
       " 'Cxcr1',\n",
       " 'Cyp11a1',\n",
       " 'Cysltr1',\n",
       " 'Cyth1',\n",
       " 'D19Bwg1357e',\n",
       " 'D630039A03Rik',\n",
       " 'Dab2',\n",
       " 'Ddc',\n",
       " 'Ddr1',\n",
       " 'Def6',\n",
       " 'Dgka',\n",
       " 'Dgkg',\n",
       " 'Dimt1',\n",
       " 'Dlg2',\n",
       " 'Dock9',\n",
       " 'Dtx3l',\n",
       " 'Dysf',\n",
       " 'Ecm1',\n",
       " 'Efemp2',\n",
       " 'Ehd2',\n",
       " 'Elovl5',\n",
       " 'Enpp2',\n",
       " 'Ept1',\n",
       " 'Esf1',\n",
       " 'F2rl1',\n",
       " 'Fah',\n",
       " 'Fam102a',\n",
       " 'Fam124b',\n",
       " 'Fam189b',\n",
       " 'Fam65b',\n",
       " 'Far1',\n",
       " 'Fbln1',\n",
       " 'Fbxo10',\n",
       " 'Fes',\n",
       " 'Fgfr1op',\n",
       " 'Flot1',\n",
       " 'Fosl2',\n",
       " 'Foxf1',\n",
       " 'Frmd6',\n",
       " 'Furin',\n",
       " 'Fut4',\n",
       " 'Fxyd5',\n",
       " 'Fxyd7',\n",
       " 'Gabarapl1',\n",
       " 'Galnt3',\n",
       " 'Galnt6',\n",
       " 'Gap43',\n",
       " 'Gas2',\n",
       " 'Gatsl2',\n",
       " 'Gcnt3',\n",
       " 'Gdi2',\n",
       " 'Gfra1',\n",
       " 'Gimap3',\n",
       " 'Gimap4',\n",
       " 'Gimap5',\n",
       " 'Gimap6',\n",
       " 'Gimap7',\n",
       " 'Glrx',\n",
       " 'Gm11110',\n",
       " 'Gm14005',\n",
       " 'Gm19705',\n",
       " 'Gm4827',\n",
       " 'Gpm6b',\n",
       " 'Gpr114',\n",
       " 'Gpr146',\n",
       " 'Gpr15',\n",
       " 'Gpr18',\n",
       " 'Gpr183',\n",
       " 'Grina',\n",
       " 'Grk5',\n",
       " 'Gsap',\n",
       " 'Gsn',\n",
       " 'Gstt1',\n",
       " 'Gtf2i',\n",
       " 'Gtpbp4',\n",
       " 'H2-Q10',\n",
       " 'H2afy',\n",
       " 'Hbegf',\n",
       " 'Hccs',\n",
       " 'Hdac5',\n",
       " 'Hecw2',\n",
       " 'Hmha1',\n",
       " 'Hopx',\n",
       " 'Hsf2bp',\n",
       " 'Hspa9',\n",
       " 'Ier5l',\n",
       " 'Ifngr1',\n",
       " 'Igfbp4',\n",
       " 'Igfbp7',\n",
       " 'Il12rb1',\n",
       " 'Il12rb2',\n",
       " 'Il13ra1',\n",
       " 'Il17a',\n",
       " 'Il17f',\n",
       " 'Il17ra',\n",
       " 'Il17re',\n",
       " 'Il22',\n",
       " 'Il23r',\n",
       " 'Il6ra',\n",
       " 'Il7r',\n",
       " 'Il9',\n",
       " 'Impa2',\n",
       " 'Inpp1',\n",
       " 'Inpp5b',\n",
       " 'Itga3',\n",
       " 'Itgb2',\n",
       " 'Itpkb',\n",
       " 'Ivns1abp',\n",
       " 'Jakmip1',\n",
       " 'Kat2b',\n",
       " 'Kcnj8',\n",
       " 'Kcnk10',\n",
       " 'Kif1a',\n",
       " 'Klf13',\n",
       " 'Klrd1',\n",
       " 'Klre1',\n",
       " 'Klrk1',\n",
       " 'Kremen2',\n",
       " 'Lad1',\n",
       " 'Lag3',\n",
       " 'Lama5',\n",
       " 'Lbh',\n",
       " 'Ldlrap1',\n",
       " 'Limd2',\n",
       " 'Lrrc32',\n",
       " 'Lrrk1',\n",
       " 'Lsp1',\n",
       " 'Ly6c1',\n",
       " 'Madd',\n",
       " 'Maml2',\n",
       " 'Maoa',\n",
       " 'Map3k5',\n",
       " 'Mapk8',\n",
       " 'Marcksl1',\n",
       " 'Mast4',\n",
       " 'Mctp2',\n",
       " 'Mdfic',\n",
       " 'Mdm1',\n",
       " 'Med30',\n",
       " 'Metrnl',\n",
       " 'Mfhas1',\n",
       " 'Mgst2',\n",
       " 'Midn',\n",
       " 'Mmachc',\n",
       " 'Mmp10',\n",
       " 'Mov10',\n",
       " 'Moxd1',\n",
       " 'Mphosph10',\n",
       " 'Mtap',\n",
       " 'Mtpap',\n",
       " 'Mxd1',\n",
       " 'Myo1e',\n",
       " 'Myo3b',\n",
       " 'Ndrg3',\n",
       " 'Ndufaf4',\n",
       " 'Ndufv3',\n",
       " 'Neat1',\n",
       " 'Neb',\n",
       " 'Nebl',\n",
       " 'Nkg7',\n",
       " 'Nln',\n",
       " 'Nlrc3',\n",
       " 'Noc3l',\n",
       " 'Nrp1',\n",
       " 'Nt5e',\n",
       " 'Olfr175-ps1',\n",
       " 'P2ry1',\n",
       " 'Pacs1',\n",
       " 'Pde2a',\n",
       " 'Pde6d',\n",
       " 'Pik3ap1',\n",
       " 'Pik3cd',\n",
       " 'Pik3ip1',\n",
       " 'Pitpnc1',\n",
       " 'Pitrm1',\n",
       " 'Plac8',\n",
       " 'Plcg1',\n",
       " 'Plek',\n",
       " 'Plin2',\n",
       " 'Pml',\n",
       " 'Pno1',\n",
       " 'Por',\n",
       " 'Pou6f1',\n",
       " 'Ppid',\n",
       " 'Ppm1h',\n",
       " 'Ppm1j',\n",
       " 'Ppp1r14c',\n",
       " 'Pros1',\n",
       " 'Prss46',\n",
       " 'Psap',\n",
       " 'Ptpn13',\n",
       " 'Ptpn5',\n",
       " 'Pxdc1',\n",
       " 'Pxmp4',\n",
       " 'Pygb',\n",
       " 'Qtrtd1',\n",
       " 'Rapgef4',\n",
       " 'Rbfox2',\n",
       " 'Rgcc',\n",
       " 'Rnf125',\n",
       " 'Rnf19a',\n",
       " 'Rpp40',\n",
       " 'Rrp15',\n",
       " 'Rsrp1',\n",
       " 'Rufy4',\n",
       " 'Rundc3a',\n",
       " 'Samhd1',\n",
       " 'Sash3',\n",
       " 'Satb1',\n",
       " 'Sbno2',\n",
       " 'Scml4',\n",
       " 'Sdc3',\n",
       " 'Sell',\n",
       " 'Selplg',\n",
       " 'Sema4d',\n",
       " 'Senp1',\n",
       " 'Sept9',\n",
       " 'Serpinb5',\n",
       " 'Sesn3',\n",
       " 'Sh2d1a',\n",
       " 'Sh3bp5',\n",
       " 'Siah3',\n",
       " 'Sipa1l1',\n",
       " 'Skap1',\n",
       " 'Sla2',\n",
       " 'Slc17a9',\n",
       " 'Slc38a3',\n",
       " 'Slc44a2',\n",
       " 'Slco3a1',\n",
       " 'Smad7',\n",
       " 'Smap2',\n",
       " 'Smox',\n",
       " 'Sox5',\n",
       " 'Spata13',\n",
       " 'Specc1',\n",
       " 'Spsb1',\n",
       " 'Ss18',\n",
       " 'St8sia1',\n",
       " 'Stard8',\n",
       " 'Stat3',\n",
       " 'Stk24',\n",
       " 'Stk32c',\n",
       " 'Stom',\n",
       " 'Stx11',\n",
       " 'Styk1',\n",
       " 'Susd3',\n",
       " 'Sv2c',\n",
       " 'Swap70',\n",
       " 'Syt11',\n",
       " 'Tasp1',\n",
       " 'Tbc1d9b',\n",
       " 'Tcp11l2',\n",
       " 'Tha1',\n",
       " 'Themis2',\n",
       " 'Tigit',\n",
       " 'Timd2',\n",
       " 'Tjp2',\n",
       " 'Tlr1',\n",
       " 'Tmem108',\n",
       " 'Tmem163',\n",
       " 'Tnfrsf1b',\n",
       " 'Tnfrsf23',\n",
       " 'Tnfrsf25',\n",
       " 'Tnfrsf26',\n",
       " 'Tnk2',\n",
       " 'Tns1',\n",
       " 'Top1',\n",
       " 'Tpd52',\n",
       " 'Tpst2',\n",
       " 'Trappc6a',\n",
       " 'Trib2',\n",
       " 'Trim37',\n",
       " 'Trpc4ap',\n",
       " 'Trub1',\n",
       " 'Tsc22d3',\n",
       " 'Tspan13',\n",
       " 'Tspan2',\n",
       " 'Tspan6',\n",
       " 'Ttc39c',\n",
       " 'Ubac2',\n",
       " 'Ube2h',\n",
       " 'Ucp2',\n",
       " 'Ugcg',\n",
       " 'Upp1',\n",
       " 'Ust',\n",
       " 'Utp20',\n",
       " 'Vasp',\n",
       " 'Vat1l',\n",
       " 'Vax2',\n",
       " 'Vill',\n",
       " 'Vps37b',\n",
       " 'Wdr12',\n",
       " 'Wdr18',\n",
       " 'Wdtc1',\n",
       " 'Whsc1l1',\n",
       " 'Wscd2',\n",
       " 'Xdh',\n",
       " 'Yipf3',\n",
       " 'Zc3h12c',\n",
       " 'Zcchc24',\n",
       " 'Zer1']"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "top_gKO_genes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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