Ensemble_to_gene_symbol.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Convert a Ensembl gene id to gene symbol\n",
    "\n",
    "This is a code snippet I find really useful when performing RNA seq. I usually end up with a counts table with Ensembl ids and when I perform differential expression I usually have to convert them to gene symbols.\n",
    "\n",
    "Below I have shown both python and an R implimentation of how this can be performed. "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Python"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Ensembl_id</th>\n",
       "      <th>baseMean</th>\n",
       "      <th>log2FoldChange</th>\n",
       "      <th>lfcSE</th>\n",
       "      <th>stat</th>\n",
       "      <th>pvalue</th>\n",
       "      <th>padj</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000115825</td>\n",
       "      <td>1349.126255</td>\n",
       "      <td>2.188251</td>\n",
       "      <td>0.224357</td>\n",
       "      <td>9.753452</td>\n",
       "      <td>1.780000e-22</td>\n",
       "      <td>1.630000e-18</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000129521</td>\n",
       "      <td>268.021678</td>\n",
       "      <td>2.765093</td>\n",
       "      <td>0.283863</td>\n",
       "      <td>9.740928</td>\n",
       "      <td>2.020000e-22</td>\n",
       "      <td>1.630000e-18</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000174697</td>\n",
       "      <td>18166.486330</td>\n",
       "      <td>3.543247</td>\n",
       "      <td>0.375474</td>\n",
       "      <td>9.436718</td>\n",
       "      <td>3.850000e-21</td>\n",
       "      <td>2.070000e-17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000123999</td>\n",
       "      <td>2094.498832</td>\n",
       "      <td>1.849762</td>\n",
       "      <td>0.204355</td>\n",
       "      <td>9.051715</td>\n",
       "      <td>1.410000e-19</td>\n",
       "      <td>5.690000e-16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000111961</td>\n",
       "      <td>4006.239649</td>\n",
       "      <td>2.415983</td>\n",
       "      <td>0.269737</td>\n",
       "      <td>8.956815</td>\n",
       "      <td>3.340000e-19</td>\n",
       "      <td>1.080000e-15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>ENSG00000126803</td>\n",
       "      <td>460.390284</td>\n",
       "      <td>1.358336</td>\n",
       "      <td>0.152744</td>\n",
       "      <td>8.892897</td>\n",
       "      <td>5.950000e-19</td>\n",
       "      <td>1.610000e-15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>ENSG00000169495</td>\n",
       "      <td>2369.954096</td>\n",
       "      <td>3.105755</td>\n",
       "      <td>0.359960</td>\n",
       "      <td>8.628059</td>\n",
       "      <td>6.240000e-18</td>\n",
       "      <td>1.440000e-14</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>ENSG00000111859</td>\n",
       "      <td>851.687123</td>\n",
       "      <td>1.611828</td>\n",
       "      <td>0.193185</td>\n",
       "      <td>8.343454</td>\n",
       "      <td>7.220000e-17</td>\n",
       "      <td>1.460000e-13</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>ENSG00000165105</td>\n",
       "      <td>772.740123</td>\n",
       "      <td>2.161641</td>\n",
       "      <td>0.260942</td>\n",
       "      <td>8.284002</td>\n",
       "      <td>1.190000e-16</td>\n",
       "      <td>2.140000e-13</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        Ensembl_id      baseMean  log2FoldChange     lfcSE      stat  \\\n",
       "0  ENSG00000115825   1349.126255        2.188251  0.224357  9.753452   \n",
       "1  ENSG00000129521    268.021678        2.765093  0.283863  9.740928   \n",
       "2  ENSG00000174697  18166.486330        3.543247  0.375474  9.436718   \n",
       "3  ENSG00000123999   2094.498832        1.849762  0.204355  9.051715   \n",
       "4  ENSG00000111961   4006.239649        2.415983  0.269737  8.956815   \n",
       "5  ENSG00000126803    460.390284        1.358336  0.152744  8.892897   \n",
       "6  ENSG00000169495   2369.954096        3.105755  0.359960  8.628059   \n",
       "7  ENSG00000111859    851.687123        1.611828  0.193185  8.343454   \n",
       "8  ENSG00000165105    772.740123        2.161641  0.260942  8.284002   \n",
       "\n",
       "         pvalue          padj  \n",
       "0  1.780000e-22  1.630000e-18  \n",
       "1  2.020000e-22  1.630000e-18  \n",
       "2  3.850000e-21  2.070000e-17  \n",
       "3  1.410000e-19  5.690000e-16  \n",
       "4  3.340000e-19  1.080000e-15  \n",
       "5  5.950000e-19  1.610000e-15  \n",
       "6  6.240000e-18  1.440000e-14  \n",
       "7  7.220000e-17  1.460000e-13  \n",
       "8  1.190000e-16  2.140000e-13  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import mygene\n",
    "import pandas as pd\n",
    "\n",
    "infile = pd.read_csv(\"data/gene_list.csv\", header = 0)\n",
    "\n",
    "infile\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0    ENSG00000115825\n",
      "1    ENSG00000129521\n",
      "2    ENSG00000174697\n",
      "3    ENSG00000123999\n",
      "4    ENSG00000111961\n",
      "5    ENSG00000126803\n",
      "6    ENSG00000169495\n",
      "7    ENSG00000111859\n",
      "8    ENSG00000165105\n",
      "Name: Ensembl_id, dtype: object\n",
      "querying 1-9...done.\n",
      "Finished.\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Ensembl_id</th>\n",
       "      <th>baseMean</th>\n",
       "      <th>log2FoldChange</th>\n",
       "      <th>lfcSE</th>\n",
       "      <th>stat</th>\n",
       "      <th>pvalue</th>\n",
       "      <th>padj</th>\n",
       "      <th>Symbol</th>\n",
       "      <th>Name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSG00000115825</td>\n",
       "      <td>1349.126255</td>\n",
       "      <td>2.188251</td>\n",
       "      <td>0.224357</td>\n",
       "      <td>9.753452</td>\n",
       "      <td>1.780000e-22</td>\n",
       "      <td>1.630000e-18</td>\n",
       "      <td>PRKD3</td>\n",
       "      <td>protein kinase D3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSG00000129521</td>\n",
       "      <td>268.021678</td>\n",
       "      <td>2.765093</td>\n",
       "      <td>0.283863</td>\n",
       "      <td>9.740928</td>\n",
       "      <td>2.020000e-22</td>\n",
       "      <td>1.630000e-18</td>\n",
       "      <td>EGLN3</td>\n",
       "      <td>egl-9 family hypoxia inducible factor 3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENSG00000174697</td>\n",
       "      <td>18166.486330</td>\n",
       "      <td>3.543247</td>\n",
       "      <td>0.375474</td>\n",
       "      <td>9.436718</td>\n",
       "      <td>3.850000e-21</td>\n",
       "      <td>2.070000e-17</td>\n",
       "      <td>LEP</td>\n",
       "      <td>leptin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ENSG00000123999</td>\n",
       "      <td>2094.498832</td>\n",
       "      <td>1.849762</td>\n",
       "      <td>0.204355</td>\n",
       "      <td>9.051715</td>\n",
       "      <td>1.410000e-19</td>\n",
       "      <td>5.690000e-16</td>\n",
       "      <td>INHA</td>\n",
       "      <td>inhibin alpha subunit</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ENSG00000111961</td>\n",
       "      <td>4006.239649</td>\n",
       "      <td>2.415983</td>\n",
       "      <td>0.269737</td>\n",
       "      <td>8.956815</td>\n",
       "      <td>3.340000e-19</td>\n",
       "      <td>1.080000e-15</td>\n",
       "      <td>SASH1</td>\n",
       "      <td>SAM and SH3 domain containing 1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>ENSG00000126803</td>\n",
       "      <td>460.390284</td>\n",
       "      <td>1.358336</td>\n",
       "      <td>0.152744</td>\n",
       "      <td>8.892897</td>\n",
       "      <td>5.950000e-19</td>\n",
       "      <td>1.610000e-15</td>\n",
       "      <td>HSPA2</td>\n",
       "      <td>heat shock protein family A (Hsp70) member 2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>ENSG00000169495</td>\n",
       "      <td>2369.954096</td>\n",
       "      <td>3.105755</td>\n",
       "      <td>0.359960</td>\n",
       "      <td>8.628059</td>\n",
       "      <td>6.240000e-18</td>\n",
       "      <td>1.440000e-14</td>\n",
       "      <td>HTRA4</td>\n",
       "      <td>HtrA serine peptidase 4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>ENSG00000111859</td>\n",
       "      <td>851.687123</td>\n",
       "      <td>1.611828</td>\n",
       "      <td>0.193185</td>\n",
       "      <td>8.343454</td>\n",
       "      <td>7.220000e-17</td>\n",
       "      <td>1.460000e-13</td>\n",
       "      <td>NEDD9</td>\n",
       "      <td>neural precursor cell expressed, developmental...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>ENSG00000165105</td>\n",
       "      <td>772.740123</td>\n",
       "      <td>2.161641</td>\n",
       "      <td>0.260942</td>\n",
       "      <td>8.284002</td>\n",
       "      <td>1.190000e-16</td>\n",
       "      <td>2.140000e-13</td>\n",
       "      <td>RASEF</td>\n",
       "      <td>RAS and EF-hand domain containing</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        Ensembl_id      baseMean  log2FoldChange     lfcSE      stat  \\\n",
       "0  ENSG00000115825   1349.126255        2.188251  0.224357  9.753452   \n",
       "1  ENSG00000129521    268.021678        2.765093  0.283863  9.740928   \n",
       "2  ENSG00000174697  18166.486330        3.543247  0.375474  9.436718   \n",
       "3  ENSG00000123999   2094.498832        1.849762  0.204355  9.051715   \n",
       "4  ENSG00000111961   4006.239649        2.415983  0.269737  8.956815   \n",
       "5  ENSG00000126803    460.390284        1.358336  0.152744  8.892897   \n",
       "6  ENSG00000169495   2369.954096        3.105755  0.359960  8.628059   \n",
       "7  ENSG00000111859    851.687123        1.611828  0.193185  8.343454   \n",
       "8  ENSG00000165105    772.740123        2.161641  0.260942  8.284002   \n",
       "\n",
       "         pvalue          padj Symbol  \\\n",
       "0  1.780000e-22  1.630000e-18  PRKD3   \n",
       "1  2.020000e-22  1.630000e-18  EGLN3   \n",
       "2  3.850000e-21  2.070000e-17    LEP   \n",
       "3  1.410000e-19  5.690000e-16   INHA   \n",
       "4  3.340000e-19  1.080000e-15  SASH1   \n",
       "5  5.950000e-19  1.610000e-15  HSPA2   \n",
       "6  6.240000e-18  1.440000e-14  HTRA4   \n",
       "7  7.220000e-17  1.460000e-13  NEDD9   \n",
       "8  1.190000e-16  2.140000e-13  RASEF   \n",
       "\n",
       "                                                Name  \n",
       "0                                  protein kinase D3  \n",
       "1            egl-9 family hypoxia inducible factor 3  \n",
       "2                                             leptin  \n",
       "3                              inhibin alpha subunit  \n",
       "4                    SAM and SH3 domain containing 1  \n",
       "5       heat shock protein family A (Hsp70) member 2  \n",
       "6                            HtrA serine peptidase 4  \n",
       "7  neural precursor cell expressed, developmental...  \n",
       "8                  RAS and EF-hand domain containing  "
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import mygene\n",
    "mg = mygene.MyGeneInfo()\n",
    "ens = infile[\"Ensembl_id\"]\n",
    "print ens\n",
    "ginfo = mg.querymany(ens, scopes='ensembl.gene')\n",
    "\n",
    "gene_symbol = []\n",
    "gene_name = []\n",
    "for g in ginfo:\n",
    "    for k, v in g.iteritems():\n",
    "        if k == \"symbol\":\n",
    "            gene_symbol.append(v)\n",
    "        elif k == \"name\":\n",
    "            gene_name.append(v)\n",
    "        \n",
    "infile[\"Symbol\"] = gene_symbol\n",
    "infile[\"Name\"] = gene_name\n",
    "\n",
    "infile"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# R"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# Add R magic command from rpy2 to allow R commands to run in the notebook\n",
    "%load_ext rpy2.ipython"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 60,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[1] \"integer\"\n",
       "       Ensembl_id   baseMean log2FoldChange     lfcSE     stat   pvalue\n",
       "1 ENSG00000111859   851.6871       1.611828 0.1931847 8.343454 7.22e-17\n",
       "2 ENSG00000111961  4006.2396       2.415983 0.2697368 8.956815 3.34e-19\n",
       "3 ENSG00000115825  1349.1263       2.188251 0.2243566 9.753452 1.78e-22\n",
       "4 ENSG00000123999  2094.4988       1.849762 0.2043549 9.051715 1.41e-19\n",
       "5 ENSG00000126803   460.3903       1.358336 0.1527440 8.892897 5.95e-19\n",
       "6 ENSG00000129521   268.0217       2.765093 0.2838634 9.740928 2.02e-22\n",
       "7 ENSG00000165105   772.7401       2.161641 0.2609417 8.284002 1.19e-16\n",
       "8 ENSG00000169495  2369.9541       3.105755 0.3599599 8.628059 6.24e-18\n",
       "9 ENSG00000174697 18166.4863       3.543247 0.3754745 9.436718 3.85e-21\n",
       "      padj SYMBOL\n",
       "1 1.46e-13  NEDD9\n",
       "2 1.08e-15  SASH1\n",
       "3 1.63e-18  PRKD3\n",
       "4 5.69e-16   INHA\n",
       "5 1.61e-15  HSPA2\n",
       "6 1.63e-18  EGLN3\n",
       "7 2.14e-13  RASEF\n",
       "8 1.44e-14  HTRA4\n",
       "9 2.07e-17    LEP\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%%R \n",
    "# %%R allows the whole cell to run as an R script\n",
    "\n",
    "library(org.Hs.eg.db)\n",
    "\n",
    "\n",
    "infile = read.csv(\"data/gene_list.csv\")\n",
    "data = infile[,\"Ensembl_id\"]\n",
    "\n",
    "# You can see that the subset data is listed as a integer, we now need to convert\n",
    "# this to a vector to pass it into the annotation mapping\n",
    "\n",
    "print(typeof(data))\n",
    "data = as.vector(data)\n",
    "\n",
    "# Using the org.Hs.eg.db we set up mapping info - if you look at the documentation you\n",
    "# can also obtain other keytypes\n",
    "\n",
    "annots <- select(org.Hs.eg.db, keys=data, \n",
    "                columns=\"SYMBOL\", keytype=\"ENSEMBL\")\n",
    "\n",
    "result <- merge(infile, annots, by.x=\"Ensembl_id\", by.y=\"ENSEMBL\")\n",
    "\n",
    "print(result)\n"
   ]
  }
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