Gene Classification Analysis.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Unnamed: 0</th>\n",
       "      <th>Gene_Names</th>\n",
       "      <th>GO</th>\n",
       "      <th>Enzyme</th>\n",
       "      <th>Metabolic</th>\n",
       "      <th>Kinase</th>\n",
       "      <th>Transcription Factor</th>\n",
       "      <th>Nucleic-Acid Binding</th>\n",
       "      <th>Signalling</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>Gene names  (primary )</td>\n",
       "      <td>Gene ontology (GO)</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>PLAA</td>\n",
       "      <td>cell [GO:0005623]; cell junction [GO:0030054];...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>NACC1</td>\n",
       "      <td>cell junction [GO:0030054]; cytoplasm [GO:0005...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>MTSS1</td>\n",
       "      <td>actin cytoskeleton [GO:0015629]; cytoplasm [GO...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>PNPLA8</td>\n",
       "      <td>endoplasmic reticulum membrane [GO:0005789]; G...</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20345</td>\n",
       "      <td>20345</td>\n",
       "      <td>GPRC5B</td>\n",
       "      <td>cell surface [GO:0009986]; cytoplasmic vesicle...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20346</td>\n",
       "      <td>20346</td>\n",
       "      <td>DNAJB12</td>\n",
       "      <td>endoplasmic reticulum [GO:0005783]; endoplasmi...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20347</td>\n",
       "      <td>20347</td>\n",
       "      <td>GCNT3</td>\n",
       "      <td>extracellular exosome [GO:0070062]; Golgi memb...</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20348</td>\n",
       "      <td>20348</td>\n",
       "      <td>DLEC1</td>\n",
       "      <td>cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20349</td>\n",
       "      <td>20349</td>\n",
       "      <td>DLG5</td>\n",
       "      <td>cell junction [GO:0030054]; cell-cell adherens...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>20350 rows × 9 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       Unnamed: 0              Gene_Names  \\\n",
       "0               0  Gene names  (primary )   \n",
       "1               1                    PLAA   \n",
       "2               2                   NACC1   \n",
       "3               3                   MTSS1   \n",
       "4               4                  PNPLA8   \n",
       "...           ...                     ...   \n",
       "20345       20345                  GPRC5B   \n",
       "20346       20346                 DNAJB12   \n",
       "20347       20347                   GCNT3   \n",
       "20348       20348                   DLEC1   \n",
       "20349       20349                    DLG5   \n",
       "\n",
       "                                                      GO  Enzyme  Metabolic  \\\n",
       "0                                     Gene ontology (GO)   False      False   \n",
       "1      cell [GO:0005623]; cell junction [GO:0030054];...   False      False   \n",
       "2      cell junction [GO:0030054]; cytoplasm [GO:0005...   False      False   \n",
       "3      actin cytoskeleton [GO:0015629]; cytoplasm [GO...   False      False   \n",
       "4      endoplasmic reticulum membrane [GO:0005789]; G...    True       True   \n",
       "...                                                  ...     ...        ...   \n",
       "20345  cell surface [GO:0009986]; cytoplasmic vesicle...   False      False   \n",
       "20346  endoplasmic reticulum [GO:0005783]; endoplasmi...   False      False   \n",
       "20347  extracellular exosome [GO:0070062]; Golgi memb...    True       True   \n",
       "20348  cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...   False      False   \n",
       "20349  cell junction [GO:0030054]; cell-cell adherens...   False      False   \n",
       "\n",
       "       Kinase  Transcription Factor  Nucleic-Acid Binding  Signalling  \n",
       "0       False                 False                 False       False  \n",
       "1       False                 False                 False        True  \n",
       "2       False                  True                 False       False  \n",
       "3       False                 False                 False        True  \n",
       "4       False                 False                 False       False  \n",
       "...       ...                   ...                   ...         ...  \n",
       "20345   False                 False                 False        True  \n",
       "20346   False                 False                 False       False  \n",
       "20347   False                 False                 False       False  \n",
       "20348   False                 False                 False       False  \n",
       "20349   False                 False                 False        True  \n",
       "\n",
       "[20350 rows x 9 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Uniprot = pd.read_csv('Uniprot_Classification.csv')\n",
    "\n",
    "Uniprot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Genes</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>TP53</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>PTEN</td>\n",
       "    </tr>\n",
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       "      <td>2</td>\n",
       "      <td>AGA</td>\n",
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       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>FBXW7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>DLD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>142</td>\n",
       "      <td>PFKFB4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>143</td>\n",
       "      <td>PRCP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>144</td>\n",
       "      <td>NAA50</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>145</td>\n",
       "      <td>NAA60</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>146</td>\n",
       "      <td>LGSN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>147 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      Genes\n",
       "0      TP53\n",
       "1      PTEN\n",
       "2       AGA\n",
       "3     FBXW7\n",
       "4       DLD\n",
       "..      ...\n",
       "142  PFKFB4\n",
       "143    PRCP\n",
       "144   NAA50\n",
       "145   NAA60\n",
       "146    LGSN\n",
       "\n",
       "[147 rows x 1 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# load genelist of genes for matrix to be created \n",
    "\n",
    "Genelist = pd.read_csv('Genelist.csv', names = ['Genes'])\n",
    "\n",
    "Genelist"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Genes</th>\n",
       "      <th>Enzyme</th>\n",
       "      <th>Metabolic</th>\n",
       "      <th>Kinase</th>\n",
       "      <th>Transcription Factor</th>\n",
       "      <th>Nucleic-Acid Binding</th>\n",
       "      <th>Signalling</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>TP53</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>PTEN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>AGA</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>FBXW7</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>DLD</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>142</td>\n",
       "      <td>PFKFB4</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>143</td>\n",
       "      <td>PRCP</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>144</td>\n",
       "      <td>NAA50</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>145</td>\n",
       "      <td>NAA60</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>146</td>\n",
       "      <td>LGSN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>147 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      Genes Enzyme Metabolic Kinase Transcription Factor Nucleic-Acid Binding  \\\n",
       "0      TP53  False     False  False                 True                 True   \n",
       "1      PTEN   True      True  False                 True                False   \n",
       "2       AGA   True      True  False                False                False   \n",
       "3     FBXW7  False     False  False                 True                False   \n",
       "4       DLD   True      True  False                False                False   \n",
       "..      ...    ...       ...    ...                  ...                  ...   \n",
       "142  PFKFB4   True      True  False                False                False   \n",
       "143    PRCP   True      True  False                False                False   \n",
       "144   NAA50   True      True  False                False                False   \n",
       "145   NAA60   True      True  False                False                False   \n",
       "146    LGSN  False     False  False                False                False   \n",
       "\n",
       "    Signalling  \n",
       "0         True  \n",
       "1         True  \n",
       "2        False  \n",
       "3         True  \n",
       "4        False  \n",
       "..         ...  \n",
       "142      False  \n",
       "143       True  \n",
       "144      False  \n",
       "145      False  \n",
       "146      False  \n",
       "\n",
       "[147 rows x 7 columns]"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "factors = [\"Enzyme\", \"Metabolic\", \"Kinase\", \"Transcription Factor\", \"Nucleic-Acid Binding\", \"Signalling\"]\n",
    "\n",
    "for item in factors: \n",
    "    count_dict = Uniprot.set_index('Gene_Names')[item].to_dict()\n",
    "    Genelist[item] = Genelist['Genes'].map(count_dict)\n",
    "\n",
    "Genelist"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      " Enzyme Genes:  95 65.00 % \n",
      " Metabolic Enzyme Genes:  79 54.0 % \n",
      " Kinase Genes:  15 10.00 % \n",
      " Transcription Factor Genes:  37 25.0 % \n",
      " Nucleic Acid Binding Genes:  41 28.000000000000004 % \n",
      " Signalling Genes:  67 46.0 % \n",
      "\n"
     ]
    }
   ],
   "source": [
    "print('\\n', 'Enzyme Genes: ', Genelist['Enzyme'].sum(), \"{0:.2f}\".format(round(Genelist['Enzyme'].sum()/Genelist['Genes'].count(),2)*100), '%', '\\n',\n",
    "      'Metabolic Enzyme Genes: ', Genelist['Metabolic'].sum(), round(Genelist['Metabolic'].sum()/Genelist['Genes'].count(),2)*100, '%', '\\n',\n",
    "      'Kinase Genes: ', Genelist['Kinase'].sum(), \"{0:.2f}\".format(round(Genelist['Kinase'].sum()/Genelist['Genes'].count(),2)*100), '%', '\\n',\n",
    "      'Transcription Factor Genes: ', Genelist['Transcription Factor'].sum(), round(Genelist['Transcription Factor'].sum()/Genelist['Genes'].count(),2)*100, '%', '\\n',\n",
    "      'Nucleic Acid Binding Genes: ', Genelist['Nucleic-Acid Binding'].sum(), round(Genelist['Nucleic-Acid Binding'].sum()/Genelist['Genes'].count(),2)*100, '%','\\n',\n",
    "     'Signalling Genes: ', Genelist['Signalling'].sum(), round(Genelist['Signalling'].sum()/Genelist['Genes'].count(),2)*100, '%', '\\n',\n",
    "     )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Also run for KEGG metabolism genes "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>GENE</th>\n",
       "      <th>PATH_TYPE</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>ADCY4</td>\n",
       "      <td>METABOLISM</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>ADCY5</td>\n",
       "      <td>METABOLISM</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>ADCY6</td>\n",
       "      <td>METABOLISM</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>ADCY7</td>\n",
       "      <td>METABOLISM</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>ADCY8</td>\n",
       "      <td>METABOLISM</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1108</td>\n",
       "      <td>NDUFB4</td>\n",
       "      <td>METABOLISM</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1109</td>\n",
       "      <td>NDUFS3</td>\n",
       "      <td>METABOLISM</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1110</td>\n",
       "      <td>NDUFB5</td>\n",
       "      <td>METABOLISM</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1111</td>\n",
       "      <td>CYC1</td>\n",
       "      <td>METABOLISM</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1112</td>\n",
       "      <td>COX11</td>\n",
       "      <td>METABOLISM</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1113 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        GENE   PATH_TYPE\n",
       "0      ADCY4  METABOLISM\n",
       "1      ADCY5  METABOLISM\n",
       "2      ADCY6  METABOLISM\n",
       "3      ADCY7  METABOLISM\n",
       "4      ADCY8  METABOLISM\n",
       "...      ...         ...\n",
       "1108  NDUFB4  METABOLISM\n",
       "1109  NDUFS3  METABOLISM\n",
       "1110  NDUFB5  METABOLISM\n",
       "1111    CYC1  METABOLISM\n",
       "1112   COX11  METABOLISM\n",
       "\n",
       "[1113 rows x 2 columns]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "KEGG_M = pd.read_csv('KEGG Pathways - Metabolism.csv')\n",
    "\n",
    "KEGG_M"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Genes</th>\n",
       "      <th>Enzyme</th>\n",
       "      <th>Metabolic</th>\n",
       "      <th>Kinase</th>\n",
       "      <th>Transcription Factor</th>\n",
       "      <th>Nucleic-Acid Binding</th>\n",
       "      <th>Signalling</th>\n",
       "      <th>KEGG Metabolic</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>TP53</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>PTEN</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>AGA</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>FBXW7</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>DLD</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>142</td>\n",
       "      <td>PFKFB4</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>143</td>\n",
       "      <td>PRCP</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>144</td>\n",
       "      <td>NAA50</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>145</td>\n",
       "      <td>NAA60</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>146</td>\n",
       "      <td>LGSN</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>147 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      Genes Enzyme Metabolic Kinase Transcription Factor Nucleic-Acid Binding  \\\n",
       "0      TP53  False     False  False                 True                 True   \n",
       "1      PTEN   True      True  False                 True                False   \n",
       "2       AGA   True      True  False                False                False   \n",
       "3     FBXW7  False     False  False                 True                False   \n",
       "4       DLD   True      True  False                False                False   \n",
       "..      ...    ...       ...    ...                  ...                  ...   \n",
       "142  PFKFB4   True      True  False                False                False   \n",
       "143    PRCP   True      True  False                False                False   \n",
       "144   NAA50   True      True  False                False                False   \n",
       "145   NAA60   True      True  False                False                False   \n",
       "146    LGSN  False     False  False                False                False   \n",
       "\n",
       "    Signalling  KEGG Metabolic  \n",
       "0         True           False  \n",
       "1         True            True  \n",
       "2        False           False  \n",
       "3         True           False  \n",
       "4        False            True  \n",
       "..         ...             ...  \n",
       "142      False            True  \n",
       "143       True           False  \n",
       "144      False           False  \n",
       "145      False           False  \n",
       "146      False           False  \n",
       "\n",
       "[147 rows x 8 columns]"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Genelist['KEGG Metabolic'] = (Genelist['Genes']).isin(KEGG_M['GENE'])\n",
    "\n",
    "Genelist"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "25 17.006802721088434 %\n"
     ]
    }
   ],
   "source": [
    "print(Genelist['KEGG Metabolic'].sum(), (Genelist['KEGG Metabolic'].sum()/Genelist['Genes'].count())*100, '%' )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "Genelist.to_csv(r'Output.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<style scoped>\n",
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       "\n",
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       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Unnamed: 0</th>\n",
       "      <th>Gene_Names</th>\n",
       "      <th>GO</th>\n",
       "      <th>Enzyme</th>\n",
       "      <th>Metabolic</th>\n",
       "      <th>Kinase</th>\n",
       "      <th>Transcription Factor</th>\n",
       "      <th>Nucleic-Acid Binding</th>\n",
       "      <th>Signalling</th>\n",
       "      <th>KEGG Metabolic</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>Gene names  (primary )</td>\n",
       "      <td>Gene ontology (GO)</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>PLAA</td>\n",
       "      <td>cell [GO:0005623]; cell junction [GO:0030054];...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>NACC1</td>\n",
       "      <td>cell junction [GO:0030054]; cytoplasm [GO:0005...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>MTSS1</td>\n",
       "      <td>actin cytoskeleton [GO:0015629]; cytoplasm [GO...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>PNPLA8</td>\n",
       "      <td>endoplasmic reticulum membrane [GO:0005789]; G...</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20345</td>\n",
       "      <td>20345</td>\n",
       "      <td>GPRC5B</td>\n",
       "      <td>cell surface [GO:0009986]; cytoplasmic vesicle...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20346</td>\n",
       "      <td>20346</td>\n",
       "      <td>DNAJB12</td>\n",
       "      <td>endoplasmic reticulum [GO:0005783]; endoplasmi...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20347</td>\n",
       "      <td>20347</td>\n",
       "      <td>GCNT3</td>\n",
       "      <td>extracellular exosome [GO:0070062]; Golgi memb...</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20348</td>\n",
       "      <td>20348</td>\n",
       "      <td>DLEC1</td>\n",
       "      <td>cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20349</td>\n",
       "      <td>20349</td>\n",
       "      <td>DLG5</td>\n",
       "      <td>cell junction [GO:0030054]; cell-cell adherens...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>20350 rows × 10 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       Unnamed: 0              Gene_Names  \\\n",
       "0               0  Gene names  (primary )   \n",
       "1               1                    PLAA   \n",
       "2               2                   NACC1   \n",
       "3               3                   MTSS1   \n",
       "4               4                  PNPLA8   \n",
       "...           ...                     ...   \n",
       "20345       20345                  GPRC5B   \n",
       "20346       20346                 DNAJB12   \n",
       "20347       20347                   GCNT3   \n",
       "20348       20348                   DLEC1   \n",
       "20349       20349                    DLG5   \n",
       "\n",
       "                                                      GO  Enzyme  Metabolic  \\\n",
       "0                                     Gene ontology (GO)   False      False   \n",
       "1      cell [GO:0005623]; cell junction [GO:0030054];...   False      False   \n",
       "2      cell junction [GO:0030054]; cytoplasm [GO:0005...   False      False   \n",
       "3      actin cytoskeleton [GO:0015629]; cytoplasm [GO...   False      False   \n",
       "4      endoplasmic reticulum membrane [GO:0005789]; G...    True       True   \n",
       "...                                                  ...     ...        ...   \n",
       "20345  cell surface [GO:0009986]; cytoplasmic vesicle...   False      False   \n",
       "20346  endoplasmic reticulum [GO:0005783]; endoplasmi...   False      False   \n",
       "20347  extracellular exosome [GO:0070062]; Golgi memb...    True       True   \n",
       "20348  cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...   False      False   \n",
       "20349  cell junction [GO:0030054]; cell-cell adherens...   False      False   \n",
       "\n",
       "       Kinase  Transcription Factor  Nucleic-Acid Binding  Signalling  \\\n",
       "0       False                 False                 False       False   \n",
       "1       False                 False                 False        True   \n",
       "2       False                  True                 False       False   \n",
       "3       False                 False                 False        True   \n",
       "4       False                 False                 False       False   \n",
       "...       ...                   ...                   ...         ...   \n",
       "20345   False                 False                 False        True   \n",
       "20346   False                 False                 False       False   \n",
       "20347   False                 False                 False       False   \n",
       "20348   False                 False                 False       False   \n",
       "20349   False                 False                 False        True   \n",
       "\n",
       "       KEGG Metabolic  \n",
       "0               False  \n",
       "1               False  \n",
       "2               False  \n",
       "3               False  \n",
       "4               False  \n",
       "...               ...  \n",
       "20345           False  \n",
       "20346           False  \n",
       "20347           False  \n",
       "20348           False  \n",
       "20349           False  \n",
       "\n",
       "[20350 rows x 10 columns]"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Uniprot['KEGG Metabolic'] = (Uniprot['Gene_Names']).isin(KEGG_M['GENE'])\n",
    "\n",
    "Uniprot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1046"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Uniprot['KEGG Metabolic'].sum()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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