notebooks/2c_U2OS_Kinase_Expression.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "795354aa",
   "metadata": {},
   "source": [
    "**Notebook - U2OS Kinase Expression**\n",
    "\n",
    "This notebook looks at the U2OS cell line and associated kinase protein expression data. This information formed part of the basis for including/excluding specific kinase inhibitors.\n",
    "\n",
    "Data Sources & Information:\n",
    "- https://depmap.org/portal/download/all/?release=CCLE+2019&file=CCLE_RPPA_20181003.csv\n",
    "- https://depmap.org/portal/cell_line/ACH-000364?tab=mutation\n",
    "- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7861052/\n",
    "- https://gracebio.com/cancer-cell-line-encyclopedia-expanded-to-include-rppa-analysis-data/\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5503cde9",
   "metadata": {},
   "source": [
    "# Imports:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "9b0dbfd0",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1948aa0f",
   "metadata": {},
   "source": [
    "# Load Data:\n",
    "Data Source: https://depmap.org/portal/download/all/?release=DepMap+Public+22Q4&file=OmicsExpressionProteinCodingGenesTPMLogp1.csv\n",
    "\n",
    "\n",
    "\"Gene expression TPM values of the protein coding genes for DepMap cell lines. Values are inferred from RNA-seq data using the RSEM tool and are reported after log2 transformation, using a pseudo-count of 1; log2(TPM+1).\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "6c1c7cf5",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(1408, 19194)\n"
     ]
    },
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>cell_type</th>\n",
       "      <th>TSPAN6 (7105)</th>\n",
       "      <th>TNMD (64102)</th>\n",
       "      <th>DPM1 (8813)</th>\n",
       "      <th>SCYL3 (57147)</th>\n",
       "      <th>C1orf112 (55732)</th>\n",
       "      <th>FGR (2268)</th>\n",
       "      <th>CFH (3075)</th>\n",
       "      <th>FUCA2 (2519)</th>\n",
       "      <th>GCLC (2729)</th>\n",
       "      <th>...</th>\n",
       "      <th>H3C2 (8358)</th>\n",
       "      <th>H3C3 (8352)</th>\n",
       "      <th>AC098582.1 (8916)</th>\n",
       "      <th>DUS4L-BCAP29 (115253422)</th>\n",
       "      <th>C8orf44-SGK3 (100533105)</th>\n",
       "      <th>ELOA3B (728929)</th>\n",
       "      <th>NPBWR1 (2831)</th>\n",
       "      <th>ELOA3D (100506888)</th>\n",
       "      <th>ELOA3 (162699)</th>\n",
       "      <th>CDR1 (1038)</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ACH-001113</td>\n",
       "      <td>4.331992</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>7.364660</td>\n",
       "      <td>2.792855</td>\n",
       "      <td>4.471187</td>\n",
       "      <td>0.028569</td>\n",
       "      <td>1.226509</td>\n",
       "      <td>3.044394</td>\n",
       "      <td>6.500005</td>\n",
       "      <td>...</td>\n",
       "      <td>2.689299</td>\n",
       "      <td>0.189034</td>\n",
       "      <td>0.201634</td>\n",
       "      <td>2.130931</td>\n",
       "      <td>0.555816</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.275007</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ACH-001289</td>\n",
       "      <td>4.567424</td>\n",
       "      <td>0.584963</td>\n",
       "      <td>7.106641</td>\n",
       "      <td>2.543496</td>\n",
       "      <td>3.504620</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.189034</td>\n",
       "      <td>3.813525</td>\n",
       "      <td>4.221877</td>\n",
       "      <td>...</td>\n",
       "      <td>1.286881</td>\n",
       "      <td>1.049631</td>\n",
       "      <td>0.321928</td>\n",
       "      <td>1.464668</td>\n",
       "      <td>0.632268</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.014355</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2 rows × 19194 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    cell_type  TSPAN6 (7105)  TNMD (64102)  DPM1 (8813)  SCYL3 (57147)  \\\n",
       "0  ACH-001113       4.331992      0.000000     7.364660       2.792855   \n",
       "1  ACH-001289       4.567424      0.584963     7.106641       2.543496   \n",
       "\n",
       "   C1orf112 (55732)  FGR (2268)  CFH (3075)  FUCA2 (2519)  GCLC (2729)  ...  \\\n",
       "0          4.471187    0.028569    1.226509      3.044394     6.500005  ...   \n",
       "1          3.504620    0.000000    0.189034      3.813525     4.221877  ...   \n",
       "\n",
       "   H3C2 (8358)  H3C3 (8352)  AC098582.1 (8916)  DUS4L-BCAP29 (115253422)  \\\n",
       "0     2.689299     0.189034           0.201634                  2.130931   \n",
       "1     1.286881     1.049631           0.321928                  1.464668   \n",
       "\n",
       "   C8orf44-SGK3 (100533105)  ELOA3B (728929)  NPBWR1 (2831)  \\\n",
       "0                  0.555816              0.0       0.275007   \n",
       "1                  0.632268              0.0       0.014355   \n",
       "\n",
       "   ELOA3D (100506888)  ELOA3 (162699)  CDR1 (1038)  \n",
       "0                 0.0             0.0          0.0  \n",
       "1                 0.0             0.0          0.0  \n",
       "\n",
       "[2 rows x 19194 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Read in gene expression data:\n",
    "u2os_omics = pd.read_csv('data/OmicsExpressionProteinCodingGenesTPMLogp1.csv')\n",
    "u2os_omics = u2os_omics.rename(columns={u2os_omics.columns[0]: 'cell_type'})\n",
    "print(u2os_omics.shape)\n",
    "u2os_omics.head(2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "c298512a",
   "metadata": {},
   "outputs": [],
   "source": [
    "# U2OS Dep-Map ID - https://depmap.org/portal/cell_line/ACH-000364?tab=mutation:\n",
    "u2os_depmap_id = 'ACH-000364'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "78e7f52b",
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>cell_type</th>\n",
       "      <th>TSPAN6 (7105)</th>\n",
       "      <th>TNMD (64102)</th>\n",
       "      <th>DPM1 (8813)</th>\n",
       "      <th>SCYL3 (57147)</th>\n",
       "      <th>C1orf112 (55732)</th>\n",
       "      <th>FGR (2268)</th>\n",
       "      <th>CFH (3075)</th>\n",
       "      <th>FUCA2 (2519)</th>\n",
       "      <th>GCLC (2729)</th>\n",
       "      <th>...</th>\n",
       "      <th>H3C2 (8358)</th>\n",
       "      <th>H3C3 (8352)</th>\n",
       "      <th>AC098582.1 (8916)</th>\n",
       "      <th>DUS4L-BCAP29 (115253422)</th>\n",
       "      <th>C8orf44-SGK3 (100533105)</th>\n",
       "      <th>ELOA3B (728929)</th>\n",
       "      <th>NPBWR1 (2831)</th>\n",
       "      <th>ELOA3D (100506888)</th>\n",
       "      <th>ELOA3 (162699)</th>\n",
       "      <th>CDR1 (1038)</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>832</th>\n",
       "      <td>ACH-000364</td>\n",
       "      <td>4.519164</td>\n",
       "      <td>0.0</td>\n",
       "      <td>6.673698</td>\n",
       "      <td>2.134221</td>\n",
       "      <td>4.107688</td>\n",
       "      <td>0.014355</td>\n",
       "      <td>0.422233</td>\n",
       "      <td>5.758889</td>\n",
       "      <td>4.806324</td>\n",
       "      <td>...</td>\n",
       "      <td>2.503349</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.863938</td>\n",
       "      <td>2.157044</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.505891</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.389567</td>\n",
       "      <td>0.097611</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1 rows × 19194 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      cell_type  TSPAN6 (7105)  TNMD (64102)  DPM1 (8813)  SCYL3 (57147)  \\\n",
       "832  ACH-000364       4.519164           0.0     6.673698       2.134221   \n",
       "\n",
       "     C1orf112 (55732)  FGR (2268)  CFH (3075)  FUCA2 (2519)  GCLC (2729)  ...  \\\n",
       "832          4.107688    0.014355    0.422233      5.758889     4.806324  ...   \n",
       "\n",
       "     H3C2 (8358)  H3C3 (8352)  AC098582.1 (8916)  DUS4L-BCAP29 (115253422)  \\\n",
       "832     2.503349          0.0           0.863938                  2.157044   \n",
       "\n",
       "     C8orf44-SGK3 (100533105)  ELOA3B (728929)  NPBWR1 (2831)  \\\n",
       "832                       0.0              0.0       0.505891   \n",
       "\n",
       "     ELOA3D (100506888)  ELOA3 (162699)  CDR1 (1038)  \n",
       "832                 0.0        0.389567     0.097611  \n",
       "\n",
       "[1 rows x 19194 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Subsetting the data to only include the U2OS cell line:\n",
    "u2os_data = u2os_omics[u2os_omics['cell_type'].str.contains(u2os_depmap_id)]\n",
    "u2os_data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "3255dc24",
   "metadata": {},
   "outputs": [
    {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>EGFR (1956)</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>832</th>\n",
       "      <td>2.163499</td>\n",
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      "text/plain": [
       "     EGFR (1956)\n",
       "832     2.163499"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Example filtering:\n",
    "u2os_data.filter(regex='EGFR')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9df6af6c",
   "metadata": {},
   "source": [
    "# Relate DepMap Data to Kinase Inhibitor Classes:\n",
    "Below are are the kinase inhibitor classes included within our dataset and their associated genes:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "a6798840",
   "metadata": {},
   "outputs": [],
   "source": [
    "ki_tgt_dict = {\n",
    "    'PI3K': 'PIK3CA|PIK3CB|PIK3CD|PIK3CG',\n",
    "    'EGFR': 'EGFR',\n",
    "    'p38 MAPK': 'MAPK11|MAPK12|MAPK13|MAPK14',\n",
    "    'JAK': 'JAK1|JAK2|JAK3|TYK2',\n",
    "    'RAF': '^ARAF|BRAF|^RAF1',\n",
    "    'AURK': 'AURKA |AURKB|AURKC',\n",
    "    'ALK': 'ALK ',\n",
    "    'SRC': '^SRC |LYN |FYN|YES1|FGR|BLK|HCK|LCK',\n",
    "    'ROCK': 'ROCK1|ROCK2',\n",
    "    'MEK': 'MAP2K1|MAP2K2',\n",
    "    'GSK': 'GSK3A|GSK3B',\n",
    "    'CDK': 'CDK1 |CDK2 |CDK4 |CDK5 |CDK6 |CDK7 |CDK9 ',\n",
    "    'VEGFR': 'FLT1|^KDR|FLT4',\n",
    "    'BCR-ABL': '^ABL1 |^ABL2 |BCR',\n",
    "    'PDGFR': 'PDGFRA|PDGFRB',\n",
    "    'FGFR': 'FGFR1 |FGFR2|FGFR3|FGFR4',\n",
    "    'BTK': '^BTK',    # '^' added to exclude IBTK\n",
    "    'AKT': 'AKT1 |AKT2|AKT3',\n",
    "    'mTOR': '^MTOR '\n",
    "    }"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "a4182e05",
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>EGFR (1956)</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>832</th>\n",
       "      <td>2.163499</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
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      "text/plain": [
       "     EGFR (1956)\n",
       "832     2.163499"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "u2os_data.filter(regex=ki_tgt_dict['EGFR'])"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9be4e06a",
   "metadata": {},
   "source": [
    "## Return Gene Expression Values:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "8e7d6c1e",
   "metadata": {},
   "outputs": [],
   "source": [
    "exp_values = []\n",
    "\n",
    "for ki in ki_tgt_dict:\n",
    "    exp_data = u2os_data.filter(regex=ki_tgt_dict[ki]).T.reset_index().values\n",
    "    exp_values.append(exp_data)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "aa5a7b64",
   "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>exp_val</th>\n",
       "      <th>k_inhib</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>PIK3CB</td>\n",
       "      <td>2.950468</td>\n",
       "      <td>PI3K</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>PIK3CG</td>\n",
       "      <td>0.028569</td>\n",
       "      <td>PI3K</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>PIK3CA</td>\n",
       "      <td>2.9241</td>\n",
       "      <td>PI3K</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>PIK3CD</td>\n",
       "      <td>2.733354</td>\n",
       "      <td>PI3K</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>EGFR</td>\n",
       "      <td>2.163499</td>\n",
       "      <td>EGFR</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     gene   exp_val k_inhib\n",
       "0  PIK3CB  2.950468    PI3K\n",
       "1  PIK3CG  0.028569    PI3K\n",
       "2  PIK3CA    2.9241    PI3K\n",
       "3  PIK3CD  2.733354    PI3K\n",
       "4    EGFR  2.163499    EGFR"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "u2os_evs_df = pd.DataFrame(np.concatenate(exp_values), columns=['gene', 'exp_val'])\n",
    "# Retain just gene names, removing numbers in brackets in original data:\n",
    "u2os_evs_df['gene'] = [x[0] for x in u2os_evs_df.gene.str.split(\" \", expand=False)]\n",
    "# Reassigning gene to kinase inhibitor in dictionary:\n",
    "ki_list = [[key for key, value in ki_tgt_dict.items() if x in value] for x in u2os_evs_df['gene']]\n",
    "u2os_evs_df['k_inhib'] = [item for sublist in ki_list for item in sublist]\n",
    "u2os_evs_df.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5d4ba3f0",
   "metadata": {},
   "source": [
    "## Group by Kinase Inhibitor Class:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "0d3f3500",
   "metadata": {},
   "outputs": [
    {
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       "        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>k_inhib</th>\n",
       "      <th>exp_val</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>MEK</td>\n",
       "      <td>6.034046</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>CDK</td>\n",
       "      <td>6.030705</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>GSK</td>\n",
       "      <td>5.909385</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AKT</td>\n",
       "      <td>5.856681</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AURK</td>\n",
       "      <td>5.759314</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>mTOR</td>\n",
       "      <td>5.100557</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>RAF</td>\n",
       "      <td>5.077632</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>ROCK</td>\n",
       "      <td>4.744178</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>FGFR</td>\n",
       "      <td>4.057675</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>p38 MAPK</td>\n",
       "      <td>3.689417</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>BCR-ABL</td>\n",
       "      <td>3.515022</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>JAK</td>\n",
       "      <td>3.309181</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>PDGFR</td>\n",
       "      <td>3.305077</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>SRC</td>\n",
       "      <td>2.444012</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>EGFR</td>\n",
       "      <td>2.163499</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>PI3K</td>\n",
       "      <td>2.159123</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>VEGFR</td>\n",
       "      <td>1.168495</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ALK</td>\n",
       "      <td>0.201634</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>BTK</td>\n",
       "      <td>0.124328</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     k_inhib   exp_val\n",
       "10       MEK  6.034046\n",
       "5        CDK  6.030705\n",
       "8        GSK  5.909385\n",
       "0        AKT  5.856681\n",
       "2       AURK  5.759314\n",
       "17      mTOR  5.100557\n",
       "13       RAF  5.077632\n",
       "14      ROCK  4.744178\n",
       "7       FGFR  4.057675\n",
       "18  p38 MAPK  3.689417\n",
       "3    BCR-ABL  3.515022\n",
       "9        JAK  3.309181\n",
       "11     PDGFR  3.305077\n",
       "15       SRC  2.444012\n",
       "6       EGFR  2.163499\n",
       "12      PI3K  2.159123\n",
       "16     VEGFR  1.168495\n",
       "1        ALK  0.201634\n",
       "4        BTK  0.124328"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "grouped_ki = pd.DataFrame(u2os_evs_df.groupby('k_inhib')['exp_val'].mean().reset_index()\n",
    "                         ).sort_values('exp_val', ascending=False)\n",
    "grouped_ki"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "7ae8bd90",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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