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kellrott/DrugScan2.ipynb

Created June 29, 2017 20:00
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DrugScan2.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 31,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"import ophion\n",
"import json\n",
"import matplotlib.pyplot as plt\n",
"import scipy.stats as stats\n",
"import pandas\n",
"import numpy as np\n",
"import itertools"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"%matplotlib inline"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"O = ophion.Ophion(\"http://bmeg.compbio.ohsu.edu\")"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"#get all CCLE samples\n",
"all_samples = O.query().has(\"gid\", \"cohort:CCLE\").outgoing(\"hasSample\").values([\"gid\"]).execute()"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"GENES = [\"CDKN2A\", \"PTEN\", \"TP53\", \"SMAD4\"]"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"CDKN2A Positive Set: 48\n",
"CDKN2A Negative Set: 998\n",
"PTEN Positive Set: 142\n",
"PTEN Negative Set: 904\n",
"TP53 Positive Set: 553\n",
"TP53 Negative Set: 493\n",
"SMAD4 Positive Set: 62\n",
"SMAD4 Negative Set: 984\n"
]
}
],
"source": [
"mut_samples = {}\n",
"norm_samples = {}\n",
"for g in GENES:\n",
" #get CCLE samples with mutation\n",
" mut_samples[g] = list(set(O.query().has(\"gid\", \"gene:%s\" % (g)).incoming(\"variantInGene\").outgoing(\"variantInBiosample\").mark(\"a\")\\\n",
" .incoming(\"hasSample\").has(\"gid\", \"cohort:CCLE\").select(\"a\").values([\"gid\"]).execute()))\n",
"\n",
" #get CCLE samples without mutation\n",
" norm_samples[g] = list(set(all_samples).difference(mut_samples[g]))\n",
" \n",
" print \"%s Positive Set: %d\" % (g, len(mut_samples[g]))\n",
" print \"%s Negative Set: %d\" % (g, len(norm_samples[g]))"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"#get response values for the positive set (samples with mutation)\n",
"#and collect AUC value by drug\n",
"pos_response = {}\n",
"for g in GENES:\n",
" pos_response[g] = {}\n",
" for row in O.query().has(\"gid\", O.within(mut_samples[g])).outEdge(\"responseToCompound\").mark(\"a\").inVertex().mark(\"b\").select([\"a\", \"b\"]).execute():\n",
" for v in json.loads(row['a']['properties']['responseSummary']):\n",
" if v['type'] == \"AUC\":\n",
" compound = row['b']['gid']\n",
" if compound not in pos_response[g]:\n",
" pos_response[g][compound] = [ v[\"value\"] ]\n",
" else:\n",
" pos_response[g][compound].append(v[\"value\"])"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"#get response values for the negative set (samples without mutation)\n",
"#and collect AUC value by drug\n",
"neg_response = {}\n",
"for g in GENES:\n",
" neg_response[g] = {}\n",
"\n",
" for row in O.query().has(\"gid\", O.within(norm_samples[g])).outEdge(\"responseToCompound\").mark(\"a\").inVertex().mark(\"b\").select([\"a\", \"b\"]).execute():\n",
" for v in json.loads(row['a']['properties']['responseSummary']):\n",
" if v['type'] == \"AUC\":\n",
" compound = row['b']['gid']\n",
" if compound not in neg_response[g]:\n",
" neg_response[g][compound] = [ v[\"value\"] ]\n",
" else:\n",
" neg_response[g][compound].append(v[\"value\"])"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"4\n",
"4\n",
"['SMAD4', 'PTEN', 'CDKN2A', 'TP53']\n"
]
}
],
"source": [
"print len(pos_response)\n",
"print len(neg_response)\n",
"print pos_response.keys()"
]
},
{
"cell_type": "code",
"execution_count": 39,
"metadata": {
"collapsed": false,
"scrolled": false
},
"outputs": [],
"source": [
"#Collect t-test statistics\n",
"drugs = set(itertools.chain.from_iterable( i.keys() for i in pos_response.values() ))\n",
"out = []\n",
"for drug in drugs:\n",
" for g in GENES:\n",
" row = {\"drug\" : drug, \"mutation\" : g}\n",
" mut_values = pos_response[g][drug]\n",
" norm_values = neg_response[g][drug]\n",
" if len(mut_values) > 5 and len(norm_values) > 5:\n",
" s = stats.ttest_ind(mut_values, norm_values, equal_var=False)\n",
" row[\"t-statistic\"] = s.statistic\n",
" row[\"t-pvalue\"] = s.pvalue\n",
" s = stats.f_oneway(mut_values, norm_values)\n",
" row[\"a-statistic\"] = s.statistic\n",
" row[\"a-pvalue\"] = s.pvalue\n",
" out.append(row)"
]
},
{
"cell_type": "code",
"execution_count": 42,
"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>drug</th>\n",
" <th>mutation</th>\n",
" <th>t-statistic</th>\n",
" <th>t-pvalue</th>\n",
" <th>a-statistic</th>\n",
" <th>a-pvalue</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>1931</th>\n",
" <td>compound:nutlin-3</td>\n",
" <td>TP53</td>\n",
" <td>10.326801</td>\n",
" <td>9.209386e-23</td>\n",
" <td>121.681037</td>\n",
" <td>2.379157e-26</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1526</th>\n",
" <td>compound:BMS-536924</td>\n",
" <td>PTEN</td>\n",
" <td>6.899566</td>\n",
" <td>9.233542e-11</td>\n",
" <td>40.151225</td>\n",
" <td>4.030042e-10</td>\n",
" </tr>\n",
" <tr>\n",
" <th>854</th>\n",
" <td>compound:pluripotin</td>\n",
" <td>PTEN</td>\n",
" <td>5.760531</td>\n",
" <td>3.527544e-08</td>\n",
" <td>26.879984</td>\n",
" <td>2.751518e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>347</th>\n",
" <td>compound:NVP-ADW742</td>\n",
" <td>PTEN</td>\n",
" <td>5.243664</td>\n",
" <td>4.789674e-07</td>\n",
" <td>25.017915</td>\n",
" <td>7.067467e-07</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1014</th>\n",
" <td>compound:navitoclax:pluripotin (1:1 mol/mol)</td>\n",
" <td>PTEN</td>\n",
" <td>4.708911</td>\n",
" <td>5.418047e-06</td>\n",
" <td>22.479716</td>\n",
" <td>2.532986e-06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>561</th>\n",
" <td>compound:linsitinib</td>\n",
" <td>PTEN</td>\n",
" <td>5.407455</td>\n",
" <td>1.765376e-07</td>\n",
" <td>19.763879</td>\n",
" <td>1.005021e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>943</th>\n",
" <td>compound:navitoclax:PLX-4032 (1:1 mol/mol)</td>\n",
" <td>TP53</td>\n",
" <td>4.296897</td>\n",
" <td>1.991386e-05</td>\n",
" <td>19.021662</td>\n",
" <td>1.469945e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2059</th>\n",
" <td>compound:dabrafenib</td>\n",
" <td>TP53</td>\n",
" <td>3.975291</td>\n",
" <td>9.566174e-05</td>\n",
" <td>18.886057</td>\n",
" <td>1.788078e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>967</th>\n",
" <td>compound:serdemetan</td>\n",
" <td>TP53</td>\n",
" <td>4.126450</td>\n",
" <td>4.235423e-05</td>\n",
" <td>18.281163</td>\n",
" <td>2.160410e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2023</th>\n",
" <td>compound:selumetinib:navitoclax (8:1 mol/mol)</td>\n",
" <td>TP53</td>\n",
" <td>4.073451</td>\n",
" <td>5.205120e-05</td>\n",
" <td>16.921041</td>\n",
" <td>4.335244e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>165</th>\n",
" <td>compound:GDC-0879</td>\n",
" <td>TP53</td>\n",
" <td>3.844640</td>\n",
" <td>1.342540e-04</td>\n",
" <td>16.079124</td>\n",
" <td>6.676160e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>718</th>\n",
" <td>compound:NVP-TAE684</td>\n",
" <td>PTEN</td>\n",
" <td>4.388090</td>\n",
" <td>2.040751e-05</td>\n",
" <td>15.777393</td>\n",
" <td>7.802296e-05</td>\n",
" </tr>\n",
" <tr>\n",
" <th>629</th>\n",
" <td>compound:selumetinib:UNC0638 (4:1 mol/mol)</td>\n",
" <td>PTEN</td>\n",
" <td>4.050775</td>\n",
" <td>7.620988e-05</td>\n",
" <td>14.624756</td>\n",
" <td>1.418611e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1358</th>\n",
" <td>compound:BMS-754807</td>\n",
" <td>PTEN</td>\n",
" <td>4.381186</td>\n",
" <td>1.922041e-05</td>\n",
" <td>13.892917</td>\n",
" <td>2.076023e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1927</th>\n",
" <td>compound:doxorubicin:navitoclax (2:1 mol/mol)</td>\n",
" <td>TP53</td>\n",
" <td>3.649277</td>\n",
" <td>2.836919e-04</td>\n",
" <td>13.834950</td>\n",
" <td>2.140654e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1483</th>\n",
" <td>compound:crizotinib:PLX-4032 (2:1 mol/mol)</td>\n",
" <td>TP53</td>\n",
" <td>3.644311</td>\n",
" <td>2.898454e-04</td>\n",
" <td>13.830982</td>\n",
" <td>2.147645e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1814</th>\n",
" <td>compound:sunitinib</td>\n",
" <td>PTEN</td>\n",
" <td>4.222549</td>\n",
" <td>3.782568e-05</td>\n",
" <td>13.379906</td>\n",
" <td>2.717217e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1571</th>\n",
" <td>compound:cytarabine hydrochloride</td>\n",
" <td>TP53</td>\n",
" <td>3.582308</td>\n",
" <td>3.652458e-04</td>\n",
" <td>13.260604</td>\n",
" <td>2.891346e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>518</th>\n",
" <td>compound:trametinib</td>\n",
" <td>PTEN</td>\n",
" <td>4.783709</td>\n",
" <td>6.508209e-06</td>\n",
" <td>13.375578</td>\n",
" <td>2.908652e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1411</th>\n",
" <td>compound:serdemetan:SCH-529074 (1:1 mol/mol)</td>\n",
" <td>TP53</td>\n",
" <td>3.462605</td>\n",
" <td>5.753622e-04</td>\n",
" <td>13.071699</td>\n",
" <td>3.197329e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1364</th>\n",
" <td>compound:L-685458</td>\n",
" <td>SMAD4</td>\n",
" <td>-2.964546</td>\n",
" <td>4.391772e-03</td>\n",
" <td>13.000899</td>\n",
" <td>3.309856e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1206</th>\n",
" <td>compound:selumetinib:piperlongumine (8:1 mol/mol)</td>\n",
" <td>PTEN</td>\n",
" <td>3.717892</td>\n",
" <td>2.783407e-04</td>\n",
" <td>12.785889</td>\n",
" <td>3.719090e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1171</th>\n",
" <td>compound:oxaliplatin</td>\n",
" <td>TP53</td>\n",
" <td>3.491766</td>\n",
" <td>5.118703e-04</td>\n",
" <td>12.630983</td>\n",
" <td>4.025980e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>979</th>\n",
" <td>compound:veliparib</td>\n",
" <td>TP53</td>\n",
" <td>3.358972</td>\n",
" <td>8.298964e-04</td>\n",
" <td>12.102088</td>\n",
" <td>5.310482e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>630</th>\n",
" <td>compound:selumetinib:UNC0638 (4:1 mol/mol)</td>\n",
" <td>TP53</td>\n",
" <td>3.388666</td>\n",
" <td>7.465367e-04</td>\n",
" <td>12.055981</td>\n",
" <td>5.452538e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1767</th>\n",
" <td>compound:FGIN-1-27</td>\n",
" <td>TP53</td>\n",
" <td>-3.504595</td>\n",
" <td>5.720758e-04</td>\n",
" <td>12.266902</td>\n",
" <td>5.602053e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>609</th>\n",
" <td>compound:tamatinib</td>\n",
" <td>PTEN</td>\n",
" <td>4.167302</td>\n",
" <td>4.592989e-05</td>\n",
" <td>11.730976</td>\n",
" <td>6.477151e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1476</th>\n",
" <td>compound:SR1001</td>\n",
" <td>SMAD4</td>\n",
" <td>3.229962</td>\n",
" <td>2.086903e-03</td>\n",
" <td>11.619238</td>\n",
" <td>6.870849e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>285</th>\n",
" <td>compound:chlorambucil</td>\n",
" <td>TP53</td>\n",
" <td>3.289987</td>\n",
" <td>1.056226e-03</td>\n",
" <td>11.234403</td>\n",
" <td>8.431888e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1515</th>\n",
" <td>compound:PD318088</td>\n",
" <td>TP53</td>\n",
" <td>3.235629</td>\n",
" <td>1.274972e-03</td>\n",
" <td>10.996403</td>\n",
" <td>9.546246e-04</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1909</th>\n",
" <td>compound:KU-55933</td>\n",
" <td>CDKN2A</td>\n",
" <td>0.020033</td>\n",
" <td>9.841059e-01</td>\n",
" <td>0.000379</td>\n",
" <td>9.844762e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>334</th>\n",
" <td>compound:Mdivi-1</td>\n",
" <td>CDKN2A</td>\n",
" <td>0.025064</td>\n",
" <td>9.801024e-01</td>\n",
" <td>0.000354</td>\n",
" <td>9.849844e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>419</th>\n",
" <td>compound:SZ4TA2</td>\n",
" <td>TP53</td>\n",
" <td>0.018763</td>\n",
" <td>9.850406e-01</td>\n",
" <td>0.000342</td>\n",
" <td>9.852587e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>264</th>\n",
" <td>compound:PF-750</td>\n",
" <td>PTEN</td>\n",
" <td>0.018285</td>\n",
" <td>9.854348e-01</td>\n",
" <td>0.000309</td>\n",
" <td>9.859871e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1432</th>\n",
" <td>compound:ML258</td>\n",
" <td>SMAD4</td>\n",
" <td>-0.021443</td>\n",
" <td>9.829618e-01</td>\n",
" <td>0.000287</td>\n",
" <td>9.864895e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>470</th>\n",
" <td>compound:YK 4-279</td>\n",
" <td>PTEN</td>\n",
" <td>-0.018823</td>\n",
" <td>9.850028e-01</td>\n",
" <td>0.000279</td>\n",
" <td>9.866878e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>694</th>\n",
" <td>compound:BRD-K02492147</td>\n",
" <td>PTEN</td>\n",
" <td>0.020152</td>\n",
" <td>9.839421e-01</td>\n",
" <td>0.000249</td>\n",
" <td>9.874154e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>872</th>\n",
" <td>compound:BRD-K20514654</td>\n",
" <td>SMAD4</td>\n",
" <td>0.013462</td>\n",
" <td>9.893769e-01</td>\n",
" <td>0.000248</td>\n",
" <td>9.874550e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>97</th>\n",
" <td>compound:dinaciclib</td>\n",
" <td>TP53</td>\n",
" <td>0.014290</td>\n",
" <td>9.886073e-01</td>\n",
" <td>0.000210</td>\n",
" <td>9.884481e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1316</th>\n",
" <td>compound:AM-580</td>\n",
" <td>SMAD4</td>\n",
" <td>-0.017044</td>\n",
" <td>9.864549e-01</td>\n",
" <td>0.000203</td>\n",
" <td>9.886368e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>936</th>\n",
" <td>compound:C6-ceramide</td>\n",
" <td>SMAD4</td>\n",
" <td>-0.016817</td>\n",
" <td>9.866374e-01</td>\n",
" <td>0.000191</td>\n",
" <td>9.889725e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>683</th>\n",
" <td>compound:FSC231</td>\n",
" <td>PTEN</td>\n",
" <td>-0.015983</td>\n",
" <td>9.872876e-01</td>\n",
" <td>0.000186</td>\n",
" <td>9.891380e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1892</th>\n",
" <td>compound:methotrexate</td>\n",
" <td>SMAD4</td>\n",
" <td>-0.015246</td>\n",
" <td>9.878897e-01</td>\n",
" <td>0.000175</td>\n",
" <td>9.894534e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>compound:CIL55A</td>\n",
" <td>SMAD4</td>\n",
" <td>-0.008349</td>\n",
" <td>9.934179e-01</td>\n",
" <td>0.000173</td>\n",
" <td>9.895070e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1860</th>\n",
" <td>compound:PF-3758309</td>\n",
" <td>SMAD4</td>\n",
" <td>0.017275</td>\n",
" <td>9.862987e-01</td>\n",
" <td>0.000158</td>\n",
" <td>9.899847e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1385</th>\n",
" <td>compound:BRD-K34099515</td>\n",
" <td>CDKN2A</td>\n",
" <td>0.013031</td>\n",
" <td>9.898089e-01</td>\n",
" <td>0.000156</td>\n",
" <td>9.900376e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>808</th>\n",
" <td>compound:docetaxel:tanespimycin (2:1 mol/mol)</td>\n",
" <td>SMAD4</td>\n",
" <td>-0.014272</td>\n",
" <td>9.886571e-01</td>\n",
" <td>0.000141</td>\n",
" <td>9.905330e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1899</th>\n",
" <td>compound:BCL-LZH-4</td>\n",
" <td>TP53</td>\n",
" <td>0.011290</td>\n",
" <td>9.909995e-01</td>\n",
" <td>0.000134</td>\n",
" <td>9.907653e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>565</th>\n",
" <td>compound:MST-312</td>\n",
" <td>PTEN</td>\n",
" <td>0.010789</td>\n",
" <td>9.914047e-01</td>\n",
" <td>0.000114</td>\n",
" <td>9.914713e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1988</th>\n",
" <td>compound:vandetanib</td>\n",
" <td>SMAD4</td>\n",
" <td>-0.010723</td>\n",
" <td>9.914836e-01</td>\n",
" <td>0.000112</td>\n",
" <td>9.915464e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>929</th>\n",
" <td>compound:lapatinib</td>\n",
" <td>CDKN2A</td>\n",
" <td>-0.010817</td>\n",
" <td>9.914143e-01</td>\n",
" <td>0.000104</td>\n",
" <td>9.918475e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>410</th>\n",
" <td>compound:staurosporine</td>\n",
" <td>PTEN</td>\n",
" <td>-0.010599</td>\n",
" <td>9.915739e-01</td>\n",
" <td>0.000095</td>\n",
" <td>9.922178e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1353</th>\n",
" <td>compound:gemcitabine</td>\n",
" <td>CDKN2A</td>\n",
" <td>-0.009935</td>\n",
" <td>9.921238e-01</td>\n",
" <td>0.000091</td>\n",
" <td>9.923832e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>96</th>\n",
" <td>compound:dinaciclib</td>\n",
" <td>PTEN</td>\n",
" <td>0.009445</td>\n",
" <td>9.924893e-01</td>\n",
" <td>0.000073</td>\n",
" <td>9.931931e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1620</th>\n",
" <td>compound:BRD-K16147474</td>\n",
" <td>SMAD4</td>\n",
" <td>0.010783</td>\n",
" <td>9.914345e-01</td>\n",
" <td>0.000058</td>\n",
" <td>9.939068e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2112</th>\n",
" <td>compound:O-6-benzylguanine</td>\n",
" <td>SMAD4</td>\n",
" <td>-0.008342</td>\n",
" <td>9.933857e-01</td>\n",
" <td>0.000040</td>\n",
" <td>9.949862e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>553</th>\n",
" <td>compound:PHA-793887</td>\n",
" <td>PTEN</td>\n",
" <td>0.005309</td>\n",
" <td>9.957701e-01</td>\n",
" <td>0.000026</td>\n",
" <td>9.959112e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>544</th>\n",
" <td>compound:STF-31</td>\n",
" <td>CDKN2A</td>\n",
" <td>-0.005057</td>\n",
" <td>9.959869e-01</td>\n",
" <td>0.000023</td>\n",
" <td>9.961368e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>821</th>\n",
" <td>compound:bortezomib</td>\n",
" <td>CDKN2A</td>\n",
" <td>0.004502</td>\n",
" <td>9.964263e-01</td>\n",
" <td>0.000013</td>\n",
" <td>9.970965e-01</td>\n",
" </tr>\n",
" <tr>\n",
" <th>481</th>\n",
" <td>compound:SGX-523</td>\n",
" <td>CDKN2A</td>\n",
" <td>0.001947</td>\n",
" <td>9.984533e-01</td>\n",
" <td>0.000001</td>\n",
" <td>9.990910e-01</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>2172 rows × 6 columns</p>\n",
"</div>"
],
"text/plain": [
" drug mutation t-statistic \\\n",
"1931 compound:nutlin-3 TP53 10.326801 \n",
"1526 compound:BMS-536924 PTEN 6.899566 \n",
"854 compound:pluripotin PTEN 5.760531 \n",
"347 compound:NVP-ADW742 PTEN 5.243664 \n",
"1014 compound:navitoclax:pluripotin (1:1 mol/mol) PTEN 4.708911 \n",
"561 compound:linsitinib PTEN 5.407455 \n",
"943 compound:navitoclax:PLX-4032 (1:1 mol/mol) TP53 4.296897 \n",
"2059 compound:dabrafenib TP53 3.975291 \n",
"967 compound:serdemetan TP53 4.126450 \n",
"2023 compound:selumetinib:navitoclax (8:1 mol/mol) TP53 4.073451 \n",
"165 compound:GDC-0879 TP53 3.844640 \n",
"718 compound:NVP-TAE684 PTEN 4.388090 \n",
"629 compound:selumetinib:UNC0638 (4:1 mol/mol) PTEN 4.050775 \n",
"1358 compound:BMS-754807 PTEN 4.381186 \n",
"1927 compound:doxorubicin:navitoclax (2:1 mol/mol) TP53 3.649277 \n",
"1483 compound:crizotinib:PLX-4032 (2:1 mol/mol) TP53 3.644311 \n",
"1814 compound:sunitinib PTEN 4.222549 \n",
"1571 compound:cytarabine hydrochloride TP53 3.582308 \n",
"518 compound:trametinib PTEN 4.783709 \n",
"1411 compound:serdemetan:SCH-529074 (1:1 mol/mol) TP53 3.462605 \n",
"1364 compound:L-685458 SMAD4 -2.964546 \n",
"1206 compound:selumetinib:piperlongumine (8:1 mol/mol) PTEN 3.717892 \n",
"1171 compound:oxaliplatin TP53 3.491766 \n",
"979 compound:veliparib TP53 3.358972 \n",
"630 compound:selumetinib:UNC0638 (4:1 mol/mol) TP53 3.388666 \n",
"1767 compound:FGIN-1-27 TP53 -3.504595 \n",
"609 compound:tamatinib PTEN 4.167302 \n",
"1476 compound:SR1001 SMAD4 3.229962 \n",
"285 compound:chlorambucil TP53 3.289987 \n",
"1515 compound:PD318088 TP53 3.235629 \n",
"... ... ... ... \n",
"1909 compound:KU-55933 CDKN2A 0.020033 \n",
"334 compound:Mdivi-1 CDKN2A 0.025064 \n",
"419 compound:SZ4TA2 TP53 0.018763 \n",
"264 compound:PF-750 PTEN 0.018285 \n",
"1432 compound:ML258 SMAD4 -0.021443 \n",
"470 compound:YK 4-279 PTEN -0.018823 \n",
"694 compound:BRD-K02492147 PTEN 0.020152 \n",
"872 compound:BRD-K20514654 SMAD4 0.013462 \n",
"97 compound:dinaciclib TP53 0.014290 \n",
"1316 compound:AM-580 SMAD4 -0.017044 \n",
"936 compound:C6-ceramide SMAD4 -0.016817 \n",
"683 compound:FSC231 PTEN -0.015983 \n",
"1892 compound:methotrexate SMAD4 -0.015246 \n",
"11 compound:CIL55A SMAD4 -0.008349 \n",
"1860 compound:PF-3758309 SMAD4 0.017275 \n",
"1385 compound:BRD-K34099515 CDKN2A 0.013031 \n",
"808 compound:docetaxel:tanespimycin (2:1 mol/mol) SMAD4 -0.014272 \n",
"1899 compound:BCL-LZH-4 TP53 0.011290 \n",
"565 compound:MST-312 PTEN 0.010789 \n",
"1988 compound:vandetanib SMAD4 -0.010723 \n",
"929 compound:lapatinib CDKN2A -0.010817 \n",
"410 compound:staurosporine PTEN -0.010599 \n",
"1353 compound:gemcitabine CDKN2A -0.009935 \n",
"96 compound:dinaciclib PTEN 0.009445 \n",
"1620 compound:BRD-K16147474 SMAD4 0.010783 \n",
"2112 compound:O-6-benzylguanine SMAD4 -0.008342 \n",
"553 compound:PHA-793887 PTEN 0.005309 \n",
"544 compound:STF-31 CDKN2A -0.005057 \n",
"821 compound:bortezomib CDKN2A 0.004502 \n",
"481 compound:SGX-523 CDKN2A 0.001947 \n",
"\n",
" t-pvalue a-statistic a-pvalue \n",
"1931 9.209386e-23 121.681037 2.379157e-26 \n",
"1526 9.233542e-11 40.151225 4.030042e-10 \n",
"854 3.527544e-08 26.879984 2.751518e-07 \n",
"347 4.789674e-07 25.017915 7.067467e-07 \n",
"1014 5.418047e-06 22.479716 2.532986e-06 \n",
"561 1.765376e-07 19.763879 1.005021e-05 \n",
"943 1.991386e-05 19.021662 1.469945e-05 \n",
"2059 9.566174e-05 18.886057 1.788078e-05 \n",
"967 4.235423e-05 18.281163 2.160410e-05 \n",
"2023 5.205120e-05 16.921041 4.335244e-05 \n",
"165 1.342540e-04 16.079124 6.676160e-05 \n",
"718 2.040751e-05 15.777393 7.802296e-05 \n",
"629 7.620988e-05 14.624756 1.418611e-04 \n",
"1358 1.922041e-05 13.892917 2.076023e-04 \n",
"1927 2.836919e-04 13.834950 2.140654e-04 \n",
"1483 2.898454e-04 13.830982 2.147645e-04 \n",
"1814 3.782568e-05 13.379906 2.717217e-04 \n",
"1571 3.652458e-04 13.260604 2.891346e-04 \n",
"518 6.508209e-06 13.375578 2.908652e-04 \n",
"1411 5.753622e-04 13.071699 3.197329e-04 \n",
"1364 4.391772e-03 13.000899 3.309856e-04 \n",
"1206 2.783407e-04 12.785889 3.719090e-04 \n",
"1171 5.118703e-04 12.630983 4.025980e-04 \n",
"979 8.298964e-04 12.102088 5.310482e-04 \n",
"630 7.465367e-04 12.055981 5.452538e-04 \n",
"1767 5.720758e-04 12.266902 5.602053e-04 \n",
"609 4.592989e-05 11.730976 6.477151e-04 \n",
"1476 2.086903e-03 11.619238 6.870849e-04 \n",
"285 1.056226e-03 11.234403 8.431888e-04 \n",
"1515 1.274972e-03 10.996403 9.546246e-04 \n",
"... ... ... ... \n",
"1909 9.841059e-01 0.000379 9.844762e-01 \n",
"334 9.801024e-01 0.000354 9.849844e-01 \n",
"419 9.850406e-01 0.000342 9.852587e-01 \n",
"264 9.854348e-01 0.000309 9.859871e-01 \n",
"1432 9.829618e-01 0.000287 9.864895e-01 \n",
"470 9.850028e-01 0.000279 9.866878e-01 \n",
"694 9.839421e-01 0.000249 9.874154e-01 \n",
"872 9.893769e-01 0.000248 9.874550e-01 \n",
"97 9.886073e-01 0.000210 9.884481e-01 \n",
"1316 9.864549e-01 0.000203 9.886368e-01 \n",
"936 9.866374e-01 0.000191 9.889725e-01 \n",
"683 9.872876e-01 0.000186 9.891380e-01 \n",
"1892 9.878897e-01 0.000175 9.894534e-01 \n",
"11 9.934179e-01 0.000173 9.895070e-01 \n",
"1860 9.862987e-01 0.000158 9.899847e-01 \n",
"1385 9.898089e-01 0.000156 9.900376e-01 \n",
"808 9.886571e-01 0.000141 9.905330e-01 \n",
"1899 9.909995e-01 0.000134 9.907653e-01 \n",
"565 9.914047e-01 0.000114 9.914713e-01 \n",
"1988 9.914836e-01 0.000112 9.915464e-01 \n",
"929 9.914143e-01 0.000104 9.918475e-01 \n",
"410 9.915739e-01 0.000095 9.922178e-01 \n",
"1353 9.921238e-01 0.000091 9.923832e-01 \n",
"96 9.924893e-01 0.000073 9.931931e-01 \n",
"1620 9.914345e-01 0.000058 9.939068e-01 \n",
"2112 9.933857e-01 0.000040 9.949862e-01 \n",
"553 9.957701e-01 0.000026 9.959112e-01 \n",
"544 9.959869e-01 0.000023 9.961368e-01 \n",
"821 9.964263e-01 0.000013 9.970965e-01 \n",
"481 9.984533e-01 0.000001 9.990910e-01 \n",
"\n",
"[2172 rows x 6 columns]"
]
},
"execution_count": 42,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"#print data sorted by statistical value\n",
"pandas.DataFrame(out, columns=[\"drug\", \"mutation\", \"t-statistic\", \"t-pvalue\", \"a-statistic\", \"a-pvalue\"]).sort_values(\"a-pvalue\")"
]
},
{
"cell_type": "code",
"execution_count": 37,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"13.534497907 0.960924747106\n",
"12.4568282282 1.70322764773\n"
]
},
{
"data": {
"image/png": 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t3vGOd3DBBRdklp+N453vfCe33lrUwbj77ru57rrrWFhY4N57713DsXQ73rNx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\nYII=\n",
"text/plain": [
"<matplotlib.figure.Figure at 0x112d8c590>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"drug = \"compound:nutlin-3\"\n",
"gene = \"TP53\"\n",
"_ = plt.hist(pos_response[gene][drug], bins=100, normed=True, color=\"R\")\n",
"_ = plt.hist(neg_response[gene][drug], bins=100, normed=True, color=\"B\")\n",
"print np.mean(pos_response[gene][drug]), np.std(pos_response[gene][drug])\n",
"print np.mean(neg_response[gene][drug]), np.std(neg_response[gene][drug])"
]
},
{
"cell_type": "code",
"execution_count": 38,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"F_onewayResult(statistic=121.68103667046283, pvalue=2.3791567976155418e-26)"
]
},
"execution_count": 38,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"stats.f_oneway(pos_response[gene][drug], neg_response[gene][drug])"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"language": "python",
"name": "python2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.12"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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