{ "cells": [ { "cell_type": "markdown", "id": "ffe44327", "metadata": { "id": "ffe44327" }, "source": [ "# Common instructions\n", "\n", "- Aim to attempt all the mandatory questions (marked with a *) in the problem set. \n", "\n", "\n", "- Only attempt optional question after you have attempted all the mandatory questions. \n", "\n", "\n", "- More credit will be given if you have successfully attempted all the mandatory questions, even if you do not attempt a single optional question, as opposed to missing even one mandatory question while attempting all the optional questions.\n", "\n", "\n", "- With the above caveat, attempt as many questions as possible within the time period. Partially attempted questions will get partial credit.\n", "\n", "\n", "- Normally, you should work through the problem set in ascending order (Q1 -> Q4).\n", "\n", "\n", "- Clean, labeled plots and clear data interpretation will boost your score. So too, will the use of functions, meaningful variable names, and readable code.\n", "\n", "\n", "- You have a maximum of 2 days to work on the assignment. We will not consider assignments submitted after the deadline. You are free to search the internet, but are not to discuss with others in any way or form, in pain of immediate disqualification.\n", "\n", "\n", "- Report the websites used to obtain help. Before the deadline, create a single .zip file with all your code submit it in the submission link provided to you in the email. DO NOT include data in your zip file. \n", "\n", "\n", "- You can use any programming language of your choice to solve all or part of the questions, preferably notebooks like Jupyter Notebook, Google Colab etc. We should be able to execute your program(s) to generate the required data and plots.\n", "\n", "\n", "- In case you are unable to complete some parts, clearly indicate how would you go about the task ? What steps would you try etc.\n" ] }, { "cell_type": "markdown", "id": "f82f0100", "metadata": { "id": "f82f0100" }, "source": [ "# Input data\n", "\n", "- The TSV file `SampleData.tsv` has the following columns\n", "\n", " - Sample: Sample IDs (S01, S02, S03...)\n", " - Treatment: Information on sample type \n", " \n", " - HF+: Blood plasma samples collected from coronary disease patients post major surgery who had a heart failure within 3 years of surgery\n", " - HF-: Blood plasma samples collected from coronary disease patients post major surgery who recovered post surgery without heart failure\n", " - HVOL: Blood plasma samples collected from individuals without any discernable coronary disease\n", " \n", " \n", " \n", "- The gzipped file `GSE208194_RawTPM.csv.gz` contains gene expression information for the sample mentioned in `SampleData.tsv` where the file structure looks like\n", "\n", "ENSEMBL ID |S01 |S02 |S03 |S04\n", ":-----------------|:--------|:--------|:--------|:--------\n", "ENSG00000000419.12|2.398878 |12.157726|1.40211 |7.667875\n", "ENSG00000000938.13|3.324077 |13.971038|1.917631 |10.225812\n", "ENSG00000001629.10|12.037059|1.453811 |12.596614|15.799738\n", "ENSG00000001631.15|1.287932 |5.842868 |1.412257 |1.526812\n", "\n", "Where each row is a feature/gene (n=4150) and each column is a sample where the features are measured.\n" ] }, { "cell_type": "code", "execution_count": 1, "id": "655809dc", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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sampletreatment
0S01HF-
1S02HF-
2S03HF-
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.........
87S88HVOL
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92 rows × 2 columns

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" ], "text/plain": [ " sample treatment\n", "0 S01 HF-\n", "1 S02 HF-\n", "2 S03 HF-\n", "3 S04 HF-\n", "4 S05 HF-\n", ".. ... ...\n", "87 S88 HVOL\n", "88 S89 HVOL\n", "89 S90 HVOL\n", "90 S95 HF-\n", "91 S96 HVOL\n", "\n", "[92 rows x 2 columns]" ] }, "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ "#Reading the SampleData file \n", "import pandas as pd\n", "path1='/raid/home/ankitsingh1/StrandAi/SampleData.tsv'\n", "SampleData_df = pd.read_csv(path1, sep='\\t') \n", "SampleData_df" ] }, { "cell_type": "code", "execution_count": 2, "id": "49ff1112", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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ENSEMBL IDS01S02S03S04S05S06S07S08S09...S83S84S85S86S87S88S89S90S95S96
0ENSG00000000419.122.39887812.1577261.4021107.6678754.1985254.0697095.5736721.2630160.000000...13.0148354.8249272.9999157.3654085.48772325.22254317.7346305.0571230.9683323.757043
1ENSG00000000938.133.32407713.9710381.91763110.2258122.8476211.7447195.5921307.5498748.696941...13.3425121.0158039.0473894.2242865.46774617.52590710.9035121.2578531.0256418.876226
2ENSG00000001629.1012.0370591.45381112.59661415.79973817.2462057.3764077.3105077.43900823.898468...15.47471524.92910615.78973222.17286715.37013389.99574832.95122612.2630585.96898114.964376
3ENSG00000001631.151.2879325.8428681.4122571.5268127.2616254.5301840.0000005.5983955.140090...4.3373784.8047293.2213803.44006010.3317367.89924711.0069746.4474972.7866515.343678
4ENSG00000002549.122.91460632.5664042.23187135.4449009.2120835.2198854.1556808.67736429.230862...14.7373668.2687947.4787536.6587929.64789928.69172033.1238146.7094701.2143853.023686
..................................................................
4145ENSG00000286834.11.446729101.31266617.106360109.49099033.0969904.78748730.19986417.30491229.437844...42.8164796.30639611.9593514.34415013.03653623.37010934.1699665.4442154.26207313.917467
4146ENSG00000287080.18.54346148.48278111.49297140.76349223.7983528.69623937.81853618.15811734.491123...21.9217596.0955911.3629755.9281430.7048422.6889189.5314082.8239520.10789412.110910
4147ENSG00000287160.13.39214357.0891397.37977867.43719717.5190942.84014710.4071368.2928865.282977...45.5157593.2037702.8021231.2864417.84843723.09488719.0405751.3243814.3294639.970802
4148ENSG00000287825.18.54341026.1981119.7316455.93931513.91137014.80715612.8842680.35344916.483560...0.00000030.60116618.95386719.68625920.5404347.1145634.66434320.3767781.6013629.273306
4149ENSG00000288560.18.3618703.2186592.5601324.1235305.0921697.4781869.5043761.7764221.402694...10.1430187.05303319.7100671.79129824.2428704.56302810.9411917.2208621.5688287.706704
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4150 rows × 90 columns

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" ], "text/plain": [ " ENSEMBL ID S01 S02 S03 S04 \\\n", "0 ENSG00000000419.12 2.398878 12.157726 1.402110 7.667875 \n", "1 ENSG00000000938.13 3.324077 13.971038 1.917631 10.225812 \n", "2 ENSG00000001629.10 12.037059 1.453811 12.596614 15.799738 \n", "3 ENSG00000001631.15 1.287932 5.842868 1.412257 1.526812 \n", "4 ENSG00000002549.12 2.914606 32.566404 2.231871 35.444900 \n", "... ... ... ... ... ... \n", "4145 ENSG00000286834.1 1.446729 101.312666 17.106360 109.490990 \n", "4146 ENSG00000287080.1 8.543461 48.482781 11.492971 40.763492 \n", "4147 ENSG00000287160.1 3.392143 57.089139 7.379778 67.437197 \n", "4148 ENSG00000287825.1 8.543410 26.198111 9.731645 5.939315 \n", "4149 ENSG00000288560.1 8.361870 3.218659 2.560132 4.123530 \n", "\n", " S05 S06 S07 S08 S09 ... S83 \\\n", "0 4.198525 4.069709 5.573672 1.263016 0.000000 ... 13.014835 \n", "1 2.847621 1.744719 5.592130 7.549874 8.696941 ... 13.342512 \n", "2 17.246205 7.376407 7.310507 7.439008 23.898468 ... 15.474715 \n", "3 7.261625 4.530184 0.000000 5.598395 5.140090 ... 4.337378 \n", "4 9.212083 5.219885 4.155680 8.677364 29.230862 ... 14.737366 \n", "... ... ... ... ... ... ... ... \n", "4145 33.096990 4.787487 30.199864 17.304912 29.437844 ... 42.816479 \n", "4146 23.798352 8.696239 37.818536 18.158117 34.491123 ... 21.921759 \n", "4147 17.519094 2.840147 10.407136 8.292886 5.282977 ... 45.515759 \n", "4148 13.911370 14.807156 12.884268 0.353449 16.483560 ... 0.000000 \n", "4149 5.092169 7.478186 9.504376 1.776422 1.402694 ... 10.143018 \n", "\n", " S84 S85 S86 S87 S88 S89 \\\n", "0 4.824927 2.999915 7.365408 5.487723 25.222543 17.734630 \n", "1 1.015803 9.047389 4.224286 5.467746 17.525907 10.903512 \n", "2 24.929106 15.789732 22.172867 15.370133 89.995748 32.951226 \n", "3 4.804729 3.221380 3.440060 10.331736 7.899247 11.006974 \n", "4 8.268794 7.478753 6.658792 9.647899 28.691720 33.123814 \n", "... ... ... ... ... ... ... \n", "4145 6.306396 11.959351 4.344150 13.036536 23.370109 34.169966 \n", "4146 6.095591 1.362975 5.928143 0.704842 2.688918 9.531408 \n", "4147 3.203770 2.802123 1.286441 7.848437 23.094887 19.040575 \n", "4148 30.601166 18.953867 19.686259 20.540434 7.114563 4.664343 \n", "4149 7.053033 19.710067 1.791298 24.242870 4.563028 10.941191 \n", "\n", " S90 S95 S96 \n", "0 5.057123 0.968332 3.757043 \n", "1 1.257853 1.025641 8.876226 \n", "2 12.263058 5.968981 14.964376 \n", "3 6.447497 2.786651 5.343678 \n", "4 6.709470 1.214385 3.023686 \n", "... ... ... ... \n", "4145 5.444215 4.262073 13.917467 \n", "4146 2.823952 0.107894 12.110910 \n", "4147 1.324381 4.329463 9.970802 \n", "4148 20.376778 1.601362 9.273306 \n", "4149 7.220862 1.568828 7.706704 \n", "\n", "[4150 rows x 90 columns]" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "#Reading the Gene Expression\n", "path2=\"/raid/home/ankitsingh1/StrandAi/GSE208194_RawTPM.csv\"\n", "Gene_exp_df= pd.read_csv(path2) \n", "Gene_exp_df" ] }, { "cell_type": "markdown", "id": "3f2b4ab9", "metadata": {}, "source": [ "# Feature filter*\n", "\n", "- Remove genes/features with very low expression values (< 1) in 70% of samples (even if they are good features they cannot be used for diagnositics)\n", "- Remove a member of feature pairs which are highly correlated\n", "- Provide the statistics with respect to the removals" ] }, { "cell_type": "code", "execution_count": 4, "id": "9b2ad9cd", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "ENSEMBL ID ENSG00000000419.12\n", "S01 2.398878\n", "S02 12.157726\n", "S03 1.40211\n", "S04 7.667875\n", " ... \n", "S88 25.222543\n", "S89 17.73463\n", "S90 5.057123\n", "S95 0.968332\n", "S96 3.757043\n", "Name: 0, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000000938.13\n", "S01 3.324077\n", "S02 13.971038\n", "S03 1.917631\n", "S04 10.225812\n", " ... \n", "S88 17.525907\n", "S89 10.903512\n", "S90 1.257853\n", "S95 1.025641\n", "S96 8.876226\n", "Name: 1, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000001629.10\n", "S01 12.037059\n", "S02 1.453811\n", "S03 12.596614\n", "S04 15.799738\n", " ... \n", "S88 89.995748\n", "S89 32.951226\n", "S90 12.263058\n", "S95 5.968981\n", "S96 14.964376\n", "Name: 2, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000001631.15\n", "S01 1.287932\n", "S02 5.842868\n", "S03 1.412257\n", "S04 1.526812\n", " ... \n", "S88 7.899247\n", "S89 11.006974\n", "S90 6.447497\n", "S95 2.786651\n", "S96 5.343678\n", "Name: 3, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000002549.12\n", "S01 2.914606\n", "S02 32.566404\n", "S03 2.231871\n", "S04 35.4449\n", " ... \n", "S88 28.69172\n", "S89 33.123814\n", "S90 6.70947\n", "S95 1.214385\n", "S96 3.023686\n", "Name: 4, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000002586.20\n", "S01 106.458644\n", "S02 40.094091\n", "S03 124.158648\n", "S04 51.141639\n", " ... \n", "S88 55.245745\n", "S89 56.911321\n", "S90 271.525037\n", "S95 154.849235\n", "S96 155.210654\n", "Name: 5, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000002834.18\n", "S01 7.243743\n", "S02 22.43391\n", "S03 5.942053\n", "S04 17.521034\n", " ... \n", "S88 42.377442\n", "S89 19.254234\n", "S90 6.904848\n", "S95 10.530023\n", "S96 14.869883\n", "Name: 6, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000003056.8\n", "S01 3.443131\n", "S02 1.512845\n", "S03 8.835538\n", "S04 6.539876\n", " ... \n", "S88 64.245814\n", "S89 5.987356\n", "S90 13.699922\n", "S95 3.465649\n", "S96 8.946997\n", "Name: 7, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000003147.19\n", "S01 6.531775\n", "S02 3.252381\n", "S03 5.433218\n", "S04 13.176043\n", " ... \n", "S88 30.129237\n", "S89 12.130276\n", "S90 7.758268\n", "S95 4.376058\n", "S96 6.206429\n", "Name: 8, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000003402.20\n", "S01 79.598523\n", "S02 122.045223\n", "S03 48.646713\n", "S04 109.224603\n", " ... \n", "S88 237.696308\n", "S89 127.585057\n", "S90 110.033203\n", "S95 49.63806\n", "S96 71.701582\n", "Name: 9, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000003436.16\n", "S01 80.166328\n", "S02 15.880695\n", "S03 114.095347\n", "S04 62.411831\n", " ... \n", "S88 43.357609\n", "S89 60.350316\n", "S90 170.117609\n", "S95 34.211417\n", "S96 79.78717\n", "Name: 10, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000003756.17\n", "S01 17.068214\n", "S02 78.228619\n", "S03 22.092087\n", "S04 65.75019\n", " ... \n", "S88 94.112517\n", "S89 119.150445\n", "S90 32.657524\n", "S95 13.900443\n", "S96 66.561672\n", "Name: 11, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000004059.11\n", "S01 10.490356\n", "S02 11.437219\n", "S03 8.897721\n", "S04 7.816751\n", " ... \n", "S88 16.536748\n", "S89 14.181463\n", "S90 20.489672\n", "S95 9.154845\n", "S96 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"ENSEMBL ID ENSG00000135655.16\n", "S01 16.808453\n", "S02 22.425698\n", "S03 24.259793\n", "S04 36.113179\n", " ... \n", "S88 47.695431\n", "S89 73.866777\n", "S90 17.139582\n", "S95 7.131522\n", "S96 13.646066\n", "Name: 1894, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000135679.25\n", "S01 11.716054\n", "S02 6.474436\n", "S03 6.004502\n", "S04 36.472123\n", " ... \n", "S88 72.597941\n", "S89 20.632971\n", "S90 20.884372\n", "S95 5.390727\n", "S96 12.785225\n", "Name: 1895, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000135709.12\n", "S01 3.249902\n", "S02 5.959034\n", "S03 10.118867\n", "S04 4.016269\n", " ... \n", "S88 5.393154\n", "S89 6.571985\n", "S90 5.886027\n", "S95 5.725055\n", "S96 6.358101\n", "Name: 1896, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000135720.13\n", "S01 5.598751\n", "S02 13.823928\n", "S03 2.350749\n", "S04 6.401682\n", " ... \n", "S88 28.113267\n", "S89 10.827338\n", "S90 2.606916\n", "S95 2.430464\n", "S96 3.986536\n", "Name: 1897, Length: 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"S89 98.140959\n", "S90 59.669901\n", "S95 8.031791\n", "S96 46.678118\n", "Name: 1913, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136021.19\n", "S01 8.596188\n", "S02 3.183735\n", "S03 13.631013\n", "S04 14.560663\n", " ... \n", "S88 7.587688\n", "S89 5.26864\n", "S90 26.267337\n", "S95 9.361773\n", "S96 16.152979\n", "Name: 1914, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136044.12\n", "S01 1.769342\n", "S02 20.384391\n", "S03 5.434918\n", "S04 4.703708\n", " ... \n", "S88 44.8632\n", "S89 1.466756\n", "S90 6.951613\n", "S95 5.782419\n", "S96 11.018665\n", "Name: 1915, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136045.12\n", "S01 1.041245\n", "S02 9.144129\n", "S03 2.381596\n", "S04 9.741259\n", " ... \n", "S88 10.319864\n", "S89 12.095596\n", "S90 3.134858\n", "S95 0.0\n", "S96 3.033476\n", "Name: 1916, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136051.14\n", "S01 2.74664\n", "S02 14.073234\n", "S03 7.150226\n", "S04 9.573702\n", " ... \n", "S88 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... \n", "S88 68.409614\n", "S89 55.628931\n", "S90 14.670357\n", "S95 2.191622\n", "S96 8.634025\n", "Name: 1921, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136147.18\n", "S01 2.803141\n", "S02 53.193411\n", "S03 9.406859\n", "S04 27.421135\n", " ... \n", "S88 90.093598\n", "S89 36.376631\n", "S90 5.733266\n", "S95 1.512059\n", "S96 9.822086\n", "Name: 1922, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136156.15\n", "S01 356.816991\n", "S02 139.819966\n", "S03 434.12544\n", "S04 217.274393\n", " ... \n", "S88 332.918457\n", "S89 251.239387\n", "S90 859.236499\n", "S95 388.743012\n", "S96 405.638031\n", "Name: 1923, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136167.14\n", "S01 25.661112\n", "S02 180.086287\n", "S03 23.290787\n", "S04 117.496464\n", " ... \n", "S88 536.755761\n", "S89 343.42916\n", "S90 24.117926\n", "S95 6.282374\n", "S96 26.904815\n", "Name: 1924, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136169.16\n", "S01 3.852261\n", "S02 24.156205\n", "S03 5.157432\n", "S04 4.763919\n", " ... \n", "S88 20.879758\n", "S89 8.615228\n", "S90 6.592091\n", "S95 2.823097\n", "S96 6.784384\n", "Name: 1925, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136231.14\n", "S01 103.916633\n", "S02 70.775178\n", "S03 166.997209\n", "S04 88.976338\n", " ... \n", "S88 121.748616\n", "S89 195.026022\n", "S90 398.24383\n", "S95 71.575744\n", "S96 134.694867\n", "Name: 1926, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136238.18\n", "S01 50.521609\n", "S02 75.160636\n", "S03 79.918641\n", "S04 99.040974\n", " ... \n", "S88 214.509621\n", "S89 97.129476\n", "S90 111.069183\n", "S95 34.617382\n", "S96 71.622096\n", "Name: 1927, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136240.10\n", "S01 10.752199\n", "S02 20.105242\n", "S03 16.564424\n", "S04 28.072194\n", " ... \n", "S88 22.26434\n", "S89 39.493845\n", "S90 21.370125\n", "S95 17.167766\n", "S96 19.922288\n", "Name: 1928, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136243.17\n", "S01 5.943446\n", "S02 29.915438\n", "S03 0.866507\n", "S04 13.048286\n", " ... \n", "S88 7.554981\n", "S89 9.646533\n", "S90 7.701983\n", "S95 5.864347\n", "S96 9.112257\n", "Name: 1929, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136247.14\n", "S01 1.507311\n", "S02 5.900513\n", "S03 1.656073\n", "S04 7.325996\n", " ... \n", "S88 7.653525\n", "S89 7.819394\n", "S90 5.208496\n", "S95 2.022145\n", "S96 3.706943\n", "Name: 1930, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136279.20\n", "S01 12.937583\n", "S02 107.875091\n", "S03 41.951676\n", "S04 44.265035\n", " ... \n", "S88 206.984644\n", "S89 114.605358\n", "S90 68.035499\n", "S95 12.764835\n", "S96 47.477927\n", "Name: 1931, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136280.16\n", "S01 2.121962\n", "S02 28.313391\n", "S03 4.577961\n", "S04 8.733281\n", " ... \n", "S88 7.388008\n", "S89 10.116374\n", "S90 2.215899\n", "S95 0.444794\n", "S96 7.475868\n", "Name: 1932, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136371.10\n", "S01 2.684918\n", "S02 50.547018\n", "S03 5.877322\n", "S04 10.758039\n", " ... \n", "S88 74.185494\n", "S89 25.322034\n", "S90 4.137277\n", "S95 1.340182\n", "S96 12.509176\n", "Name: 1933, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136404.16\n", "S01 6.627083\n", "S02 1.526482\n", "S03 7.763469\n", "S04 10.368454\n", " ... \n", "S88 5.208483\n", "S89 16.239461\n", "S90 23.174448\n", "S95 6.490639\n", "S96 24.255848\n", "Name: 1934, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136436.14\n", "S01 15.741811\n", "S02 60.127878\n", "S03 12.434619\n", "S04 58.454304\n", " ... \n", "S88 137.462373\n", "S89 66.093035\n", "S90 13.496764\n", "S95 4.628101\n", "S96 16.642871\n", "Name: 1935, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136448.12\n", "S01 3.332901\n", "S02 3.704822\n", "S03 3.472375\n", "S04 10.230578\n", " ... \n", "S88 29.32335\n", "S89 37.253966\n", "S90 5.857674\n", "S95 1.884426\n", "S96 6.623171\n", "Name: 1936, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136450.13\n", "S01 5.015985\n", "S02 25.533398\n", "S03 5.461676\n", "S04 22.855428\n", " ... \n", "S88 19.559806\n", "S89 14.717101\n", "S90 1.700844\n", "S95 4.109243\n", "S96 6.589526\n", "Name: 1937, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136490.9\n", "S01 5.655217\n", "S02 29.257664\n", "S03 5.254029\n", "S04 20.408167\n", " ... \n", "S88 78.191641\n", "S89 59.989444\n", "S90 1.664264\n", "S95 5.630291\n", "S96 8.432462\n", "Name: 1938, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136521.13\n", "S01 2.549157\n", "S02 35.20821\n", "S03 4.269027\n", "S04 24.285489\n", " ... \n", "S88 51.231615\n", "S89 57.322972\n", "S90 4.054543\n", "S95 2.072269\n", "S96 7.092052\n", "Name: 1939, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136522.14\n", "S01 1.215221\n", "S02 5.5352\n", "S03 3.509059\n", "S04 6.190453\n", " ... \n", "S88 29.099005\n", "S89 20.858781\n", "S90 3.533369\n", "S95 1.279195\n", "S96 1.045852\n", "Name: 1940, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136527.18\n", "S01 31.971122\n", "S02 44.069173\n", "S03 30.135488\n", "S04 66.626679\n", " ... \n", "S88 48.86067\n", "S89 35.291665\n", "S90 60.465026\n", "S95 17.647436\n", "S96 45.049938\n", "Name: 1941, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136536.15\n", "S01 1.529841\n", "S02 10.459172\n", "S03 5.999082\n", "S04 13.307312\n", " ... \n", "S88 14.0706\n", "S89 11.160845\n", "S90 1.646488\n", "S95 1.301455\n", "S96 4.555217\n", "Name: 1942, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136560.14\n", "S01 10.533995\n", "S02 44.984924\n", "S03 10.794799\n", "S04 10.838258\n", " ... \n", "S88 101.249959\n", "S89 74.488058\n", "S90 17.587851\n", "S95 5.450218\n", "S96 16.052297\n", "Name: 1943, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136603.14\n", "S01 4.37591\n", "S02 21.419216\n", "S03 3.734226\n", "S04 7.087773\n", " ... \n", "S88 16.410143\n", "S89 22.51013\n", "S90 3.509533\n", "S95 4.977305\n", "S96 1.808996\n", "Name: 1944, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136628.18\n", "S01 2.543893\n", "S02 9.946548\n", "S03 1.139588\n", "S04 2.214551\n", " ... \n", "S88 4.551438\n", "S89 18.286785\n", "S90 3.108838\n", "S95 0.426113\n", "S96 1.443354\n", "Name: 1945, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136643.12\n", "S01 1.862268\n", "S02 2.47244\n", "S03 2.237621\n", "S04 5.672387\n", " ... \n", "S88 2.113168\n", "S89 4.869166\n", "S90 2.226627\n", "S95 1.233386\n", "S96 2.8499\n", "Name: 1946, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136682.15\n", "S01 4.917027\n", "S02 22.484016\n", "S03 4.292453\n", "S04 25.322478\n", " ... \n", "S88 24.185464\n", "S89 16.547885\n", "S90 5.34323\n", "S95 1.365008\n", "S96 5.561408\n", "Name: 1947, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136709.12\n", "S01 2.083784\n", "S02 3.131257\n", "S03 2.331781\n", "S04 1.444822\n", " ... \n", "S88 13.614882\n", "S89 1.593081\n", "S90 1.963875\n", "S95 2.513673\n", "S96 3.88053\n", "Name: 1948, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136731.13\n", "S01 9.356758\n", "S02 2.334318\n", "S03 7.057712\n", "S04 11.839393\n", " ... \n", "S88 15.493417\n", "S89 6.511397\n", "S90 15.615409\n", "S95 3.787273\n", "S96 12.347472\n", "Name: 1949, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136732.16\n", "S01 5.755202\n", "S02 50.542288\n", "S03 10.82278\n", "S04 42.118785\n", " ... \n", "S88 76.199389\n", "S89 64.522465\n", "S90 3.079872\n", "S95 2.313955\n", "S96 14.736496\n", "Name: 1950, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136738.15\n", "S01 4.098539\n", "S02 5.537755\n", "S03 4.831501\n", "S04 8.061264\n", " ... \n", "S88 5.83124\n", "S89 16.665805\n", "S90 6.308335\n", "S95 1.375039\n", "S96 2.229686\n", "Name: 1951, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136754.17\n", "S01 12.998036\n", "S02 9.185315\n", "S03 16.250681\n", "S04 18.721384\n", " ... \n", "S88 21.276567\n", "S89 32.810699\n", "S90 30.662672\n", "S95 9.477297\n", "S96 22.674381\n", "Name: 1952, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136758.18\n", "S01 4.974011\n", "S02 7.908659\n", "S03 4.822639\n", "S04 16.455786\n", " ... \n", "S88 16.851596\n", "S89 8.616622\n", "S90 5.646218\n", "S95 2.723118\n", "S96 4.956161\n", "Name: 1953, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136770.11\n", "S01 1.786921\n", "S02 5.695712\n", "S03 3.695873\n", "S04 2.806024\n", " ... \n", "S88 9.516371\n", "S89 1.742773\n", "S90 2.695519\n", "S95 1.018875\n", "S96 1.615572\n", "Name: 1954, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136783.10\n", "S01 1.527653\n", "S02 3.001943\n", "S03 3.973856\n", "S04 6.946056\n", " ... \n", "S88 16.64594\n", "S89 7.465284\n", "S90 5.967673\n", "S95 0.577625\n", "S96 6.341669\n", "Name: 1955, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136810.13\n", "S01 23.853456\n", "S02 110.198519\n", "S03 25.340689\n", "S04 56.293334\n", " ... \n", "S88 121.586524\n", "S89 113.863439\n", "S90 47.530398\n", "S95 12.856812\n", "S96 26.397615\n", "Name: 1956, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136811.16\n", "S01 2.580304\n", "S02 5.939719\n", "S03 3.920903\n", "S04 5.433455\n", " ... \n", "S88 17.566678\n", "S89 4.338907\n", "S90 4.473023\n", "S95 2.446828\n", "S96 4.237804\n", "Name: 1957, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136813.14\n", "S01 4.676631\n", "S02 18.578492\n", "S03 2.644971\n", "S04 2.2382\n", " ... \n", "S88 5.04087\n", "S89 18.342194\n", "S90 3.875986\n", "S95 1.472229\n", "S96 3.936606\n", "Name: 1958, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136819.15\n", "S01 52.751422\n", "S02 137.633864\n", "S03 32.253651\n", "S04 138.154316\n", " ... \n", "S88 282.115594\n", "S89 304.453615\n", "S90 35.650325\n", "S95 17.491203\n", "S96 58.996982\n", "Name: 1959, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136861.18\n", "S01 7.273594\n", "S02 9.651457\n", "S03 6.408209\n", "S04 4.668763\n", " ... \n", "S88 14.611113\n", "S89 14.877755\n", "S90 12.096755\n", "S95 4.435016\n", "S96 10.489578\n", "Name: 1960, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136874.11\n", "S01 6.736495\n", "S02 33.61422\n", "S03 2.693196\n", "S04 15.101009\n", " ... \n", "S88 6.647898\n", "S89 1.979677\n", "S90 8.281591\n", "S95 1.956159\n", "S96 10.79924\n", "Name: 1961, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136888.7\n", "S01 16.582384\n", "S02 80.394169\n", "S03 22.238186\n", "S04 54.685015\n", " ... \n", "S88 149.900118\n", "S89 76.766368\n", "S90 51.911217\n", "S95 13.753022\n", "S96 43.98553\n", "Name: 1962, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136897.8\n", "S01 0.387715\n", "S02 10.848338\n", "S03 0.858927\n", "S04 3.683902\n", " ... \n", "S88 10.413629\n", "S89 17.151866\n", "S90 1.132153\n", "S95 0.016418\n", "S96 2.543598\n", "Name: 1963, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136929.13\n", "S01 53.110685\n", "S02 82.258977\n", "S03 107.531733\n", "S04 99.237385\n", " ... \n", "S88 111.861439\n", "S89 107.984459\n", "S90 67.983941\n", "S95 15.035834\n", "S96 72.020496\n", "Name: 1964, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136930.13\n", "S01 2.463287\n", "S02 30.059015\n", "S03 2.87231\n", "S04 2.980459\n", " ... \n", "S88 34.664752\n", "S89 17.963106\n", "S90 1.319367\n", "S95 1.255288\n", "S96 3.974677\n", "Name: 1965, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136935.14\n", "S01 12.147075\n", "S02 20.186463\n", "S03 10.697878\n", "S04 26.591286\n", " ... \n", "S88 27.257416\n", "S89 17.74445\n", "S90 22.747758\n", "S95 14.409777\n", "S96 21.086192\n", "Name: 1966, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136936.10\n", "S01 1.764337\n", "S02 23.066032\n", "S03 5.029449\n", "S04 16.755326\n", " ... \n", "S88 43.671387\n", "S89 23.162273\n", "S90 2.506809\n", "S95 0.417513\n", "S96 3.465178\n", "Name: 1967, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136938.9\n", "S01 73.568259\n", "S02 194.782062\n", "S03 85.848194\n", "S04 177.911897\n", " ... \n", "S88 348.437108\n", "S89 256.419272\n", "S90 128.68647\n", "S95 45.933894\n", "S96 117.939117\n", "Name: 1968, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000136942.15\n", "S01 258.850943\n", "S02 1784.230483\n", "S03 278.061899\n", "S04 1129.338358\n", " ... \n", "S88 3280.664966\n", "S89 1995.060809\n", "S90 206.135054\n", "S95 75.778231\n", "S96 298.894583\n", "Name: 1969, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137073.22\n", "S01 89.681582\n", "S02 70.062753\n", "S03 87.15873\n", "S04 89.756112\n", " ... \n", "S88 104.45589\n", "S89 86.052956\n", "S90 144.763782\n", "S95 83.547845\n", "S96 140.959726\n", "Name: 1970, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137075.18\n", "S01 4.671901\n", "S02 3.008535\n", "S03 6.464437\n", "S04 10.206141\n", " ... \n", "S88 11.836431\n", "S89 19.619912\n", "S90 6.1001\n", "S95 3.791935\n", "S96 9.759006\n", "Name: 1971, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137076.21\n", "S01 34.712827\n", "S02 34.187951\n", "S03 141.953408\n", "S04 49.217315\n", " ... \n", "S88 47.618339\n", "S89 41.669287\n", "S90 221.791181\n", "S95 111.678693\n", "S96 82.375424\n", "Name: 1972, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137100.16\n", "S01 4.457226\n", "S02 24.706932\n", "S03 2.577393\n", "S04 15.187557\n", " ... \n", "S88 27.018531\n", "S89 17.656067\n", "S90 2.492213\n", "S95 1.919805\n", "S96 9.684323\n", "Name: 1973, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137145.20\n", "S01 3.160604\n", "S02 2.641468\n", "S03 5.308082\n", "S04 2.962009\n", " ... \n", "S88 2.83155\n", "S89 17.149785\n", "S90 5.69208\n", "S95 1.369884\n", "S96 3.444186\n", "Name: 1974, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137154.13\n", "S01 97.631565\n", "S02 839.326446\n", "S03 102.071745\n", "S04 518.86306\n", " ... \n", "S88 1572.654431\n", "S89 842.91497\n", "S90 77.028162\n", "S95 25.038179\n", "S96 129.656246\n", "Name: 1975, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137161.17\n", "S01 4.026788\n", "S02 13.428686\n", "S03 8.847004\n", "S04 10.126614\n", " ... \n", "S88 27.75559\n", "S89 15.736226\n", "S90 5.86833\n", "S95 3.473871\n", "S96 10.865618\n", "Name: 1976, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137198.10\n", "S01 9.051639\n", "S02 25.353283\n", "S03 24.769453\n", "S04 9.884649\n", " ... \n", "S88 13.072346\n", "S89 12.1433\n", "S90 54.618471\n", "S95 14.606022\n", "S96 24.85843\n", "Name: 1977, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137207.12\n", "S01 3.769178\n", "S02 4.077572\n", "S03 4.887531\n", "S04 13.189725\n", " ... \n", "S88 6.662688\n", "S89 1.919724\n", "S90 4.69549\n", "S95 7.73296\n", "S96 8.347359\n", "Name: 1978, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137210.14\n", "S01 3.794094\n", "S02 29.569493\n", "S03 4.736849\n", "S04 12.226268\n", " ... \n", "S88 49.464429\n", "S89 39.664306\n", "S90 2.303238\n", "S95 0.942547\n", "S96 3.323844\n", "Name: 1979, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137288.10\n", "S01 2.129653\n", "S02 17.47078\n", "S03 1.451457\n", "S04 11.888149\n", " ... \n", "S88 43.171279\n", "S89 15.297686\n", "S90 1.83979\n", "S95 3.690715\n", "S96 4.105157\n", "Name: 1980, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137312.15\n", "S01 3.514551\n", "S02 15.171658\n", "S03 6.649416\n", "S04 31.372709\n", " ... \n", "S88 60.043096\n", "S89 21.934327\n", "S90 4.552056\n", "S95 2.121752\n", "S96 8.557328\n", "Name: 1981, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137478.15\n", "S01 7.687689\n", "S02 13.642285\n", "S03 15.201694\n", "S04 39.833538\n", " ... \n", "S88 28.225916\n", "S89 24.045419\n", "S90 26.322492\n", "S95 3.287446\n", "S96 14.39572\n", "Name: 1982, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137486.17\n", "S01 6.19604\n", "S02 16.629835\n", "S03 12.760493\n", "S04 20.922629\n", " ... \n", "S88 25.268169\n", "S89 20.13161\n", "S90 19.413271\n", "S95 6.68167\n", "S96 9.586311\n", "Name: 1983, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137492.8\n", "S01 3.445758\n", "S02 24.297853\n", "S03 4.791394\n", "S04 11.038377\n", " ... \n", "S88 11.402938\n", "S89 1.053469\n", "S90 6.98414\n", "S95 1.048729\n", "S96 7.142544\n", "Name: 1984, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137497.17\n", "S01 0.698927\n", "S02 10.676927\n", "S03 1.675082\n", "S04 7.435078\n", " ... \n", "S88 17.621763\n", "S89 5.13607\n", "S90 1.008334\n", "S95 1.896239\n", "S96 2.049129\n", "Name: 1985, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137500.9\n", "S01 14.584664\n", "S02 37.700061\n", "S03 14.386363\n", "S04 56.720558\n", " ... \n", "S88 38.931346\n", "S89 63.383233\n", "S90 27.448203\n", "S95 9.049842\n", "S96 27.544483\n", "Name: 1986, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137502.10\n", "S01 9.040962\n", "S02 5.375059\n", "S03 13.539726\n", "S04 20.206104\n", " ... \n", "S88 60.209708\n", "S89 34.079239\n", "S90 11.496093\n", "S95 4.413731\n", "S96 6.830137\n", "Name: 1987, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137575.12\n", "S01 32.298544\n", "S02 70.755247\n", "S03 27.421626\n", "S04 52.426543\n", " ... \n", "S88 164.114597\n", "S89 74.082997\n", "S90 33.90987\n", "S95 14.651054\n", "S96 17.687092\n", "Name: 1988, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137601.16\n", "S01 7.206192\n", "S02 6.094632\n", "S03 4.828743\n", "S04 5.658311\n", " ... \n", "S88 17.603576\n", "S89 11.230356\n", "S90 12.72199\n", "S95 3.61252\n", "S96 6.514039\n", "Name: 1989, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137710.16\n", "S01 4.116318\n", "S02 11.147753\n", "S03 3.690861\n", "S04 18.334864\n", " ... \n", "S88 37.617574\n", "S89 19.438387\n", "S90 10.067875\n", "S95 3.363644\n", "S96 5.590025\n", "Name: 1990, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137752.24\n", "S01 6.895312\n", "S02 22.358224\n", "S03 3.268519\n", "S04 15.002616\n", " ... \n", "S88 15.280428\n", "S89 30.669847\n", "S90 4.211884\n", "S95 4.360948\n", "S96 5.651646\n", "Name: 1991, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137764.20\n", "S01 5.380146\n", "S02 8.35076\n", "S03 8.691347\n", "S04 3.339213\n", " ... \n", "S88 9.347852\n", "S89 20.276512\n", "S90 7.128136\n", "S95 2.077429\n", "S96 6.892803\n", "Name: 1992, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137770.14\n", "S01 5.380412\n", "S02 4.558284\n", "S03 2.360258\n", "S04 16.431639\n", " ... \n", "S88 10.496382\n", "S89 30.810897\n", "S90 3.920041\n", "S95 4.224643\n", "S96 3.893618\n", "Name: 1993, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137776.17\n", "S01 189.713447\n", "S02 240.754462\n", "S03 181.925609\n", "S04 206.11155\n", " ... \n", "S88 365.081632\n", "S89 276.894496\n", "S90 369.917269\n", "S95 97.4139\n", "S96 297.477791\n", "Name: 1994, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137801.11\n", "S01 16.366807\n", "S02 4.148494\n", "S03 42.912373\n", "S04 17.443949\n", " ... \n", "S88 14.970296\n", "S89 4.921397\n", "S90 39.323822\n", "S95 27.921646\n", "S96 35.439618\n", "Name: 1995, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137804.14\n", "S01 2.075186\n", "S02 2.517665\n", "S03 2.764625\n", "S04 15.10892\n", " ... \n", "S88 15.920653\n", "S89 24.950447\n", "S90 3.388077\n", "S95 0.884134\n", "S96 3.820147\n", "Name: 1996, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137812.19\n", "S01 7.599669\n", "S02 0.699477\n", "S03 4.327187\n", "S04 3.082995\n", " ... \n", "S88 0.560931\n", "S89 26.698866\n", "S90 6.417732\n", "S95 2.856766\n", "S96 14.370346\n", "Name: 1997, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137815.14\n", "S01 5.791171\n", "S02 10.119228\n", "S03 1.526229\n", "S04 5.142867\n", " ... \n", "S88 13.850097\n", "S89 10.979435\n", "S90 1.892503\n", "S95 2.094253\n", "S96 3.175044\n", "Name: 1998, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137818.12\n", "S01 226.613621\n", "S02 1514.846925\n", "S03 208.154622\n", "S04 1163.419194\n", " ... \n", "S88 3867.531129\n", "S89 1147.407564\n", "S90 118.737282\n", "S95 55.215388\n", "S96 183.59643\n", "Name: 1999, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137822.12\n", "S01 2.932008\n", "S02 14.208196\n", "S03 3.868678\n", "S04 8.550825\n", " ... \n", "S88 3.480437\n", "S89 7.233292\n", "S90 6.481488\n", "S95 2.147596\n", "S96 3.602388\n", "Name: 2000, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137831.15\n", "S01 3.064208\n", "S02 21.530176\n", "S03 6.780568\n", "S04 18.12565\n", " ... \n", "S88 28.912866\n", "S89 12.20264\n", "S90 5.274271\n", "S95 2.314805\n", "S96 2.615793\n", "Name: 2001, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137845.15\n", "S01 11.164086\n", "S02 18.423136\n", "S03 33.561379\n", "S04 24.237662\n", " ... \n", "S88 27.37501\n", "S89 19.793263\n", "S90 39.11641\n", "S95 15.517711\n", "S96 36.591672\n", "Name: 2002, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000137871.20\n", "S01 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"S88 577.722022\n", "S89 251.476064\n", "S90 73.826906\n", "S95 7.715376\n", "S96 44.747207\n", "Name: 4122, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000278705.1\n", "S01 61.526441\n", "S02 567.442598\n", "S03 64.542938\n", "S04 295.032534\n", " ... \n", "S88 725.781424\n", "S89 278.02524\n", "S90 46.218386\n", "S95 43.005212\n", "S96 165.136535\n", "Name: 4123, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000278828.1\n", "S01 117.63984\n", "S02 54.443288\n", "S03 165.214929\n", "S04 87.259243\n", " ... \n", "S88 195.718868\n", "S89 186.192015\n", "S90 457.069382\n", "S95 59.69337\n", "S96 345.474513\n", "Name: 4124, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000280800.1\n", "S01 5.715291\n", "S02 20.679962\n", "S03 5.534207\n", "S04 12.000328\n", " ... \n", "S88 9.526345\n", "S89 39.459917\n", "S90 21.31847\n", "S95 6.795015\n", "S96 21.736379\n", "Name: 4125, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000281501.1\n", "S01 3.413084\n", "S02 23.239169\n", "S03 1.376445\n", "S04 6.535886\n", " ... \n", "S88 0.960481\n", "S89 3.462836\n", "S90 13.195915\n", "S95 0.249542\n", "S96 12.069031\n", "Name: 4126, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000282508.2\n", "S01 4.329421\n", "S02 13.242666\n", "S03 9.757549\n", "S04 21.77835\n", " ... \n", "S88 5.467054\n", "S89 0.522939\n", "S90 3.662294\n", "S95 6.668907\n", "S96 11.315744\n", "Name: 4127, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000282885.2\n", "S01 75.910309\n", "S02 97.708653\n", "S03 71.358165\n", "S04 62.561343\n", " ... \n", "S88 94.695298\n", "S89 121.3767\n", "S90 162.35816\n", "S95 258.540697\n", "S96 170.10865\n", "Name: 4128, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000283633.1\n", "S01 23.347516\n", "S02 25.745014\n", "S03 69.513013\n", "S04 25.666181\n", " ... \n", "S88 31.070003\n", "S89 22.792831\n", "S90 70.461584\n", "S95 79.23306\n", "S96 47.914348\n", "Name: 4129, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000283907.1\n", "S01 1551.902572\n", "S02 5776.878761\n", "S03 2045.300449\n", "S04 1924.482864\n", " ... \n", "S88 1543.019304\n", "S89 4507.294843\n", "S90 1286.101741\n", "S95 1453.669903\n", "S96 2125.38655\n", "Name: 4130, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000284196.3\n", "S01 0.881197\n", "S02 6.125912\n", "S03 1.805723\n", "S04 6.067895\n", " ... \n", "S88 3.587343\n", "S89 2.795492\n", "S90 1.9553\n", "S95 0.688148\n", "S96 1.548496\n", "Name: 4131, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000284634.1\n", "S01 0.193346\n", "S02 17.569602\n", "S03 1.829062\n", "S04 3.630899\n", " ... \n", "S88 1.22953\n", "S89 7.916768\n", "S90 2.717358\n", "S95 1.394298\n", "S96 7.010212\n", "Name: 4132, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000284770.2\n", "S01 2.286874\n", "S02 3.021524\n", "S03 2.865297\n", "S04 1.687029\n", " ... \n", "S88 3.64196\n", "S89 8.227829\n", "S90 5.276986\n", "S95 1.922482\n", "S96 2.831849\n", "Name: 4133, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000284809.1\n", "S01 2.10143\n", "S02 79.508964\n", "S03 18.811116\n", "S04 128.032804\n", " ... \n", "S88 26.795235\n", "S89 64.156015\n", "S90 2.286713\n", "S95 3.233638\n", "S96 8.297921\n", "Name: 4134, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000284874.1\n", "S01 1.454187\n", "S02 0.516431\n", "S03 5.9613\n", "S04 2.242609\n", " ... \n", "S88 6.52894\n", "S89 3.040584\n", "S90 9.681206\n", "S95 4.203609\n", "S96 8.978747\n", "Name: 4135, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000284959.2\n", "S01 3.818503\n", "S02 7.670754\n", "S03 6.573182\n", "S04 5.024401\n", " ... \n", "S88 4.459959\n", "S89 3.83891\n", "S90 9.367243\n", "S95 2.328772\n", "S96 6.29211\n", "Name: 4136, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000285756.2\n", "S01 10.719458\n", "S02 18.280204\n", "S03 13.687993\n", "S04 19.905845\n", " ... \n", "S88 31.79922\n", "S89 21.999797\n", "S90 3.724749\n", "S95 6.310617\n", "S96 24.491164\n", "Name: 4137, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000285774.2\n", "S01 10.118388\n", "S02 8.798636\n", "S03 23.047404\n", "S04 5.058205\n", " ... \n", "S88 15.120421\n", "S89 19.235443\n", "S90 24.984497\n", "S95 8.582279\n", "S96 11.68162\n", "Name: 4138, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000285884.1\n", "S01 11.527974\n", "S02 2.21428\n", "S03 10.603282\n", "S04 2.302238\n", " ... \n", "S88 50.115171\n", "S89 19.366971\n", "S90 19.058147\n", "S95 5.182737\n", "S96 19.591224\n", "Name: 4139, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000285976.2\n", "S01 4.386403\n", "S02 10.137873\n", "S03 3.925357\n", "S04 5.49431\n", " ... \n", "S88 7.294156\n", "S89 6.30509\n", "S90 10.17373\n", "S95 3.98307\n", "S96 6.404164\n", "Name: 4140, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000286021.2\n", "S01 2.951689\n", "S02 69.319858\n", "S03 6.950649\n", "S04 67.810987\n", " ... \n", "S88 15.54745\n", "S89 22.10011\n", "S90 1.974481\n", "S95 1.428419\n", "S96 2.48381\n", "Name: 4141, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000286147.1\n", "S01 2.780988\n", "S02 66.183243\n", "S03 12.663118\n", "S04 88.524134\n", " ... \n", "S88 9.409992\n", "S89 19.978202\n", "S90 3.483134\n", "S95 4.340778\n", "S96 8.868814\n", "Name: 4142, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000286171.1\n", "S01 22.090146\n", "S02 79.348496\n", "S03 18.383923\n", "S04 34.275493\n", " ... \n", "S88 10.441533\n", "S89 31.744585\n", "S90 27.933352\n", "S95 15.813597\n", "S96 94.583754\n", "Name: 4143, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000286522.1\n", "S01 38.558169\n", "S02 285.735258\n", "S03 36.159325\n", "S04 125.344512\n", " ... \n", "S88 559.390098\n", "S89 387.044359\n", "S90 89.231794\n", "S95 27.761897\n", "S96 49.83076\n", "Name: 4144, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000286834.1\n", "S01 1.446729\n", "S02 101.312666\n", "S03 17.10636\n", "S04 109.49099\n", " ... \n", "S88 23.370109\n", "S89 34.169966\n", "S90 5.444215\n", "S95 4.262073\n", "S96 13.917467\n", "Name: 4145, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000287080.1\n", "S01 8.543461\n", "S02 48.482781\n", "S03 11.492971\n", "S04 40.763492\n", " ... \n", "S88 2.688918\n", "S89 9.531408\n", "S90 2.823952\n", "S95 0.107894\n", "S96 12.11091\n", "Name: 4146, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000287160.1\n", "S01 3.392143\n", "S02 57.089139\n", "S03 7.379778\n", "S04 67.437197\n", " ... \n", "S88 23.094887\n", "S89 19.040575\n", "S90 1.324381\n", "S95 4.329463\n", "S96 9.970802\n", "Name: 4147, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000287825.1\n", "S01 8.54341\n", "S02 26.198111\n", "S03 9.731645\n", "S04 5.939315\n", " ... \n", "S88 7.114563\n", "S89 4.664343\n", "S90 20.376778\n", "S95 1.601362\n", "S96 9.273306\n", "Name: 4148, Length: 90, dtype: object\n", "ENSEMBL ID ENSG00000288560.1\n", "S01 8.36187\n", "S02 3.218659\n", "S03 2.560132\n", "S04 4.12353\n", " ... \n", "S88 4.563028\n", "S89 10.941191\n", "S90 7.220862\n", "S95 1.568828\n", "S96 7.706704\n", "Name: 4149, Length: 90, dtype: object\n" ] } ], "source": [ "\n", "for index, row in Gene_exp_df.iterrows():\n", " print(row[])" ] }, { "cell_type": "code", "execution_count": 3, "id": "81406851", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "['ENSEMBL ID', 'S01', 'S02', 'S03', 'S04', 'S05', 'S06', 'S07', 'S08', 'S09', 'S10', 'S11', 'S12', 'S13', 'S14', 'S15', 'S16', 'S17', 'S18', 'S19', 'S20', 'S21', 'S22', 'S23', 'S24', 'S26', 'S27', 'S28', 'S29', 'S30', 'S31', 'S32', 'S33', 'S34', 'S35', 'S36', 'S37', 'S38', 'S39', 'S40', 'S41', 'S42', 'S44', 'S45', 'S46', 'S47', 'S48', 'S49', 'S50', 'S51', 'S52', 'S53', 'S54', 'S55', 'S56', 'S57', 'S58', 'S59', 'S60', 'S61', 'S62', 'S63', 'S64', 'S65', 'S66', 'S67', 'S68', 'S69', 'S70', 'S71', 'S72', 'S73', 'S74', 'S75', 'S77', 'S78', 'S79', 'S80', 'S81', 'S82', 'S83', 'S84', 'S85', 'S86', 'S87', 'S88', 'S89', 'S90', 'S95', 'S96']\n", "['S01', 'S02', 'S03', 'S04', 'S05', 'S06', 'S07', 'S08', 'S09', 'S10', 'S11', 'S12', 'S13', 'S14', 'S15', 'S16', 'S17', 'S18', 'S19', 'S20', 'S21', 'S22', 'S23', 'S24', 'S26', 'S27', 'S28', 'S29', 'S30', 'S31', 'S32', 'S33', 'S34', 'S35', 'S36', 'S37', 'S38', 'S39', 'S40', 'S41', 'S42', 'S44', 'S45', 'S46', 'S47', 'S48', 'S49', 'S50', 'S51', 'S52', 'S53', 'S54', 'S55', 'S56', 'S57', 'S58', 'S59', 'S60', 'S61', 'S62', 'S63', 'S64', 'S65', 'S66', 'S67', 'S68', 'S69', 'S70', 'S71', 'S72', 'S73', 'S74', 'S75', 'S77', 'S78', 'S79', 'S80', 'S81', 'S82', 'S83', 'S84', 'S85', 'S86', 'S87', 'S88', 'S89', 'S90', 'S95', 'S96']\n" ] } ], "source": [ "# Place your code here\n", "\n", "genes=[]\n", "genes_cols= Gene_exp_df.columns.values.tolist()\n", "\n", "print(genes_cols)\n", "genes_cols.remove(\"ENSEMBL ID\")\n", "print(genes_cols)" ] }, { "cell_type": "code", "execution_count": 4, "id": "63e5b93d", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "0 3.852019\n", "1 1.473123\n", "2 14.680768\n", "3 1.117000\n", "4 4.570469\n", " ... \n", "4145 6.152377\n", "4146 24.942787\n", "4147 3.686996\n", "4148 18.347209\n", "4149 4.514240\n", "Name: S14, Length: 4150, dtype: float64" ] }, "execution_count": 4, "metadata": {}, "output_type": "execute_result" } ], "source": [ "Gene_exp_df['S14']" ] }, { "cell_type": "code", "execution_count": 5, "id": "bcac89f0", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "4150" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "Gene_exp_df.shape[0]" ] }, { "cell_type": "code", "execution_count": 6, "id": "e53a4ad1", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "107\n", "63\n", "59\n", "21\n", "62\n", "16\n", "90\n", "38\n", "290\n", "52\n", "52\n", "33\n", "104\n", "48\n", "80\n", "74\n", "109\n", "6\n", "320\n", "80\n", "132\n", "41\n", "158\n", "74\n", "35\n", "99\n", "80\n", "40\n", "67\n", "28\n", "29\n", "13\n", "129\n", "91\n", "120\n", "47\n", "84\n", "129\n", "47\n", "238\n", "39\n", "69\n", "45\n", "174\n", "95\n", "127\n", "28\n", "132\n", "38\n", "85\n", "162\n", "65\n", "41\n", "207\n", "13\n", "57\n", "320\n", "91\n", "246\n", "3\n", "8\n", "64\n", "42\n", "15\n", "9\n", "12\n", "106\n", "18\n", "15\n", "36\n", "13\n", "11\n", "8\n", "3\n", "9\n", "24\n", "36\n", "8\n", "154\n", "118\n", "22\n", "15\n", "8\n", "3\n", "45\n", "23\n", "73\n", "456\n", "18\n" ] } ], "source": [ "#Gene_exp_df.shape[0]= 4150\n", "thresold= 2905 #This is 70% of 4150 (total rows):\n", "remove_genes=[]\n", "new_genes=[]\n", "for g in genes_cols:\n", " count=0\n", " # df=Gene_exp_df[g]\n", " for i in range(Gene_exp_df.shape[0]):\n", " if Gene_exp_df[g][i] <1 :\n", " count+=1\n", " if count >=thresold:\n", " remove_genes.append(g)\n", " print(count)\n", " else:\n", " new_genes.append(g)\n", " print(count)" ] }, { "cell_type": "code", "execution_count": 7, "id": "5d1a4e5b", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "[]" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "\n", "remove_genes" ] }, { "cell_type": "code", "execution_count": 8, "id": "073aca5a", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "89" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "len(new_genes)" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "markdown", "id": "b4ebb19a", "metadata": { "id": "b4ebb19a" }, "source": [ "# Feature elimination*\n", "\n", "From the feature matrix `GSE208194_RawTPM.csv.gz`, split the samples into training and test and on the training set \n", "- using recursive feature elimination identify the optimal number of features out of the 4150, which can predict the status of a particular individual to be \n", " - Having the likelihood of coronary disease which can lead to heart failure (HF+)\n", " - Having the likelihood of coronary disease which may not lead to heart failure (HF-)\n", " - Healthy indiviual (HVOL)\n", " \n", "- Show the relative accuracy of the model as different number of features are used as a plot." ] }, { "cell_type": "code", "execution_count": null, "id": "5d4ae96e", "metadata": { "id": "5d4ae96e" }, "outputs": [], "source": [ "# Place your code here" ] }, { "cell_type": "markdown", "id": "5bb0af3f", "metadata": { "id": "5bb0af3f" }, "source": [ "# Model building*\n", "\n", "With N optimal features identified, used a feature selection method of choice to select the top N features and build a multi-class classifier with cross-validation and report its accuracy and any other metric deemed suitable.\n" ] }, { "cell_type": "code", "execution_count": null, "id": "8634f46c", "metadata": { "id": "8634f46c" }, "outputs": [], "source": [ "# Place your code here" ] }, { "cell_type": "markdown", "id": "ba72d9b9", "metadata": { "id": "ba72d9b9" }, "source": [ "# Model evaluation*\n", "\n", "- Apply the model on the test set and report the accuracy and per class sensitivity i.e the total number of samples in a given class within the test set, and how many were predicted accurately.\n", "- Also report as a binary matrix how many samples were correctly identified as HF+/HF- and HVOL\n", "\n", "| | HF+/- | HVOL |\n", "|----------|:-------------:|------:|\n", "| HF+/- | . | . |\n", "| HVOL | . | . |\n" ] }, { "cell_type": "code", "execution_count": null, "id": "277533a0", "metadata": { "id": "277533a0" }, "outputs": [], "source": [ "# Place your code here" ] }, { "cell_type": "markdown", "id": "46e6f4ce", "metadata": {}, "source": [ "# Biological significance of features\n", "\n", "- Take the top 5 features and search for their gene names in [Gene Cards](https://www.genecards.org/) with using the suffix for example:\n", " ENSG00000000419.12 -> ENSG00000000419\t\n", " \n", "- Take the gene names identified and search in [Pubmed](https://pubmed.ncbi.nlm.nih.gov/) as \n", " \"Gene name\" AND \"coronary disease\"\n", " \n", "- Report if anything of interest is found by reading the abstract of the top hits in pubmed." ] }, { "cell_type": "code", "execution_count": null, "id": "8c1bf912", "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "colab": { "name": "AssignmentMotifDiscovery.ipynb", "provenance": [] }, "kernelspec": { "display_name": "Python 3.9.12 ('base')", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.12" }, "toc": { "base_numbering": 1, "nav_menu": {}, "number_sections": true, "sideBar": true, "skip_h1_title": false, "title_cell": "Table of Contents", "title_sidebar": "Contents", "toc_cell": false, "toc_position": {}, "toc_section_display": true, "toc_window_display": false }, "vscode": { "interpreter": { "hash": "67225e902c436798ce86437353744102e33ba4d68fae561004183084f442db90" } } }, 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