{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "data": { "text/html": [ "" ], "text/vnd.plotly.v1+html": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
" ], "text/plain": [ "\n", " | GSM1846906 | \n", "GSM1846907 | \n", "GSM1846905 | \n", "GSM1846909 | \n", "GSM1846910 | \n", "GSM1846915 | \n", "GSM1846919 | \n", "GSM1846914 | \n", "GSM1846911 | \n", "GSM1846912 | \n", "GSM1846913 | \n", "GSM1846920 | \n", "GSM1846916 | \n", "GSM1846908 | \n", "GSM1846918 | \n", "GSM1846917 | \n", "GSM1846904 | \n", "GSM1846921 | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
A1BG | \n", "280 | \n", "84 | \n", "334 | \n", "170 | \n", "424 | \n", "503 | \n", "221 | \n", "619 | \n", "932 | \n", "561 | \n", "985 | \n", "332 | \n", "222 | \n", "354 | \n", "282 | \n", "291 | \n", "167 | \n", "268 | \n", "
A1CF | \n", "2 | \n", "2 | \n", "11 | \n", "10 | \n", "4 | \n", "2 | \n", "6 | \n", "3 | \n", "10 | \n", "4 | \n", "3 | \n", "9 | \n", "7 | \n", "10 | \n", "2 | \n", "6 | \n", "4 | \n", "3 | \n", "
A2M | \n", "8 | \n", "40 | \n", "8 | \n", "49 | \n", "10704 | \n", "10969 | \n", "5479 | \n", "11670 | \n", "10334 | \n", "7303 | \n", "25299 | \n", "4313 | \n", "3252 | \n", "72 | \n", "3021 | \n", "2109 | \n", "40 | \n", "3438 | \n", "
A2ML1 | \n", "8 | \n", "4 | \n", "18 | \n", "25 | \n", "7 | \n", "5 | \n", "16 | \n", "7 | \n", "17 | \n", "15 | \n", "5 | \n", "10 | \n", "8 | \n", "11 | \n", "9 | \n", "7 | \n", "14 | \n", "9 | \n", "
A2MP1 | \n", "2 | \n", "0 | \n", "1 | \n", "2 | \n", "34 | \n", "26 | \n", "11 | \n", "31 | \n", "29 | \n", "14 | \n", "50 | \n", "20 | \n", "10 | \n", "2 | \n", "6 | \n", "10 | \n", "1 | \n", "2 | \n", "
\n", " | Sample Title | \n", "cell type | \n", "infected shrna | \n", "melanoma mutation | \n", "passage | \n", "
---|---|---|---|---|---|
Sample_geo_accession | \n", "\n", " | \n", " | \n", " | \n", " | \n", " |
GSM1846906 | \n", "MM13_shKMT2D_RNAseq_rp3 | \n", "patient derived xenograft cells | \n", "shKMT2D | \n", "NRASQ61L | \n", "2 | \n", "
GSM1846907 | \n", "MM13_shLuc_RNAseq_rp1 | \n", "patient derived xenograft cells | \n", "shLuc | \n", "NRASQ61L | \n", "2 | \n", "
GSM1846905 | \n", "MM13_shKMT2D_RNAseq_rp2 | \n", "patient derived xenograft cells | \n", "shKMT2D | \n", "NRASQ61L | \n", "2 | \n", "
GSM1846909 | \n", "MM13_shLuc_RNAseq_rp3 | \n", "patient derived xenograft cells | \n", "shLuc | \n", "NRASQ61L | \n", "2 | \n", "
GSM1846910 | \n", "MM16_shKMT2D_RNAseq_rp1 | \n", "patient derived xenograft cells | \n", "shKMT2D | \n", "NRASQ61K | \n", "2 | \n", "
GSM1846915 | \n", "MM16_shLuc_RNAseq_rp3 | \n", "patient derived xenograft cells | \n", "shLuc | \n", "NRASQ61K | \n", "2 | \n", "
GSM1846919 | \n", "MM27_shLuc_RNAseq_rp1 | \n", "patient derived xenograft cells | \n", "shLuc | \n", "BRAFV600E | \n", "2 | \n", "
GSM1846914 | \n", "MM16_shLuc_RNAseq_rp2 | \n", "patient derived xenograft cells | \n", "shLuc | \n", "NRASQ61K | \n", "2 | \n", "
GSM1846911 | \n", "MM16_shKMT2D_RNAseq_rp2 | \n", "patient derived xenograft cells | \n", "shKMT2D | \n", "NRASQ61K | \n", "2 | \n", "
GSM1846912 | \n", "MM16_shKMT2D_RNAseq_rp3 | \n", "patient derived xenograft cells | \n", "shKMT2D | \n", "NRASQ61K | \n", "2 | \n", "
GSM1846913 | \n", "MM16_shLuc_RNAseq_rp1 | \n", "patient derived xenograft cells | \n", "shLuc | \n", "NRASQ61K | \n", "2 | \n", "
GSM1846920 | \n", "MM27_shLuc_RNAseq_rp2 | \n", "patient derived xenograft cells | \n", "shLuc | \n", "BRAFV600E | \n", "2 | \n", "
GSM1846916 | \n", "MM27_shKMT2D_RNAseq_rp1 | \n", "patient derived xenograft cells | \n", "shKMT2D | \n", "BRAFV600E | \n", "2 | \n", "
GSM1846908 | \n", "MM13_shLuc_RNAseq_rp2 | \n", "patient derived xenograft cells | \n", "shLuc | \n", "NRASQ61L | \n", "2 | \n", "
GSM1846918 | \n", "MM27_shKMT2D_RNAseq_rp3 | \n", "patient derived xenograft cells | \n", "shKMT2D | \n", "BRAFV600E | \n", "2 | \n", "
GSM1846917 | \n", "MM27_shKMT2D_RNAseq_rp2 | \n", "patient derived xenograft cells | \n", "shKMT2D | \n", "BRAFV600E | \n", "2 | \n", "
GSM1846904 | \n", "MM13_shKMT2D_RNAseq_rp1 | \n", "patient derived xenograft cells | \n", "shKMT2D | \n", "NRASQ61L | \n", "2 | \n", "
GSM1846921 | \n", "MM27_shLuc_RNAseq_rp3 | \n", "patient derived xenograft cells | \n", "shLuc | \n", "BRAFV600E | \n", "2 | \n", "
\n", " | logFC | \n", "AveExpr | \n", "P-value | \n", "FDR | \n", "
---|---|---|---|---|
Gene | \n", "\n", " | \n", " | \n", " | \n", " |
*CSF3 | \n", "4.98 | \n", "-0.61 | \n", "7.988621e-08 | \n", "0.000702 | \n", "
*DEFB103B | \n", "4.66 | \n", "2.08 | \n", "1.038521e-07 | \n", "0.000702 | \n", "
*ELOVL2 | \n", "-3.31 | \n", "4.45 | \n", "1.063014e-07 | \n", "0.000702 | \n", "
*KIF20A | \n", "-2.83 | \n", "5.20 | \n", "1.187809e-07 | \n", "0.000702 | \n", "
*NDC80 | \n", "-2.76 | \n", "4.23 | \n", "1.675947e-07 | \n", "0.000702 | \n", "
*CDK1 | \n", "-2.61 | \n", "5.19 | \n", "2.099340e-07 | \n", "0.000702 | \n", "
*DEFB103A | \n", "4.64 | \n", "1.08 | \n", "2.162027e-07 | \n", "0.000702 | \n", "
*NCAPG | \n", "-2.54 | \n", "4.93 | \n", "2.271055e-07 | \n", "0.000702 | \n", "
*SPAG5 | \n", "-2.20 | \n", "5.14 | \n", "2.379365e-07 | \n", "0.000702 | \n", "
*NUF2 | \n", "-2.59 | \n", "4.07 | \n", "2.670675e-07 | \n", "0.000702 | \n", "
*PADI3 | \n", "-3.42 | \n", "1.03 | \n", "2.741276e-07 | \n", "0.000702 | \n", "
*RRM2 | \n", "-3.14 | \n", "5.16 | \n", "2.749318e-07 | \n", "0.000702 | \n", "
*KIF23 | \n", "-2.13 | \n", "5.38 | \n", "2.794625e-07 | \n", "0.000702 | \n", "
*PBK | \n", "-2.71 | \n", "4.34 | \n", "2.893579e-07 | \n", "0.000702 | \n", "
*CDC25C | \n", "-2.99 | \n", "1.86 | \n", "2.989265e-07 | \n", "0.000702 | \n", "
*BMP2 | \n", "2.30 | \n", "5.57 | \n", "3.558851e-07 | \n", "0.000751 | \n", "
*CDKN2C | \n", "-3.65 | \n", "2.64 | \n", "3.731138e-07 | \n", "0.000751 | \n", "
*CDKN3 | \n", "-2.80 | \n", "3.87 | \n", "4.323315e-07 | \n", "0.000751 | \n", "
*CDC6 | \n", "-2.46 | \n", "4.69 | \n", "4.338553e-07 | \n", "0.000751 | \n", "
*TMEM71 | \n", "-2.47 | \n", "2.69 | \n", "4.510800e-07 | \n", "0.000751 | \n", "
*PPL | \n", "-2.60 | \n", "4.86 | \n", "4.842187e-07 | \n", "0.000751 | \n", "
*ZWINT | \n", "-2.20 | \n", "4.88 | \n", "4.929842e-07 | \n", "0.000751 | \n", "
*CCNB1 | \n", "-1.84 | \n", "6.13 | \n", "5.770819e-07 | \n", "0.000751 | \n", "
*FABP3 | \n", "-2.74 | \n", "1.95 | \n", "5.888300e-07 | \n", "0.000751 | \n", "
*IL1B | \n", "2.10 | \n", "7.56 | \n", "5.888948e-07 | \n", "0.000751 | \n", "
*MAPK8IP2 | \n", "-2.25 | \n", "2.78 | \n", "6.164419e-07 | \n", "0.000751 | \n", "
*NUSAP1 | \n", "-2.60 | \n", "5.30 | \n", "6.166006e-07 | \n", "0.000751 | \n", "
*LMNB1 | \n", "-2.21 | \n", "4.84 | \n", "6.320962e-07 | \n", "0.000751 | \n", "
*GATSL3 | \n", "2.35 | \n", "4.13 | \n", "6.469384e-07 | \n", "0.000751 | \n", "
*NMU | \n", "-4.08 | \n", "-1.83 | \n", "6.883912e-07 | \n", "0.000751 | \n", "
*GPSM2 | \n", "-2.73 | \n", "4.30 | \n", "7.020776e-07 | \n", "0.000751 | \n", "
*FAM72B | \n", "-2.55 | \n", "2.36 | \n", "7.465090e-07 | \n", "0.000751 | \n", "
*TYMS | \n", "-1.80 | \n", "6.03 | \n", "8.134943e-07 | \n", "0.000751 | \n", "
*NEIL3 | \n", "-2.61 | \n", "1.29 | \n", "8.255161e-07 | \n", "0.000751 | \n", "
*CCNB2 | \n", "-2.39 | \n", "4.71 | \n", "8.270063e-07 | \n", "0.000751 | \n", "
*PPM1E | \n", "-3.42 | \n", "0.46 | \n", "8.708551e-07 | \n", "0.000751 | \n", "
*APOBEC3B | \n", "-3.12 | \n", "3.18 | \n", "8.734778e-07 | \n", "0.000751 | \n", "
*FAM111B | \n", "-3.04 | \n", "3.40 | \n", "9.140102e-07 | \n", "0.000751 | \n", "
*CENPA | \n", "-2.40 | \n", "3.08 | \n", "9.485570e-07 | \n", "0.000751 | \n", "
*HMMR | \n", "-2.59 | \n", "4.07 | \n", "9.776581e-07 | \n", "0.000751 | \n", "
*OLFML2A | \n", "-3.33 | \n", "2.91 | \n", "9.930159e-07 | \n", "0.000751 | \n", "
*DLGAP5 | \n", "-2.50 | \n", "4.55 | \n", "9.949078e-07 | \n", "0.000751 | \n", "
*KIFC1 | \n", "-2.73 | \n", "5.18 | \n", "1.045586e-06 | \n", "0.000751 | \n", "
*NEK2 | \n", "-2.58 | \n", "3.69 | \n", "1.063784e-06 | \n", "0.000751 | \n", "
*GMNN | \n", "-1.88 | \n", "5.47 | \n", "1.066635e-06 | \n", "0.000751 | \n", "
*TPX2 | \n", "-2.35 | \n", "6.21 | \n", "1.071492e-06 | \n", "0.000751 | \n", "
*TTK | \n", "-2.51 | \n", "4.15 | \n", "1.083748e-06 | \n", "0.000751 | \n", "
*RAD51 | \n", "-2.53 | \n", "2.95 | \n", "1.086303e-06 | \n", "0.000751 | \n", "
*SKA3 | \n", "-2.40 | \n", "3.63 | \n", "1.088784e-06 | \n", "0.000751 | \n", "
*SOD2 | \n", "2.37 | \n", "9.24 | \n", "1.091390e-06 | \n", "0.000751 | \n", "
*SPC25 | \n", "-2.52 | \n", "3.03 | \n", "1.139658e-06 | \n", "0.000751 | \n", "
*CDC45 | \n", "-2.40 | \n", "3.52 | \n", "1.157999e-06 | \n", "0.000751 | \n", "
*ANGPTL4 | \n", "3.32 | \n", "1.41 | \n", "1.164318e-06 | \n", "0.000751 | \n", "
*ITGA7 | \n", "-1.97 | \n", "5.30 | \n", "1.187852e-06 | \n", "0.000751 | \n", "
*CEP55 | \n", "-2.69 | \n", "5.62 | \n", "1.187904e-06 | \n", "0.000751 | \n", "
*CLDN1 | \n", "2.59 | \n", "2.23 | \n", "1.193546e-06 | \n", "0.000751 | \n", "
*CDCA8 | \n", "-2.79 | \n", "3.47 | \n", "1.236268e-06 | \n", "0.000759 | \n", "
*CENPF | \n", "-2.22 | \n", "6.78 | \n", "1.248938e-06 | \n", "0.000759 | \n", "
*AC004381.6 | \n", "-2.05 | \n", "2.67 | \n", "1.345565e-06 | \n", "0.000804 | \n", "
*IQGAP3 | \n", "-2.24 | \n", "5.04 | \n", "1.431250e-06 | \n", "0.000822 | \n", "
*GINS2 | \n", "-1.99 | \n", "3.32 | \n", "1.432323e-06 | \n", "0.000822 | \n", "
*DEPDC1B | \n", "-2.38 | \n", "2.58 | \n", "1.446979e-06 | \n", "0.000822 | \n", "
*CCNA2 | \n", "-2.52 | \n", "4.36 | \n", "1.531383e-06 | \n", "0.000852 | \n", "
*KIF11 | \n", "-2.46 | \n", "5.22 | \n", "1.546659e-06 | \n", "0.000852 | \n", "
*NCAPG2 | \n", "-2.61 | \n", "4.43 | \n", "1.671211e-06 | \n", "0.000885 | \n", "
*FBXO43 | \n", "-2.65 | \n", "0.59 | \n", "1.675541e-06 | \n", "0.000885 | \n", "
*SDC2 | \n", "2.77 | \n", "3.28 | \n", "1.706618e-06 | \n", "0.000885 | \n", "
*MALL | \n", "-3.22 | \n", "2.11 | \n", "1.715640e-06 | \n", "0.000885 | \n", "
*CDCA3 | \n", "-2.56 | \n", "3.62 | \n", "1.747172e-06 | \n", "0.000885 | \n", "
*HJURP | \n", "-2.77 | \n", "5.30 | \n", "1.758300e-06 | \n", "0.000885 | \n", "
*CNTRL | \n", "-1.76 | \n", "4.76 | \n", "1.788160e-06 | \n", "0.000887 | \n", "
*EXO1 | \n", "-2.60 | \n", "3.27 | \n", "1.901500e-06 | \n", "0.000931 | \n", "
*CIT | \n", "-2.78 | \n", "5.35 | \n", "1.970083e-06 | \n", "0.000951 | \n", "
*KIF2C | \n", "-2.70 | \n", "4.63 | \n", "2.113863e-06 | \n", "0.000970 | \n", "
*TCF19 | \n", "-2.56 | \n", "4.94 | \n", "2.118624e-06 | \n", "0.000970 | \n", "
*FAM46B | \n", "-2.48 | \n", "0.32 | \n", "2.137942e-06 | \n", "0.000970 | \n", "
*UBE2T | \n", "-1.84 | \n", "4.03 | \n", "2.151694e-06 | \n", "0.000970 | \n", "
*RAD51AP1 | \n", "-2.11 | \n", "3.39 | \n", "2.198760e-06 | \n", "0.000970 | \n", "
*FAM64A | \n", "-2.88 | \n", "3.33 | \n", "2.220530e-06 | \n", "0.000970 | \n", "
*MELK | \n", "-2.30 | \n", "4.26 | \n", "2.230197e-06 | \n", "0.000970 | \n", "
*TNFAIP6 | \n", "4.34 | \n", "-1.47 | \n", "2.231709e-06 | \n", "0.000970 | \n", "
*NEURL1B | \n", "-4.02 | \n", "1.57 | \n", "2.257868e-06 | \n", "0.000970 | \n", "
*WDR76 | \n", "-2.67 | \n", "3.42 | \n", "2.400674e-06 | \n", "0.001019 | \n", "
*BORA | \n", "-1.90 | \n", "3.09 | \n", "2.437616e-06 | \n", "0.001023 | \n", "
*OSBP2 | \n", "-1.96 | \n", "4.10 | \n", "2.497887e-06 | \n", "0.001036 | \n", "
*SGO1 | \n", "-2.40 | \n", "2.61 | \n", "2.629448e-06 | \n", "0.001077 | \n", "
*PTPRH | \n", "-1.99 | \n", "2.87 | \n", "2.749500e-06 | \n", "0.001114 | \n", "
*ARNT2 | \n", "-2.16 | \n", "2.94 | \n", "2.820754e-06 | \n", "0.001125 | \n", "
*FAM72A | \n", "-2.10 | \n", "2.40 | \n", "2.842528e-06 | \n", "0.001125 | \n", "
*GTSE1 | \n", "-2.49 | \n", "4.25 | \n", "2.993814e-06 | \n", "0.001160 | \n", "
*FAM72D | \n", "-2.36 | \n", "1.78 | \n", "2.996688e-06 | \n", "0.001160 | \n", "
*PHGDH | \n", "-2.19 | \n", "5.14 | \n", "3.037237e-06 | \n", "0.001163 | \n", "
*PLK4 | \n", "-2.16 | \n", "2.92 | \n", "3.175932e-06 | \n", "0.001192 | \n", "
*PRC1 | \n", "-2.09 | \n", "6.54 | \n", "3.179518e-06 | \n", "0.001192 | \n", "
*MCM3 | \n", "-1.63 | \n", "7.21 | \n", "3.306676e-06 | \n", "0.001217 | \n", "
*IL32 | \n", "2.80 | \n", "2.02 | \n", "3.315727e-06 | \n", "0.001217 | \n", "
*CDCA2 | \n", "-2.38 | \n", "3.84 | \n", "3.387261e-06 | \n", "0.001225 | \n", "
*HS3ST2 | \n", "2.60 | \n", "-0.44 | \n", "3.407397e-06 | \n", "0.001225 | \n", "
*HELLS | \n", "-1.89 | \n", "3.99 | \n", "3.465145e-06 | \n", "0.001233 | \n", "
*KIF15 | \n", "-2.68 | \n", "3.06 | \n", "3.500165e-06 | \n", "0.001233 | \n", "