Note: C1=relapse. C2=disease-free.
ALL OLD DATA
Top three genes w/ PPDE=1 and FDR=0.01 by individual sample gene count
## R_80 R_83 R_84 R_86 R_87 R_88
## CPS1 41.116515 26.82607 24.761282 32.824674 22.01996 61.654563
## LGALS4 8.410196 39.34490 10.425803 1.025771 17.43247 1.100974
## ERN2 40.182049 181.52305 5.212901 2.051542 31.19494 49.543845
## R_89 R_95 R_98 R_99 DF_76 DF_77
## CPS1 6750.24393 67.24642 24375.42750 271.063114 95.22258 16.833054
## LGALS4 10.94930 42.24454 44.92550 17.363474 59.10367 8.416527
## ERN2 73.90778 71.55709 28.67585 1.929275 54.72562 100.998325
## DF_78 DF_79 DF_81 DF_93 DF_97 DF_109
## CPS1 39.84806 33.672503 46.95468 61.29114 194.90850 10.218931
## LGALS4 6.97341 12.772329 4896.70204 53.11899 22.45859 8.646788
## ERN2 1138.65819 2.322242 918.01185 1.63443 62.56322 2050.074720
## DF_110 DF_111 DF_112
## CPS1 16.58887 15.92699 3.541365
## LGALS4 1745.51775 86.46080 41.315925
## ERN2 1782.38190 410.68878 2699.700575
MINUS SAMPLES 81 AND 110 OLD DATA
Top three genes w/ PPDE=1 and FDR=0.01 by individual sample gene count
## R_80 R_83 R_84 R_86 R_87 R_88
## CPS1 40.711084 26.6909468 24.6224295 32.575943 21.74890 61.061383
## PRR4 22.011743 3.1406347 0.4924486 11.269240 25.03842 93.652896
## SEC14L5 9.252519 0.8896982 3.8877520 1.017998 12.68686 5.451909
## R_89 R_95 R_98 R_99 DF_76 DF_77
## CPS1 6683.813436 66.80147 24196.605852 268.05464 94.630357 16.662914
## PRR4 224.962091 5.13001 9.127930 17.17076 4.535731 5.369161
## SEC14L5 1.355193 12.84644 5.693096 17.17076 3.263116 7.405740
## DF_78 DF_79 DF_93 DF_97 DF_109 DF_111
## CPS1 39.637803 33.472277 60.82883 193.032811 10.13538 15.75034
## PRR4 26.260045 2.019879 5.88012 16.538861 88.09983 14345.41206
## SEC14L5 9.909451 2.308433 15.40997 3.971869 10.13538 3037.56608
## DF_112
## CPS1 3.51441
## PRR4 9.37176
## SEC14L5 8.20029
ALL OLD DATA
In the "ALL OLD DATA" FDR=0.01 set, I located the top 3 PPDE genes located in both sets. All five genes appear (one gene--CPS1--was located in both sets; thus 5 genes instead of 6 genes):
## R_80 R_83 R_84 R_86 R_87 R_88
## CPS1 41.116515 26.8260667 24.7612818 32.824674 22.01996 61.654563
## ERN2 40.182049 181.5230511 5.2129014 2.051542 31.19494 49.543845
## LGALS4 8.410196 39.3448978 10.4258029 1.025771 17.43247 1.100974
## PRR4 22.230952 3.1565338 0.4952256 11.355286 25.35048 94.562685
## SEC14L5 9.344663 0.8942022 3.9096761 1.025771 12.84498 5.504872
## R_89 R_95 R_98 R_99 DF_76 DF_77
## CPS1 6750.243931 67.24642 24375.427496 271.063114 95.222582 16.833054
## ERN2 73.907780 71.55709 28.675849 1.929275 54.725622 100.998325
## LGALS4 10.949301 42.24454 44.925497 17.363474 59.103672 8.416527
## PRR4 227.197991 5.16418 9.195389 17.363474 4.564117 5.423984
## SEC14L5 1.368663 12.93200 5.735170 17.363474 3.283537 7.481357
## DF_78 DF_79 DF_81 DF_93 DF_97 DF_109
## CPS1 39.848056 33.672503 46.95468 61.29114 194.908496 10.218931
## ERN2 1138.658193 2.322242 918.01185 1.63443 62.563221 2050.074720
## LGALS4 6.973410 12.772329 4896.70204 53.11899 22.458592 8.646788
## PRR4 26.399337 2.031961 19.37599 5.92481 16.699567 88.826090
## SEC14L5 9.962014 2.322242 7.66607 15.52709 4.010463 10.218931
## DF_110 DF_111 DF_112
## CPS1 16.58887 15.92699 3.541365
## ERN2 1782.38190 410.68878 2699.700575
## LGALS4 1745.51775 86.46080 41.315925
## PRR4 50.31957 14506.30139 9.443640
## SEC14L5 47.92340 3071.63355 8.263185
ALL OLD DATA
Here's the same info, but with category means instead of individual gene counts. All genes got a high PPDE value of 1.
## PPEE PPDE PostFC RealFC R_mean DF_mean
## CPS1 3.562706e-13 1 59.64331905 65.10844237 3167.318402 48.63697
## ERN2 1.128785e-08 1 0.06010448 0.05795638 48.577832 838.34181
## LGALS4 9.827360e-09 1 0.03324738 0.03063491 19.322292 631.04426
## PRR4 1.266588e-08 1 0.03135086 0.03106728 41.607219 1339.57368
## SEC14L5 4.894100e-08 1 0.03141410 0.02450313 7.092347 289.84471
MINUS SAMPLES 81 AND 110 OLD DATA
In the "MINUS SAMPLES 81 AND 110 OLD DATA" w/ FDR=0.01, I tried to locate the same five genes, but I could only locate four of them. The "NA" field is where I called for gene LGALS4, but couldn't find it in the FDR=0.01 set. So, I located it in the entire set, i.e. no FDR cutoff. See code chunk after this one for those values.
## R_80 R_83 R_84 R_86 R_87 R_88
## CPS1 40.711084 26.6909468 24.6224295 32.575943 21.74890 61.061383
## ERN2 39.785832 180.6087402 5.1836694 2.035996 30.81094 49.067182
## NA NA NA NA NA NA NA
## PRR4 22.011743 3.1406347 0.4924486 11.269240 25.03842 93.652896
## SEC14L5 9.252519 0.8896982 3.8877520 1.017998 12.68686 5.451909
## R_89 R_95 R_98 R_99 DF_76 DF_77
## CPS1 6683.813436 66.80147 24196.605852 268.054641 94.630357 16.662914
## ERN2 73.180439 71.08361 28.465479 1.907862 54.385262 99.977487
## NA NA NA NA NA NA NA
## PRR4 224.962091 5.13001 9.127930 17.170760 4.535731 5.369161
## SEC14L5 1.355193 12.84644 5.693096 17.170760 3.263116 7.405740
## DF_78 DF_79 DF_93 DF_97 DF_109 DF_111
## CPS1 39.637803 33.472277 60.828829 193.032811 10.13538 15.75034
## ERN2 1132.650228 2.308433 1.622102 61.961149 2033.31300 406.13383
## NA NA NA NA NA NA NA
## PRR4 26.260045 2.019879 5.880120 16.538861 88.09983 14345.41206
## SEC14L5 9.909451 2.308433 15.409970 3.971869 10.13538 3037.56608
## DF_112
## CPS1 3.51441
## ERN2 2679.15203
## NA NA
## PRR4 9.37176
## SEC14L5 8.20029
MINUS SAMPLES 81 AND 110 OLD DATA
Here's LGALS4 in the entire dataset, i.e. no FDR cutoff. Below are the individual gene counts. Look three code chunks down to see that it got a NASTY PPDE value. Guess EBSeq decided it didn't like it anymore.
## R_80 R_83 R_84 R_86 R_87 R_88 R_89
## LGALS4 8.327267 39.14672 10.36734 1.017998 17.21788 1.090382 10.84155
## R_95 R_98 R_99 DF_76 DF_77 DF_78 DF_79
## LGALS4 41.96502 44.59592 17.17076 58.73608 8.331457 6.936616 12.69638
## DF_93 DF_97 DF_109 DF_111 DF_112
## LGALS4 52.71832 22.24246 8.57609 85.50186 41.00145
MINUS SAMPLES 81 AND 110 OLD DATA
Here's the same info, but with category means instead of individual gene counts. Note that 4 of the 5 genes got high PPDE values. Here, again, "NA" is where I called for LGALS4, but it wasn't in the FDR=0.01 dataset. See the code chunk after this one where I pulled it from the entire dataset summary instead of trying to pull from the FDR=0.01 set.
## PPEE PPDE PostFC RealFC R_mean
## CPS1 1.547984e-10 1.0000000 60.29428913 60.46006989 3142.268608
## ERN2 3.407147e-06 0.9999966 0.07149434 0.06706336 48.212975
## NA NA NA NA NA NA
## PRR4 3.744038e-09 1.0000000 0.02847894 0.02557207 41.199617
## SEC14L5 1.514887e-08 1.0000000 0.02840156 0.02043631 7.025222
## DF_mean
## CPS1 51.96279
## ERN2 719.05595
## NA NA
## PRR4 1611.49861
## SEC14L5 344.24115
## PPEE PPDE PostFC RealFC C1Mean C2Mean
## LGALS4 0.9873388 0.01266119 0.6074723 0.5816674 19.17408 32.97119
And here are the TPM values for those five genes. Sorry! This is really ugly!
## gene_id DF_109_TPM DF_110_TPM DF_111_TPM DF_112_TPM DF_76_TPM
## 3930 CPS1 0.18 0.38 0.29 0.08 2.05
## DF_77_TPM DF_78_TPM DF_79_TPM R_80_TPM DF_81_TPM R_83_TPM R_84_TPM
## 3930 0.42 1.13 0.9 0.88 1.04 0.56 0.62
## R_86_TPM R_87_TPM R_88_TPM R_89_TPM DF_93_TPM R_95_TPM DF_97_TPM
## 3930 0.58 0.58 1.52 160.19 1.37 1.34 4.38
## R_98_TPM R_99_TPM
## 3930 585.48 7.83
## gene_id DF_109_TPM DF_110_TPM DF_111_TPM DF_112_TPM DF_76_TPM
## 5583 ERN2 49.56 55.58 10.96 81.67 1.99
## DF_77_TPM DF_78_TPM DF_79_TPM R_80_TPM DF_81_TPM R_83_TPM R_84_TPM
## 5583 3.41 48.62 0.1 1.38 32.99 5.35 0.19
## R_86_TPM R_87_TPM R_88_TPM R_89_TPM DF_93_TPM R_95_TPM DF_97_TPM
## 5583 0.06 1.25 2.06 2.56 0.06 2.3 2.36
## R_98_TPM R_99_TPM
## 5583 1.14 0.09
## gene_id DF_109_TPM DF_110_TPM DF_111_TPM DF_112_TPM DF_76_TPM
## 9598 LGALS4 0.65 167.48 7.09 3.88 6.42
## DF_77_TPM DF_78_TPM DF_79_TPM R_80_TPM DF_81_TPM R_83_TPM R_84_TPM
## 9598 0.87 0.92 1.71 0.88 551.13 3.58 1.19
## R_86_TPM R_87_TPM R_88_TPM R_89_TPM DF_93_TPM R_95_TPM DF_97_TPM
## 9598 0.09 2.2 0.14 1.18 6.08 4.29 2.56
## R_98_TPM R_99_TPM
## 9598 5.54 2.39
## gene_id DF_109_TPM DF_110_TPM DF_111_TPM DF_112_TPM DF_76_TPM
## 18167 PRR4 20.55 14.03 4056.61 2.49 1.41
## DF_77_TPM DF_78_TPM DF_79_TPM R_80_TPM DF_81_TPM R_83_TPM R_84_TPM
## 18167 1.58 9.87 0.77 6.6 6.42 0.82 0.17
## R_86_TPM R_87_TPM R_88_TPM R_89_TPM DF_93_TPM R_95_TPM DF_97_TPM
## 18167 3.55 9.19 35.98 84.29 2.02 1.53 5.46
## R_98_TPM R_99_TPM
## 18167 3.33 7.08
## gene_id DF_109_TPM DF_110_TPM DF_111_TPM DF_112_TPM DF_76_TPM
## 19888 SEC14L5 0.13 0.8 43.96 0.14 0.06
## DF_77_TPM DF_78_TPM DF_79_TPM R_80_TPM DF_81_TPM R_83_TPM R_84_TPM
## 19888 0.14 0.23 0.05 0.17 0.15 0.01 0.08
## R_86_TPM R_87_TPM R_88_TPM R_89_TPM DF_93_TPM R_95_TPM DF_97_TPM
## 19888 0.02 0.28 0.12 0.03 0.31 0.23 0.08
## R_98_TPM R_99_TPM
## 19888 0.12 0.41
ALL OLD DATA
All gene counts for genes at FDR=0.01
## R_80 R_83 R_84 R_86 R_87
## ABCC6 6.656203e+01 2.614111e+02 220.6099886 41.666820 4.405827e+01
## ADGRB1 5.700244e+01 7.779559e+01 69.0709440 24.618505 1.743247e+01
## ALOX12 1.093326e+02 2.682607e+00 2.6064507 9.231940 1.100998e+01
## ARHGAP40 1.214806e+01 1.225057e+02 212.4257333 49.237011 1.834997e+00
## BAMBI 2.280098e+02 1.126695e+02 84.7096483 67.700890 6.238988e+01
## BPIFA1 2.990292e+01 1.429588e+05 23.4580564 60.520493 1.834997e+00
## C16orf89 5.401215e+02 1.320737e+03 247.6128180 9.231940 4.587491e+00
## CLCA2 3.057574e+03 2.682607e+00 35.1870847 376.457979 2.385495e+01
## COL17A1 3.975219e+03 2.146085e+01 7135.1588335 8387.729953 2.201996e+01
## CPS1 4.111652e+01 2.682607e+01 24.7612818 32.824674 2.201996e+01
## DNAH17 2.691263e+02 9.120863e+01 40.3999861 478.009314 2.128596e+02
## DSC3 4.000525e+03 1.537134e+01 43.9447591 5747.200350 1.648891e+03
## DSG3 4.154076e+03 1.899286e+01 22.3112181 6434.661856 6.238071e+01
## ERN2 4.018205e+01 1.815231e+02 5.2129014 2.051542 3.119494e+01
## ERVH48-1 9.344663e-01 1.609564e+01 5.2129014 5.128855 1.009248e+01
## FAT2 1.230692e+03 2.682607e+00 302.3482830 548.787517 1.541397e+02
## FCGBP 1.532525e+02 2.414346e+02 132.9289865 208.231525 8.991483e+01
## FMO5 4.859225e+01 3.782475e+02 165.5096204 15.386566 8.991483e+01
## FRZB 1.971724e+02 4.444185e+02 153.7805922 104.628648 1.027598e+02
## HAP1 4.251821e+02 8.673762e+01 2.6064507 24.618505 2.966272e+03
## HHLA2 4.049042e+01 1.073043e+01 86.0128736 5.098082 2.167131e+01
## HLA-G 5.067610e+01 1.586315e+01 2537.5882875 66.418676 2.770845e+00
## HMGA2 4.034558e+02 1.402109e+01 682.9813132 3521.831067 4.479043e+02
## HOXD1 1.214806e+01 1.028333e+02 23.4580564 4.103084 7.064737e+01
## HPGD 2.831433e+02 4.623025e+02 1363.1737242 15.386566 5.229740e+01
## ICAM4 7.382283e+01 9.210283e+01 9.1225775 65.649348 1.372577e+01
## IL1A 2.812743e+02 9.836224e+00 201.9999304 766.250981 1.651497e+01
## KCMF1 1.324129e+03 1.007417e+03 1512.8230920 1217.590248 1.426031e+03
## KLK11 1.317597e+02 7.266287e+03 99.0451272 4.103084 8.624484e+01
## KRT17 9.720572e+04 4.077562e+02 131.6257611 16825.773977 1.348447e+04
## LGALS4 8.410196e+00 3.934490e+01 10.4258029 1.025771 1.743247e+01
## LILRA2 3.177185e+01 7.174345e+03 36.4903100 61.536006 8.220784e+02
## LIPH 1.046602e+02 2.324926e+02 188.9676769 50.262782 2.385495e+01
## LRAT 1.336287e+02 1.788404e+00 10.4258029 5.128855 9.376832e+02
## MAN1C1 3.177185e+02 1.654274e+02 115.9870568 123.092527 6.422488e+01
## METTL7B 1.775486e+01 5.633474e+01 29.9741832 33.850445 8.257484e+00
## MMP1 7.184177e+03 1.019391e+03 591.6643124 16684.166282 1.438637e+03
## MMP12 4.349940e+03 1.341303e+01 2349.7153200 834.977642 3.614943e+02
## MSMP 3.214564e+00 2.272168e+01 23.7317338 17.550943 1.639569e+01
## MUC5B 7.045876e+02 2.627166e+03 43.0064368 107.705961 8.257484e+00
## NKD1 8.690536e+01 5.365213e+01 32.5936662 31.798903 2.110246e+01
## NPTX1 1.027913e+01 6.313068e+02 14.3354789 27.695819 1.834997e+01
## PRR4 2.223095e+01 3.156534e+00 0.4952256 11.355286 2.535048e+01
## RBM28 5.700244e+02 5.096953e+02 755.8707075 509.808217 4.532441e+02
## RET 1.588593e+01 4.023910e+01 54.7354650 18.463879 2.752495e+00
## RRM2 5.980023e+02 6.751227e+02 720.7748486 1313.828088 1.544663e+03
## SCN3A 2.903387e+01 8.047820e+00 1044.1180921 11.283482 8.330884e+00
## SEC14L5 9.344663e+00 8.942022e-01 3.9096761 1.025771 1.284498e+01
## SELE 4.887258e+02 2.772027e+02 24.7612818 167.200683 9.174983e-01
## SHISA3 1.682039e+01 3.576809e+00 9.1225775 1.025771 1.834997e+00
## SLC16A9 8.783983e+01 6.080575e+01 119.8967329 9.231940 1.009248e+01
## SLC1A7 4.672331e+01 9.299703e+01 248.9160433 11.283482 1.009248e+01
## SLC6A20 4.952671e+01 9.836224e+00 36.4903100 12.309253 3.761743e+01
## SOX15 1.513835e+02 3.576809e+00 80.7999722 410.308424 2.523120e+02
## SULT1C2 6.634710e+01 8.942022e+01 50.8257890 1.025771 2.752495e+00
## TMEM130 7.767283e+01 4.373543e+01 24.2530239 21.059080 5.388467e+01
## TMEM40 1.476457e+02 8.942022e+00 374.0256777 337.478679 1.293673e+02
## TNPO3 1.014830e+03 8.879428e+02 1219.8189348 1000.126783 1.074390e+03
## UPK1B 2.094139e+01 1.471857e+01 18.9879935 11.293739 3.713115e+01
## R_88 R_89 R_95 R_98 R_99
## ABCC6 103.337451 134.963819 461.732873 123.411295 85.621217
## ADGRB1 41.837025 429.760056 68.970685 4975.259798 36.656222
## ALOX12 8.807795 8.211976 32.761075 3.823447 1373.643681
## ARHGAP40 124.410100 88.963069 7.759202 69.777899 25.080573
## BAMBI 103.491587 121.810971 204.325655 86.027547 188.104296
## BPIFA1 1084.459718 3821.305973 164.667511 36146.863503 13.504924
## C16orf89 475.620912 662.432697 2352.762497 1109.755356 245.982541
## CLCA2 7771.777815 57.483829 23.277606 3.823447 8726.110072
## COL17A1 5421.197615 32.847902 12.932003 18.161371 10792.363418
## CPS1 61.654563 6750.243931 67.246418 24375.427496 271.063114
## DNAH17 74.866255 269.626532 148.286973 8610.133946 140.837063
## DSC3 835.033983 34.189192 26.131268 21.067190 5441.992340
## DSG3 1032.438681 12.167410 21.587824 36.580825 13906.174414
## ERN2 49.543845 73.907780 71.557086 28.675849 1.929275
## ERVH48-1 2.201949 1653.344418 12.069870 17.205509 10.611012
## FAT2 2089.649284 5.474650 25.864007 7.646893 1587.793188
## FCGBP 320.383531 350.377625 613.839098 69.777899 105.145478
## FMO5 154.136407 80.751093 290.539011 438.740489 27.974485
## FRZB 177.256868 52.009179 284.504076 140.511660 145.660250
## HAP1 6.605846 42.428541 12.932003 30.587572 291.320500
## HHLA2 59.738867 24.635927 71.238096 11.604160 65.373478
## HLA-G 24.375572 9.197413 95.576127 13.592352 48.270456
## HMGA2 1771.500731 10.415522 10.862883 11.862243 353.992993
## HOXD1 30.827281 19.161276 18.104805 28.675849 10.611012
## HPGD 137.621792 147.815561 904.378109 697.778992 218.972694
## ICAM4 40.736050 56.115167 162.943244 11.470340 11.575649
## IL1A 2234.977896 109.493008 13.794137 2.867585 82.958818
## KCMF1 1312.746746 903.317314 797.887371 1125.680010 1528.959952
## KLK11 41.837025 602.211543 599.182827 3148.608218 564.312889
## KRT17 10566.050672 295.631121 529.350009 96.542025 75106.669266
## LGALS4 1.100974 10.949301 42.244545 44.925497 17.363474
## LILRA2 104.647610 95.861128 215.257508 3454.493499 8.334467
## LIPH 181.660765 281.944495 260.364336 18.161371 132.155326
## LRAT 8.807795 2.737325 6.034935 6.691031 8.575627
## MAN1C1 171.751996 88.963069 364.682498 143.379245 97.688831
## METTL7B 58.351640 39.691215 25.864007 46.837220 14.469561
## MMP1 16999.043699 6657.174875 18.104805 96.542025 1484.576984
## MMP12 317.080608 4909.392738 38.796010 2976.553124 650.165619
## MSMP 12.848370 24.964406 9.423120 18.515040 17.826499
## MUC5B 286.253327 1472.680955 413.824111 3236.547488 33.762310
## NKD1 95.784767 69.801792 486.243330 140.511660 81.029543
## NPTX1 23.120461 262.783219 12.069870 1761.652989 11.575649
## PRR4 94.562685 227.197991 5.164180 9.195389 17.363474
## RBM28 407.360503 572.100966 293.987545 648.074187 433.122200
## RET 34.130204 213.511365 35.347476 2851.335250 25.080573
## RRM2 583.516396 1055.663148 65.522151 1092.253529 1821.245089
## SCN3A 25.322410 249.096593 18.104805 1869.521974 1.929275
## SEC14L5 5.504872 1.368663 12.932003 5.735170 17.363474
## SELE 570.304704 68.433130 278.469141 39.190327 8.681737
## SHISA3 15.413641 5.474650 181.048049 7.646893 5.787825
## SLC16A9 14.312666 30.110577 42.244545 134.776490 112.862578
## SLC1A7 12.110718 2.737325 31.036808 16.249648 5.787825
## SLC6A20 59.452614 17.792614 106.904562 35.366880 30.964861
## SOX15 31.928256 50.640516 18.104805 5.735170 1041.808410
## SULT1C2 44.038973 49.271854 27.588274 26.764126 48.231871
## TMEM130 61.830719 10.182850 223.197758 10.351981 70.823679
## TMEM40 404.057580 120.442309 14.656271 7.646893 285.532675
## TNPO3 927.020388 1198.948436 744.883400 1229.238060 827.658904
## UPK1B 37.917556 27.195326 24.156982 22.032611 6283.406973
## DF_76 DF_77 DF_78 DF_79 DF_81
## ABCC6 462.245437 505.954850 377.689834 272.433769 6.613423e+02
## ADGRB1 40.496960 77.619083 40.844257 25.544657 7.666070e+01
## ALOX12 18.606711 5.611018 14.943021 17.416812 7.666070e+00
## ARHGAP40 140.097592 476.936535 393.499550 220.612949 1.293649e+02
## BAMBI 268.155547 231.922080 71.726500 1511.779260 7.186940e+01
## BPIFA1 70.048796 370.327192 706.306788 4.644483 9.774239e+01
## C16orf89 2781.156100 2580.133139 7710.598786 265.896659 1.887770e+03
## CLCA2 93.033557 43.017805 12.950618 3.483362 4.791294e+00
## COL17A1 518.798895 597.573424 300.852821 3595.991066 6.190351e+02
## CPS1 95.222582 16.833054 39.848056 33.672503 4.695468e+01
## DNAH17 110.545756 107.544513 68.737896 99.856387 3.928861e+01
## DSC3 82.734195 36.340694 141.400826 189.494912 1.907893e+01
## DSG3 183.111931 26.605577 44.061988 18.728878 3.588679e+01
## ERN2 54.725622 100.998325 1138.658193 2.322242 9.180119e+02
## ERVH48-1 12.039637 13.092375 8.965813 3.483362 4.791294e+00
## FAT2 49.253060 93.516968 37.855653 71.989489 3.833035e+01
## FCGBP 495.814134 4670.237367 1464.416049 924.252144 3.037680e+02
## FMO5 383.079353 579.805200 1102.794943 1221.499064 1.857105e+03
## FRZB 414.820213 626.563684 820.869948 202.035016 5.567483e+02
## HAP1 30.646348 14.962715 7.969611 26.705778 1.149910e+01
## HHLA2 45.947632 490.412330 616.678549 67.345005 1.704551e+02
## HLA-G 83.182945 15.795016 37.975197 15.187460 3.601136e+01
## HMGA2 118.480971 166.263817 91.919503 39.315550 3.281078e+01
## HOXD1 16.417687 126.247906 434.343808 146.301219 3.833035e+00
## HPGD 276.911646 374.067871 2056.159676 3633.146931 1.074208e+03
## ICAM4 86.466482 271.199206 285.909800 75.472851 1.437388e+01
## IL1A 5.472562 6.546188 20.920229 160.234668 1.629040e+01
## KCMF1 681.881248 596.030394 623.532414 888.106454 7.411652e+02
## KLK11 6.567075 40.212296 26.897438 56.894918 2.874776e+01
## KRT17 4014.671616 638.720889 247.057946 87.084059 9.074710e+02
## LGALS4 59.103672 8.416527 6.973410 12.772329 4.896702e+03
## LILRA2 72.237821 185.921083 65.749292 74.996791 1.820692e+01
## LIPH 348.054955 390.900925 388.518543 521.343232 4.015104e+02
## LRAT 3.283537 17.768224 28.889840 10.124973 1.916517e+00
## MAN1C1 554.917805 531.176376 296.868015 159.073547 3.258080e+02
## METTL7B 71.143308 721.950991 106.593549 258.929935 4.283416e+02
## MMP1 128.057955 289.902600 600.709440 2621.810729 1.379893e+02
## MMP12 171.838452 16.833054 40.844257 832.523602 4.963780e+02
## MSMP 36.031349 19.853652 19.097181 18.554710 2.899691e+01
## MUC5B 29.551836 34095.351251 6217.292897 4.644483 2.057190e+04
## NKD1 93.033557 201.126942 143.453001 40.639227 9.969724e+01
## NPTX1 20.795736 14.962715 82.684716 77.795092 4.216338e+01
## PRR4 4.564117 5.423984 26.399337 2.031961 1.937599e+01
## RBM28 341.487880 304.865315 251.042751 394.781066 2.913106e+02
## RET 38.307935 63.591538 22.912632 18.577933 1.533214e+01
## RRM2 359.492610 250.475846 132.972962 599.149935 2.111715e+02
## SCN3A 40.332783 2.805509 20.471939 12.876829 1.551421e+01
## SEC14L5 3.283537 7.481357 9.962014 2.322242 7.666070e+00
## SELE 18.606711 31.795769 67.741695 661.838847 6.995289e+01
## SHISA3 113.829293 123.442397 242.076939 62.700522 4.791294e+01
## SLC16A9 21.890249 276.810224 662.473927 1004.369478 7.378592e+01
## SLC1A7 35.024398 4655.274652 959.341942 199.712775 8.049373e+01
## SLC6A20 65.670746 293.736796 453.271634 812.784548 6.132856e+01
## SOX15 16.417687 2.805509 16.935424 40.639227 3.833035e+00
## SULT1C2 364.472641 71.072895 367.598314 139.334494 2.903524e+02
## TMEM130 134.329511 999.995639 213.187098 52.227213 2.129251e+02
## TMEM40 14.228662 1.870339 14.943021 37.155865 9.582587e-01
## TNPO3 693.920885 687.349713 662.473927 869.679467 8.039791e+02
## UPK1B 255.098013 19.329957 29.248473 11.692486 1.904060e+01
## DF_93 DF_97 DF_109 DF_110 DF_111
## ABCC6 390.694253 91.590951 6.086867e+02 7.307397e+02 379.653907
## ADGRB1 39.226331 6.416741 5.895537e+01 5.621784e+01 25.028125
## ALOX12 12.258228 16.843944 1.021893e+01 1.105925e+01 6.825852
## ARHGAP40 4.086076 8.823018 1.304093e+03 4.654100e+02 6.825852
## BAMBI 263.143301 552.641784 5.659715e+01 2.561137e+03 4064.795067
## BPIFA1 6.537722 125.928534 3.851751e+01 3.906679e+03 5524.389825
## C16orf89 1452.191447 176.596722 1.960620e+04 1.610687e+04 3870.258275
## CLCA2 17.161520 972.136200 2.829858e+01 2.488330e+01 13.651705
## COL17A1 17.161520 668.143114 2.389658e+02 4.792340e+01 98.974859
## CPS1 61.291142 194.908496 1.021893e+01 1.658887e+01 15.926989
## DNAH17 196.131653 70.584147 5.659715e+01 8.478756e+01 87.598438
## DSC3 27.188750 1601.065008 1.726213e+01 1.039569e+01 18.327414
## DSG3 25.529803 1251.657441 1.389775e+01 8.193058e+00 30.693583
## ERN2 1.634430 62.563221 2.050075e+03 1.782382e+03 410.688782
## ERVH48-1 13.892659 5.614648 2.358215e+00 4.608019e+00 26.165767
## FAT2 8.172152 231.002661 2.122393e+01 5.529623e+00 18.202273
## FCGBP 102.969118 294.367975 2.058722e+03 1.566727e+03 352.669037
## FMO5 331.789380 38.500444 1.402352e+03 1.345542e+02 191.123865
## FRZB 552.437489 206.939884 5.549665e+02 4.930581e+02 242.317758
## HAP1 27.785317 187.689662 3.144286e+00 8.294435e+00 18.202273
## HHLA2 22.277287 10.475329 2.199428e+01 6.826320e+01 37.667328
## HLA-G 28.929419 22.458592 7.373352e+00 3.797008e+00 36.324911
## HMGA2 19.229074 161.332900 1.715208e+01 3.760144e+00 18.782470
## HOXD1 111.141270 2.406278 6.209966e+01 2.847756e+02 73.946734
## HPGD 4018.247239 197.314773 2.657944e+04 5.492759e+02 532.416482
## ICAM4 3387.357089 14.437666 4.716430e+01 3.308558e+02 200.225002
## IL1A 219.830894 58.552758 1.336322e+01 9.216039e-01 17.064631
## KCMF1 1018.544362 937.341424 1.000716e+03 8.662063e+02 755.394325
## KLK11 129.937220 54.542295 2.751251e+01 2.460682e+02 290.098724
## KRT17 109.506840 15236.550539 4.181901e+02 3.317774e+02 757.669609
## LGALS4 53.118989 22.458592 8.646788e+00 1.745518e+03 86.460796
## LILRA2 407.120279 28.081261 3.458715e+01 7.004189e+01 103.502674
## LIPH 230.454692 177.262459 4.276229e+02 2.414602e+02 675.759381
## LRAT 16.344304 37.690330 6.563698e+00 9.216039e-01 1.137642
## MAN1C1 310.590817 520.558081 3.207172e+02 4.165650e+02 294.649293
## METTL7B 28.602533 34.489981 7.782109e+01 1.972232e+02 262.795315
## MMP1 307.272923 4551.073266 4.008965e+01 6.451227e+01 62.570313
## MMP12 8.989367 1277.733471 6.052751e+01 2.764812e+01 137.654689
## MSMP 27.997793 12.416393 1.039973e+03 1.302226e+01 19.931489
## MUC5B 14.709874 105.074127 4.679091e+04 2.250557e+03 756.531967
## NKD1 410.242041 35.292073 1.108361e+02 6.083507e+01 13830.314478
## NPTX1 23.699241 8.020926 2.358215e+01 6.082586e+01 22.752841
## PRR4 5.924810 16.699567 8.882609e+01 5.031957e+01 14506.301388
## RBM28 305.638492 314.420289 2.971351e+02 2.451466e+02 279.859946
## RET 15.527089 7.218833 2.358215e+00 1.207301e+02 25.028125
## RRM2 36.022847 588.760012 1.856858e+02 7.255787e+01 271.919204
## SCN3A 14.709874 16.106019 3.160008e+01 1.843208e+01 4.550568
## SEC14L5 15.527089 4.010463 1.021893e+01 4.792340e+01 3071.633552
## SELE 20647.759760 91.438553 6.131358e+01 2.672651e+01 23.890483
## SHISA3 92.345320 20.052314 6.885987e+02 1.972232e+02 32.991620
## SLC16A9 40.043546 52.938110 3.380108e+01 8.755237e+01 19.339915
## SLC1A7 40.043546 14.437666 9.432859e+01 2.709515e+02 25.028125
## SLC6A20 81.721522 28.875333 2.248165e+02 7.925793e+01 69.418918
## SOX15 29.419748 202.127329 7.074644e+00 4.608019e+00 21.615199
## SULT1C2 57.205065 68.177869 6.760216e+01 1.105925e+01 79.634944
## TMEM130 315.992609 64.833143 2.757303e+02 1.978942e+03 242.408769
## TMEM40 13.075444 75.396702 7.860716e-01 3.962897e+01 35.266904
## TNPO3 760.010155 601.569431 7.719223e+02 6.829085e+02 536.967051
## UPK1B 20.446725 300.840862 1.986403e+01 1.869934e+01 43.844725
## DF_112
## ABCC6 771.368317
## ADGRB1 87.353670
## ALOX12 38.955015
## ARHGAP40 1287.876400
## BAMBI 312.820574
## BPIFA1 489.888823
## C16orf89 4393.665298
## CLCA2 7.082730
## COL17A1 335.249219
## CPS1 3.541365
## DNAH17 81.451395
## DSC3 31.459126
## DSG3 44.845485
## ERN2 2699.700575
## ERVH48-1 4.721820
## FAT2 9.443640
## FCGBP 914.852622
## FMO5 5314.408390
## FRZB 423.783343
## HAP1 4.721820
## HHLA2 1163.291180
## HLA-G 30.337693
## HMGA2 21.484281
## HOXD1 1934.765738
## HPGD 3556.710901
## ICAM4 74.368665
## IL1A 2.360910
## KCMF1 740.464005
## KLK11 4.721820
## KRT17 136.932779
## LGALS4 41.315925
## LILRA2 54.300930
## LIPH 880.619427
## LRAT 37.774560
## MAN1C1 540.648388
## METTL7B 123.947775
## MMP1 12.985005
## MMP12 33.052740
## MSMP 5.902275
## MUC5B 12674.545287
## NKD1 48.398655
## NPTX1 15.345915
## PRR4 9.443640
## RBM28 239.632364
## RET 8.263185
## RRM2 158.251797
## SCN3A 17.706825
## SEC14L5 8.263185
## SELE 9.443640
## SHISA3 4056.043365
## SLC16A9 3484.703147
## SLC1A7 54.300930
## SLC6A20 106.240950
## SOX15 29.511375
## SULT1C2 1888.727993
## TMEM130 174.872603
## TMEM40 14.165460
## TNPO3 700.009812
## UPK1B 37.160723
MINUS SAMPLES 81 AND 110 OLD DATA
All gene counts for genes at FDR=0.01
## R_80 R_83 R_84 R_86 R_87
## ADGRB1 56.4403659 7.740375e+01 68.6836191 24.431958 17.217876
## AKR7A3 10.1777709 2.577367e+02 25.9183468 7.125988 57.090853
## ALOX12 108.2544723 2.669095e+00 2.5918347 9.161984 10.874448
## ARHGAP40 12.0282747 1.218887e+02 211.2345267 48.863915 1.812408
## BPIFA1 29.6080608 1.422387e+05 23.3265122 60.061896 1.812408
## CLCA2 3027.4242176 2.669095e+00 34.9897682 373.605351 23.561305
## CPS1 40.7110836 2.669095e+01 24.6224295 32.575943 21.748897
## DNAH17 266.4725473 9.074922e+01 40.1734376 474.387176 210.239334
## DNAJC12 37.9353279 2.447560e+03 9.0714214 22.395961 26.279917
## DSC3 3961.0774051 1.529391e+01 43.6983328 5703.650673 1628.593623
## DSG3 4113.1147974 1.889719e+01 22.1861049 6385.902908 61.612812
## ERN2 39.7858317 1.806087e+02 5.1836694 2.035996 30.810937
## ERVH48-1 0.9252519 1.601457e+01 5.1836694 5.089991 9.968244
## FAT2 1218.5567526 2.669095e+00 300.6528233 544.629054 152.242276
## HAP1 420.9896146 8.630073e+01 2.5918347 24.431958 2929.757609
## HHLA2 40.0911648 1.067638e+01 85.5305446 5.059451 21.404539
## HLA-G 50.1764106 1.578325e+01 2523.3584115 65.915386 2.736736
## HMGA2 399.4775079 1.395047e+01 679.1514014 3495.144229 442.390680
## HOXD1 12.0282747 1.023153e+02 23.3265122 4.071993 69.777710
## HPGD 280.3513258 4.599740e+02 1355.5295396 15.269973 51.653629
## ICAM4 73.0949001 9.163892e+01 9.0714214 65.151887 13.556812
## KLK11 130.4605179 7.229688e+03 98.4897180 4.071993 85.183178
## LILRA2 31.4585646 7.138209e+03 36.2856856 61.069714 811.958805
## MSMP 3.1828665 2.260723e+01 23.5986548 17.417950 16.193866
## MUC5B 697.6399328 2.613933e+03 42.7652723 106.889814 8.155836
## NKD1 86.0484267 5.338189e+01 32.4108927 31.557945 20.842693
## NPTX1 10.1777709 6.281269e+02 14.2550908 27.485952 18.124080
## PGC 488.5330033 1.930788e+05 171.0610891 2.035996 0.906204
## PRR4 22.0117427 3.140635e+00 0.4924486 11.269240 25.038417
## RBM28 564.4036592 5.071280e+02 751.6320583 505.945121 447.664788
## RET 15.7292823 4.003642e+01 54.4285284 18.323968 2.718612
## SCN3A 28.7475765 8.007284e+00 1038.2630560 11.197981 8.228333
## SEC14L5 9.2525190 8.896982e-01 3.8877520 1.017998 12.686856
## SELE 483.9067438 2.758065e+02 24.6224295 165.933712 0.906204
## SHISA3 16.6545342 3.558793e+00 9.0714214 1.017998 1.812408
## SLC16A9 86.9736786 6.049948e+01 119.2243955 9.161984 9.968244
## SLC1A7 46.2625950 9.252862e+01 247.5202123 11.197981 9.968244
## SLC6A20 49.0383507 9.786681e+00 36.2856856 12.215979 37.154365
## SULT1C2 65.6928849 8.896982e+01 50.5407763 1.017998 2.718612
## TNPO3 1004.8235637 8.834703e+02 1212.9786320 992.548276 1061.164912
## R_88 R_89 R_95 R_98 R_99
## ADGRB1 41.434510 425.530701 68.514326 4938.760577 36.249382
## AKR7A3 2.180764 988.532213 6.654454 1499.978918 17.790815
## ALOX12 8.723055 8.131160 32.544305 3.795397 1358.397896
## ARHGAP40 123.213147 88.087566 7.707862 69.265998 24.802209
## BPIFA1 1074.026106 3783.699739 163.577953 35881.684911 13.355035
## CLCA2 7697.005361 56.918119 23.123585 3.795397 8629.260791
## CPS1 61.061383 6683.813436 66.801468 24196.605852 268.054641
## DNAH17 74.145965 266.973083 147.305800 8546.968765 139.273942
## DNAJC12 50.157564 565.115613 10.277149 1118.693318 10.493242
## DSC3 827.000101 33.852729 25.958365 20.912638 5381.592799
## DSG3 1022.505564 12.047669 21.444984 36.312462 13751.832677
## ERN2 49.067182 73.180439 71.083613 28.465479 1.907862
## ERVH48-1 2.180764 1637.073526 11.990007 17.079287 10.493242
## FAT2 2069.544720 5.420773 25.692872 7.590794 1570.170602
## HAP1 6.542291 42.010993 12.846436 30.363177 288.087194
## HHLA2 59.164118 24.393480 70.766734 11.519030 64.647911
## HLA-G 24.141054 9.106899 94.943727 13.492637 47.734713
## HMGA2 1754.457081 10.313021 10.791006 11.775220 350.064098
## HOXD1 30.530691 18.972706 17.985011 28.465479 10.493242
## HPGD 136.297729 146.360878 898.394096 692.659985 216.542361
## ICAM4 40.344128 55.562926 161.865095 11.386192 11.447173
## KLK11 41.434510 596.285059 595.218205 3125.509575 558.049697
## LILRA2 103.640793 94.917740 213.833211 3429.150838 8.241965
## MSMP 12.724756 24.718726 9.360770 18.379211 17.628647
## MUC5B 283.499277 1458.188008 411.085954 3212.803710 33.387589
## NKD1 94.863219 69.114859 483.025997 139.480846 80.130213
## NPTX1 22.898018 260.197117 11.990007 1748.729249 11.447173
## PGC 912.649594 315.760043 2620.672960 6998.712394 50.558349
## PRR4 93.652896 224.962091 5.130010 9.127930 17.170760
## RBM28 403.441278 566.470806 292.042313 643.319821 428.315067
## RET 33.801837 211.410157 35.113592 2830.417445 24.802209
## SCN3A 25.078782 246.645184 17.985011 1855.806892 1.907862
## SEC14L5 5.451909 1.355193 12.846436 5.693096 17.170760
## SELE 564.817790 67.759666 276.626590 38.902821 8.585380
## SHISA3 15.265346 5.420773 179.850105 7.590794 5.723587
## SLC16A9 14.174964 29.814253 41.965025 133.787750 111.609939
## SLC1A7 11.994200 2.710387 30.831447 16.130438 5.723587
## SLC6A20 58.880619 17.617513 106.197205 35.107424 30.621189
## SULT1C2 43.615273 48.786959 27.405730 26.567780 47.696555
## TNPO3 918.101504 1187.149345 739.954718 1220.220192 818.472890
## DF_76 DF_77 DF_78 DF_79 DF_93
## ADGRB1 40.245094 76.834550 40.628748 25.392762 38.930450
## AKR7A3 1.087705 35.177264 14.864176 13.492790 7.299459
## ALOX12 18.490989 5.554305 14.864176 17.313247 12.165766
## ARHGAP40 139.226272 472.115910 391.423307 219.301127 4.055255
## BPIFA1 69.613136 366.584118 702.580062 4.616866 6.488408
## CLCA2 92.454946 42.583004 12.882286 3.462649 17.032072
## CPS1 94.630357 16.662914 39.637803 33.472277 60.828829
## DNAH17 109.858230 106.457509 68.375211 99.262615 194.652252
## DNAJC12 1.087705 75.908833 210.080357 151.202356 4.055255
## DSC3 82.219640 35.973381 140.654745 188.368126 26.983668
## DSG3 181.973088 26.336662 43.829501 18.617511 25.337235
## ERN2 54.385262 99.977487 1132.650228 2.308433 1.622102
## ERVH48-1 11.964758 12.960045 8.918506 3.462649 13.787868
## FAT2 48.946736 92.571747 37.655913 71.561420 8.110510
## HAP1 30.455747 14.811480 7.927561 26.546979 27.575736
## HHLA2 45.661866 485.455499 613.424734 66.944555 22.109252
## HLA-G 82.665599 15.635368 37.774826 15.097151 28.711207
## HMGA2 117.744093 164.583309 91.434503 39.081769 19.084031
## HOXD1 16.315579 124.971859 432.052055 145.431274 110.302943
## HPGD 275.189428 370.286988 2045.310647 3611.543295 3987.938011
## ICAM4 85.928715 268.458067 284.401238 75.024070 3361.806600
## KLK11 6.526231 39.805851 26.755517 56.556606 128.957117
## LILRA2 71.788546 184.041890 65.402375 74.550841 404.049412
## MSMP 35.807257 19.652982 18.996417 18.444379 27.786609
## MUC5B 29.368042 33750.733267 6184.488251 4.616866 14.598919
## NKD1 92.454946 199.094056 142.696092 40.397576 407.147627
## NPTX1 20.666400 14.811480 82.248442 77.332503 23.520480
## PGC 910.409294 561.910505 336.921328 9.233732 3197.974288
## PRR4 4.535731 5.369161 26.260045 2.019879 5.880120
## RBM28 339.364038 301.783895 249.718160 392.433596 303.333093
## RET 38.069684 62.948788 22.791737 18.467463 15.409970
## SCN3A 40.081938 2.777152 20.363921 12.800261 14.598919
## SEC14L5 3.263116 7.405740 9.909451 2.308433 15.409970
## SELE 18.490989 31.474394 67.384266 657.903381 20492.015818
## SHISA3 113.121346 122.194706 240.799655 62.327689 91.648769
## SLC16A9 21.754105 274.012371 658.978479 998.397236 39.741501
## SLC1A7 34.806568 4608.221569 954.280113 198.525231 39.741501
## SLC6A20 65.262315 290.767858 450.880012 807.951520 81.105105
## SULT1C2 362.205848 70.354528 365.658735 138.505975 56.773573
## TNPO3 689.605128 680.402341 658.978479 864.508127 754.277476
## DF_97 DF_109 DF_111 DF_112
## ADGRB1 6.354990 58.473342 24.750538 86.68878
## AKR7A3 18.270595 12.248216 9.000196 23.42940
## ALOX12 16.681848 10.135379 6.750147 38.65851
## ARHGAP40 8.738111 1293.430314 6.750147 1278.07384
## BPIFA1 124.716672 38.202583 5463.118842 486.16008
## CLCA2 962.780935 28.067204 13.500294 7.02882
## CPS1 193.032811 10.135379 15.750343 3.51441
## DNAH17 69.904886 56.134408 86.626884 80.83143
## DNAJC12 42.101807 35.084005 6.750147 23.42940
## DSC3 1585.657305 17.120994 18.124144 31.21968
## DSG3 1239.612229 13.784116 30.353160 44.50415
## ERN2 61.961149 2033.312996 406.133835 2679.15203
## ERVH48-1 5.560616 2.338934 25.875563 4.68588
## FAT2 228.779628 21.050403 18.000392 9.37176
## HAP1 185.883448 3.118578 18.000392 4.68588
## HHLA2 10.374521 21.814455 37.249560 1154.43689
## HLA-G 22.242464 7.313066 35.922031 30.10678
## HMGA2 159.780328 17.011844 18.574154 21.32076
## HOXD1 2.383121 61.591920 73.126591 1920.03943
## HPGD 195.415932 26362.121290 526.511453 3529.63930
## ICAM4 14.298727 46.778673 198.004307 73.80261
## KLK11 54.017412 27.287559 286.881241 4.68588
## LILRA2 27.811024 34.304360 102.354727 53.88762
## MSMP 12.296905 1031.469744 19.710429 5.85735
## MUC5B 104.062956 46408.342051 748.141275 12578.07405
## NKD1 34.952443 109.929882 13676.922520 48.03027
## NPTX1 7.943737 23.389337 22.500489 15.22911
## PGC 56.400533 274.434883 1702.162028 1018.00748
## PRR4 16.538861 88.099835 14345.412062 9.37176
## RBM28 311.394494 294.705641 276.756020 237.80842
## RET 7.149363 2.338934 24.750538 8.20029
## SCN3A 15.951024 31.341711 4.500098 17.57205
## SEC14L5 3.971869 10.135379 3037.566077 8.20029
## SELE 90.558603 60.812275 23.625514 9.37176
## SHISA3 19.859343 682.968629 32.625710 4025.17113
## SLC16A9 52.428665 33.524716 19.125416 3458.17962
## SLC1A7 14.298727 93.557346 24.750538 53.88762
## SLC6A20 28.597454 222.978342 68.648993 105.43231
## SULT1C2 67.521765 67.049432 78.751713 1874.35210
## TNPO3 595.780282 765.610952 531.011551 694.68175