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Last data update: 2014.03.03

R: Build a gene expression based classifier

buildClassifier

R Documentation

Build a gene expression based classifier

Description

This function employs PAM to build a gene expression based classifier.

Usage

buildClassifier(sigMat, clus.f, nfold=10, nboot=100)
figPAMCV(err)

Arguments

`sigMat`	a matrix of median centered expression values of selected genes (by function `filterDiffGenes`) for selected cancer samples (by function `filterSamples`).
`clus.f`	a numeric vector of cluster labels for selected cancer samples.
`nfold`	an integer value specifying the fold of cross validation.
`nboot`	an integer value specifying the number of bootstraps.
`err`	a matrix of cross validation error rates for different shrinkage thresholds.

Details

The expression data of the retained most predictive genes were trained by PAM to build a robust classifier. To select the optimal threshold for centroid shrinkage, we performed 10-fold cross-validation over a range of shirnkage thresholds for 1000 iterations, and selected the one yielding a good performance (error rate < 2%) with the least number of genes.

Value

This function will return a list including signature (a character vector of signature genes), pam.rslt (an list of training results returned by pamr.train), thresh (the selected shrinkage threshold), err (a matrix of cross validation error rates for different shrinkage thresholds), cents (a numeric matrix of PAM centroids for three subtypes).

Author(s)

Xin Wang xw264@cam.ac.uk

References

De Sousa E Melo, F. and Wang, X. and Jansen, M. et al. Poor prognosis colon cancer is defined by a molecularly distinct subtype and precursor lesion. accepted

Tibshirani, Robert and Hastie, Trevor and Narasimhan, Balasubramanian and Chu, Gilbert (2002). Diagnosis of multiple cancer types by shrunken centroids of gene expression. PNAS, 99(10), 6567-6572.

Examples

data(diffGenes.f, package="DeSousa2013")
data(silh, package="DeSousa2013")
sigMat <- sdat.f[diffGenes.f, names(clus.f)]
##set a small number of bootstraps, only for testing the function
classifier <- buildClassifier(sigMat, clus.f, nboot=10)
data(classifier, package="DeSousa2013")
figPAMCV(err)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(DeSousa2013)

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DeSousa2013/buildClassifier.Rd_%03d_medium.png", width=480, height=480)
> ### Name: buildClassifier
> ### Title: Build a gene expression based classifier
> ### Aliases: buildClassifier figPAMCV
> 
> ### ** Examples
> 
> data(diffGenes.f, package="DeSousa2013")
> data(silh, package="DeSousa2013")
> sigMat <- sdat.f[diffGenes.f, names(clus.f)]
> ##set a small number of bootstraps, only for testing the function
> classifier <- buildClassifier(sigMat, clus.f, nboot=10)
123456789101112131415161718192021222324252627282930123Fold 1 :123456789101112131415161718192021222324252627282930
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123Fold 1 :123456789101112131415161718192021222324252627282930
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123Fold 1 :123456789101112131415161718192021222324252627282930
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123Fold 1 :123456789101112131415161718192021222324252627282930
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       id           1-score 2-score 3-score
  [1,] SRSF6        -0.4878 1.3762  -0.3869
  [2,] HNRNPL       -0.3976 1.3079  -0.4854
  [3,] ZIC2         -0.5618 1.2151  -0.108 
  [4,] EIF5A        -0.4426 1.2072  -0.3132
  [5,] TOB1         0.5199  -1.2008 0.1697 
  [6,] KIAA0226L    0.8295  -1.1985 -0.3844
  [7,] ITCH         0.5528  -1.1891 0.1002 
  [8,] QPRT         0.7594  -1.1737 -0.2821
  [9,] CYP1B1       -0.6275 -0.0445 1.1593 
 [10,] RBM6         0.4362  -1.136  0.2596 
 [11,] PSIP1        -0.353  1.1132  -0.3871
 [12,] NUTF2        -0.2763 1.0736  -0.4877
 [13,] SEMA5A       0.5755  -1.0574 -0.0605
 [14,] HTR2B        -0.4448 -0.2866 1.0545 
 [15,] GAS1         -0.7269 0.2939  1.0274 
 [16,] VAV3         0.6489  -1.0268 -0.2193
 [17,] MDM4         0.3899  -1.0028 0.2206 
 [18,] ECM2         -0.4249 -0.264  0.9986 
 [19,] TRIM7        -0.5372 0.9919  0.0519 
 [20,] PRPF39       -0.4225 0.9832  -0.1447
 [21,] KHDRBS3      0.4682  -0.9771 0.0575 
 [22,] AMFR         -0.3074 0.976   -0.3431
 [23,] AXIN2        0.725   -0.9757 -0.4016
 [24,] KCNE4        -0.5181 -0.0508 0.97   
 [25,] RGS4         -0.5038 -0.0725 0.9643 
 [26,] PDGFRL       -0.5548 0.0394  0.9529 
 [27,] CFH          -0.4206 -0.2219 0.9524 
 [28,] ATP10B       0.6502  -0.9507 -0.2911
 [29,] CASP2        -0.2928 0.9483  -0.3439
 [30,] STON1        -0.3965 -0.2534 0.9381 
 [31,] ZNF827       0.4735  -0.9367 0.0112 
 [32,] PMEPA1       0.2865  -0.9316 0.3398 
 [33,] PPP1R14C     0.7513  -0.9306 -0.4895
 [34,] NAP1L3       -0.3252 -0.3841 0.9304 
 [35,] CCDC80       -0.4328 -0.1708 0.9274 
 [36,] ISM1         -0.3298 -0.3679 0.9238 
 [37,] PLN          -0.3796 -0.2642 0.9178 
 [38,] PCDH7        -0.3078 -0.3898 0.9046 
 [39,] MSRB3        -0.355  -0.2936 0.901  
 [40,] CXCL12       -0.3881 -0.226  0.8981 
 [41,] ZNF529       0.3085  -0.8953 0.2675 
 [42,] ZFPM2        -0.4125 -0.1722 0.8925 
 [43,] VGLL3        -0.5949 0.1898  0.8872 
 [44,] NAA15        -0.1674 0.8847  -0.5094
 [45,] GPR126       -0.3508 0.8844  -0.1822
 [46,] PTGIS        -0.2997 -0.3804 0.8816 
 [47,] COLEC12      -0.5713 0.15    0.8814 
 [48,] SYK          0.3347  -0.8793 0.2061 
 [49,] HSD17B6      -0.2422 -0.4901 0.8792 
 [50,] VMP1         0.2613  -0.866  0.3248 
 [51,] SET          -0.3311 0.8643  -0.1989
 [52,] PDGFC        -0.3131 -0.3346 0.8637 
 [53,] HOPX         -0.4539 -0.0551 0.8594 
 [54,] SEC22B       0.2704  -0.8593 0.3025 
 [55,] HPSE         -0.4811 0.8579  0.0742 
 [56,] ALYREF       -0.1106 0.8544  -0.583 
 [57,] CYR61        -0.4384 -0.0787 0.8534 
 [58,] TXNDC9       0.3427  -0.8528 0.1678 
 [59,] EPM2AIP1     0.3587  -0.852  0.1386 
 [60,] KIAA1967     -0.1869 0.8513  -0.4442
 [61,] C1orf174     -0.2134 0.8513  -0.3968
 [62,] FAP          -0.557  0.1596  0.8471 
 [63,] DOK5         -0.3835 -0.1791 0.8471 
 [64,] CAB39L       0.341   -0.8469 0.1654 
 [65,] PRRX1        -0.5702 0.1861  0.8465 
 [66,] C10orf99     0.7565  -0.8432 -0.5786
 [67,] TYMS         -0.2769 0.8408  -0.274 
 [68,] CBX5         0.24    -0.8405 0.3396 
 [69,] BHLHE41      -0.4421 -0.056  0.8392 
 [70,] F13A1        -0.3981 -0.1411 0.8385 
 [71,] AMACR        0.6301  -0.8385 -0.3576
 [72,] FERMT2       -0.3593 -0.216  0.8377 
 [73,] KANSL1L      0.3509  -0.8346 0.1364 
 [74,] DACT1        -0.3413 -0.2471 0.834  
 [75,] NR1I2        0.56    -0.8284 -0.2418
 [76,] ARL4C        -0.5035 0.0765  0.8277 
 [77,] RPL22L1      -0.2595 0.8269  -0.2924
 [78,] SSPN         -0.2787 -0.3612 0.8265 
 [79,] LOC100130275 -0.3435 0.826   -0.1418
 [80,] ZNF573       0.3044  -0.8259 0.2115 
 [81,] INHBA        -0.4902 0.0562  0.8226 
 [82,] LINC00094    0.3324  -0.822  0.1581 
 [83,] UQCRC2       0.3265  -0.8213 0.168  
 [84,] VCAN         -0.3821 -0.1521 0.8199 
 [85,] NNMT         -0.4709 0.0239  0.8176 
 [86,] PLAGL2       0.7255  -0.8127 -0.5512
 [87,] ATP9A        0.483   -0.8125 -0.1192
 [88,] PHACTR2      0.3133  -0.8085 0.1797 
 [89,] FRMD6        -0.4601 0.0131  0.8083 
 [90,] ULBP2        -0.5745 0.8078  0.2866 
 [91,] PEG3         -0.3305 -0.2371 0.8057 
 [92,] SYNC         -0.3669 -0.1658 0.8054 
 [93,] RNF43        0.6679  -0.8022 -0.4581
 [94,] PRKD1        -0.3504 -0.1929 0.8008 
 [95,] LMCD1        -0.4607 0.0238  0.7995 
 [96,] C20orf112    0.4871  -0.7995 -0.1383
 [97,] PDLIM3       -0.296  -0.2973 0.7992 
 [98,] PRR15        0.6044  -0.7991 -0.3479
 [99,] DUSP4        -0.5942 0.7936  0.3345 
[100,] SAMD4B       0.3775  -0.7891 0.0476 
[101,] ZHX1         0.2694  -0.7858 0.2373 
[102,] BAG4         -0.3063 0.7854  -0.1711
[103,] TMEM245      0.2664  -0.7834 0.2403 
[104,] ANGPTL1      -0.353  -0.1657 0.7805 
[105,] MAP1B        -0.3712 -0.1296 0.7801 
[106,] UBE2QL1      -0.3695 -0.1291 0.7765 
[107,] SRGAP2C      -0.4391 0.007   0.7763 
[108,] INO80D       0.3445  -0.7727 0.0914 
[109,] CYBRD1       -0.2943 -0.2716 0.7727 
[110,] MUM1         0.2716  -0.7726 0.2213 
[111,] ASCL2        0.6585  -0.7715 -0.4695
[112,] DFNA5        -0.4568 0.0483  0.7702 
[113,] PGGT1B       0.3104  -0.7682 0.148  
[114,] RAB31        -0.4373 0.0133  0.7674 
[115,] DUSP18       0.506   -0.7673 -0.2014
[116,] PLXDC2       -0.5117 0.1601  0.7659 
[117,] LOC100509635 -0.4065 -0.045  0.7658 
[118,] EFEMP1       -0.243  -0.3642 0.7658 
[119,] FBN1         -0.3479 -0.1573 0.7638 
[120,] IL1R1        -0.3578 -0.1336 0.7598 
[121,] TAGLN        -0.3289 -0.1896 0.7594 
[122,] SKA1         -0.1529 0.758   -0.4195
[123,] ZNF165       -0.2659 0.7579  -0.218 
[124,] AKAP12       -0.3143 -0.2159 0.7574 
[125,] NLGN4X       -0.3023 -0.2393 0.7574 
[126,] CEP68        0.3089  -0.7571 0.1407 
[127,] PLA2G5       -0.3269 -0.1906 0.7567 
[128,] CDH11        -0.3199 -0.2042 0.7566 
[129,] RNLS         0.4014  -0.7561 -0.0251
[130,] HSPA4L       -0.2919 0.756   -0.1699
[131,] TMEM45A      -0.6115 0.3661  0.7557 
[132,] TMEM106B     0.2741  -0.7552 0.201  
[133,] XRCC5        0.3157  -0.755  0.1265 
[134,] DCAKD        -0.1861 0.7534  -0.3561
[135,] CDHR1        0.635   -0.7533 -0.4443
[136,] C5orf46      -0.5368 0.2233  0.7529 
[137,] TSPAN6       0.5898  -0.7526 -0.3642
[138,] FRZB         0.2317  -0.7517 0.2733 
[139,] MARCH6       0.2914  -0.7508 0.1662 
[140,] MEOX2        -0.3967 -0.0477 0.7507 
[141,] GLT8D2       -0.2768 -0.2805 0.7495 
[142,] MXRA7        -0.3543 -0.1283 0.7488 
[143,] DPYSL3       -0.314  -0.2054 0.7473 
[144,] TUG1         0.4022  -0.7467 -0.0352
[145,] HOXC6        -0.7153 0.7447  0.5951 
[146,] KLHL3        0.3678  -0.7447 0.0242 
[147,] GPC6         -0.3397 -0.1519 0.7443 
[148,] ANTXR1       -0.3225 -0.1851 0.7439 
[149,] RNF19B       -0.2241 0.7401  -0.2762
[150,] SLC38A1      0.3943  -0.74   -0.0273
[151,] C5orf4       0.1457  -0.7395 0.4154 
[152,] ZNF521       -0.2779 -0.2673 0.7394 
[153,] PPP1CB       0.2992  -0.7389 0.1412 
[154,] SPP1         -0.7282 0.6127  0.7385 
[155,] HNRNPH1      0.2959  -0.7379 0.1462 
[156,] LAYN         -0.3536 -0.1164 0.7366 
[157,] CNRIP1       -0.2908 -0.2375 0.7353 
[158,] CACNA2D1     -0.3322 -0.1552 0.7338 
[159,] DCN          -0.2998 -0.2144 0.7301 
[160,] MORC4        -0.2638 0.7295  -0.1958
[161,] LHFP         -0.2736 -0.2596 0.7247 
[162,] DDR2         -0.3463 -0.109  0.7168 
[163,] ENGASE       0.4842  -0.7162 -0.2093
[164,] DSE          -0.5214 0.2337  0.7162 
[165,] ETV5         -0.566  0.7152  0.3559 
[166,] CRYAB        -0.2895 -0.2174 0.7146 
[167,] OXCT1        -0.3599 0.713   -0.0093
[168,] SESN1        0.3808  -0.7112 -0.0295
[169,] FITM2        0.6617  -0.7108 -0.5306
[170,] RECK         -0.2463 -0.2952 0.7085 
[171,] SGCE         -0.3126 -0.1652 0.708  
[172,] MAGI2-AS3    -0.3017 -0.1832 0.7052 
[173,] ZMYND8       0.4217  -0.7034 -0.1095
[174,] SLC5A3       0.289   -0.7033 0.1269 
[175,] ZNF148       0.2434  -0.7008 0.2061 
[176,] HCG11        0.3565  -0.7001 0.0037 
[177,] RAB32        0.3314  -0.6981 0.0466 
[178,] MEIS2        -0.6017 0.4136  0.6949 
[179,] FUT8         -0.2668 0.6943  -0.1584
[180,] BMPR1B       -0.2268 -0.3162 0.6931 
[181,] PMP22        -0.4184 0.0595  0.6914 
[182,] NPIPL3       0.2458  -0.6912 0.193  
[183,] PRLR         0.5858  -0.6909 -0.4134
[184,] BOC          -0.2165 -0.333  0.69   
[185,] AKT3         -0.3351 -0.0975 0.6863 
[186,] CYB5D1       -0.2691 0.6846  -0.1453
[187,] PPP1R14D     0.6103  -0.6845 -0.463 
[188,] CDCA2        -0.1246 0.684   -0.4025
[189,] E2F7         -0.1699 0.6836  -0.3213
[190,] ACTA2        -0.2405 -0.279  0.6835 
[191,] C20orf194    -0.2838 -0.1941 0.6832 
[192,] TIPIN        -0.1963 0.682   -0.2727
[193,] MPDZ         -0.2974 -0.166  0.6817 
[194,] TRIB2        -0.4974 0.6813  0.2646 
[195,] CDK2         -0.2046 0.6813  -0.2572
[196,] TP73-AS1     -0.2632 -0.2315 0.6805 
[197,] PBX1         0.1563  -0.6738 0.3367 
[198,] TUBB6        -0.3848 0.0161  0.6713 
[199,] SEH1L        -0.1775 0.6696  -0.2949
[200,] ENO2         -0.5395 0.6677  0.3521 
[201,] CLEC5A       -0.6562 0.5508  0.667  
[202,] CLIP4        -0.3334 -0.0791 0.6666 
[203,] TUBA1A       -0.3074 -0.1295 0.6663 
[204,] TSHZ3        -0.3113 -0.1204 0.6648 
[205,] IHH          0.5761  -0.6642 -0.4205
[206,] FEZ1         -0.2673 -0.205  0.6636 
[207,] ELK3         -0.3651 -0.0133 0.6629 
[208,] DEPDC1       -0.1556 0.661   -0.3262
[209,] FECH         -0.3749 0.6606  0.0651 
[210,] NR3C1        -0.3046 -0.128  0.6598 
[211,] POSTN        -0.5082 0.27    0.6594 
[212,] ID3          0.1954  -0.6552 0.2499 
[213,] TSHZ2        -0.2728 -0.1842 0.6544 
[214,] LOC100505702 -0.4799 0.222   0.6527 
[215,] PCMTD2       0.3246  -0.6512 0.0158 
[216,] SFXN1        -0.2128 0.6507  -0.2149
[217,] CCDC170      0.4009  -0.6487 -0.1223
[218,] PIAS2        -0.2295 0.6483  -0.1828
[219,] CYS1         -0.2057 -0.3054 0.6455 
[220,] EMILIN3      0.3557  -0.6454 -0.0448
[221,] C1QBP        -0.1336 0.6452  -0.3509
[222,] GGT7         0.3714  -0.6449 -0.0733
[223,] AMOTL1       -0.2557 -0.2064 0.6442 
[224,] FAT4         0.1993  -0.6424 0.2314 
[225,] PPIB         -0.237  0.642   -0.1637
[226,] PDZD2        0.2665  -0.6413 0.1104 
[227,] ETV6         0.2728  -0.6369 0.0952 
[228,] CENPM        -0.1315 0.6367  -0.347 
[229,] WDHD1        -0.2385 0.6364  -0.1559
[230,] ZNF141       0.3499  -0.6344 -0.0444
[231,] DDC          0.6334  -0.5723 -0.6065
[232,] FYN          -0.4864 0.2563  0.633  
[233,] NUP50        -0.1877 0.6286  -0.2394
[234,] CALD1        -0.2814 -0.1388 0.6284 
[235,] SRPRB        -0.1695 0.6283  -0.2715
[236,] FOXO3        0.2474  -0.6281 0.1325 
[237,] RAB34        -0.2775 -0.1447 0.6268 
[238,] DPYD         -0.5467 0.3812  0.6264 
[239,] PRDX5        0.6241  -0.5627 -0.5988
[240,] CHMP4B       0.3794  -0.623  -0.1075
[241,] C14orf101    0.3389  -0.6211 -0.037 
[242,] SNRPD1       -0.189  0.6197  -0.2289
[243,] LSMD1        -0.2662 0.6195  -0.0911
[244,] SERINC3      0.3531  -0.6176 -0.0656
[245,] DKK3         -0.2166 -0.2511 0.6154 
[246,] BCL6         -0.4805 0.2647  0.6149 
[247,] PRKCI        0.3256  -0.6111 -0.0224
[248,] TREM1        -0.6096 0.5859  0.5518 
[249,] SLC39A5      0.4568  -0.6086 -0.2586
[250,] NFATC3       0.2376  -0.6086 0.132  
[251,] PALLD        -0.3427 0.0033  0.6079 
[252,] GRM8         0.4793  -0.6064 -0.3007
[253,] TNFAIP6      -0.6038 0.5167  0.6046 
[254,] NDN          -0.2242 -0.224  0.6042 
[255,] SFR1         -0.1977 0.604   -0.1991
[256,] MED31        -0.3247 0.6028  0.0285 
[257,] ZNF232       -0.3102 0.6019  0.0034 
[258,] EXO1         -0.2109 0.5995  -0.1714
[259,] FHOD3        0.3102  -0.5993 -0.0058
[260,] NDUFV2       -0.204  0.5987  -0.1829
[261,] ITGAM        -0.5055 0.3313  0.5986 
[262,] FSCN1        -0.5975 0.5179  0.5922 
[263,] TSR1         -0.1869 0.5912  -0.2067
[264,] RPL15        0.2879  -0.5891 0.0246 
[265,] TRNP1        -0.5454 0.5888  0.4346 
[266,] MITF         -0.3636 0.0683  0.5859 
[267,] FZD1         -0.2739 -0.1057 0.5847 
[268,] SUMF2        -0.1868 0.5846  -0.2008
[269,] RAP2A        0.2026  -0.5793 0.1678 
[270,] RUFY2        0.1742  -0.5791 0.2183 
[271,] SLC11A1      -0.5208 0.3876  0.5746 
[272,] STK38        0.3328  -0.5728 -0.0703
[273,] GATAD1       0.2717  -0.5727 0.0386 
[274,] S100A16      -0.4525 0.5726  0.2838 
[275,] LOC157860    0.5706  -0.5209 -0.5416
[276,] DDX27        0.3854  -0.5695 -0.1671
[277,] AIFM3        0.5691  -0.5684 -0.4955
[278,] AVPR1A       -0.5475 0.4466  0.5682 
[279,] SLC5A6       0.558   -0.4675 -0.5678
[280,] NUCB2        -0.4287 0.5669  0.2466 
[281,] RPN1         -0.1506 0.5663  -0.2486
[282,] POFUT1       0.4878  -0.5614 -0.3571
[283,] DIO3OS       0.3608  -0.5575 -0.1341
[284,] SPATA2       0.4498  -0.5561 -0.2942
[285,] GGH          0.5291  -0.4288 -0.5517
[286,] SPHK1        -0.5447 0.5498  0.469  
[287,] ATF6         0.159   -0.5486 0.2176 
[288,] ARFGEF2      0.3875  -0.5476 -0.1907
[289,] AUNIP        -0.1909 0.5388  -0.1516
[290,] EPB41L4B     0.5163  -0.5372 -0.4298
[291,] GSTZ1        -0.1528 0.5346  -0.2158
[292,] AKAP1        0.4617  -0.5346 -0.335 
[293,] KCNJ15       -0.483  0.3598  0.5326 
[294,] DDAH1        0.2664  -0.5319 0.0107 
[295,] PIK3AP1      -0.5258 0.5139  0.468  
[296,] FCGR2A       -0.521  0.4543  0.5139 
[297,] ANO9         0.5157  -0.4892 -0.4727
[298,] FHDC1        0.5076  -0.515  -0.4346
[299,] ARID3A       0.4713  -0.5141 -0.3707
[300,] SLC2A3       -0.5135 0.4673  0.4888 
[301,] SALL4        0.1306  -0.5135 0.236  
[302,] COMMD7       0.27    -0.513  -0.0128
[303,] CALM1        -0.1563 0.5083  -0.1854
[304,] LOC440894    0.207   0.1511  -0.5068
[305,] ACSL5        0.4993  -0.4386 -0.4896
[306,] AHR          -0.4267 0.4987  0.3053 
[307,] KIF1B        -0.3991 0.2348  0.4971 
[308,] CDX2         0.4817  -0.4504 -0.4474
[309,] OVOL1        0.4637  -0.4803 -0.388 
[310,] IKBIP        -0.4721 0.472   0.4106 
[311,] CEP170       -0.4599 0.3927  0.4612 
[312,] PLEKHG6      0.4448  -0.3651 -0.4595
[313,] BNIP3L       -0.4135 0.3061  0.4577 
[314,] CEP85L       -0.4574 0.4208  0.4311 
[315,] DAPK2        0.4293  -0.4545 -0.3503
[316,] NFATC1       -0.4536 0.3965  0.4466 
[317,] CASP6        0.4452  -0.4063 -0.4226
[318,] ADAM8        -0.415  0.3324  0.4363 
[319,] LOC440944    0.4077  -0.433  -0.3314
[320,] TAF4         0.4158  -0.3896 -0.3855
[321,] DUSP16       0.4126  -0.391  -0.3785
[322,] SLC2A8       0.3948  -0.3688 -0.367 
[323,] SHROOM1      0.3747  -0.3546 -0.3442
       id           1-score 2-score 3-score
  [1,] SRSF6        -0.4592 1.328   -0.3416
  [2,] HNRNPL       -0.369  1.2597  -0.4401
  [3,] ZIC2         -0.5332 1.1669  -0.0627
  [4,] EIF5A        -0.414  1.159   -0.2679
  [5,] TOB1         0.4913  -1.1526 0.1243 
  [6,] KIAA0226L    0.8009  -1.1503 -0.339 
  [7,] ITCH         0.5242  -1.1409 0.0549 
  [8,] QPRT         0.7308  -1.1255 -0.2368
  [9,] CYP1B1       -0.5989 0       1.114  
 [10,] RBM6         0.4076  -1.0878 0.2143 
 [11,] PSIP1        -0.3244 1.065   -0.3418
 [12,] NUTF2        -0.2477 1.0254  -0.4423
 [13,] SEMA5A       0.5469  -1.0092 -0.0151
 [14,] HTR2B        -0.4162 -0.2384 1.0092 
 [15,] GAS1         -0.6983 0.2457  0.982  
 [16,] VAV3         0.6203  -0.9786 -0.1739
 [17,] MDM4         0.3613  -0.9546 0.1753 
 [18,] ECM2         -0.3963 -0.2158 0.9533 
 [19,] TRIM7        -0.5085 0.9436  0.0066 
 [20,] PRPF39       -0.3939 0.935   -0.0993
 [21,] KHDRBS3      0.4396  -0.9289 0.0122 
 [22,] AMFR         -0.2788 0.9278  -0.2977
 [23,] AXIN2        0.6964  -0.9275 -0.3563
 [24,] KCNE4        -0.4895 -0.0026 0.9247 
 [25,] RGS4         -0.4752 -0.0243 0.919  
 [26,] PDGFRL       -0.5262 0       0.9076 
 [27,] CFH          -0.392  -0.1737 0.907  
 [28,] ATP10B       0.6216  -0.9025 -0.2458
 [29,] CASP2        -0.2642 0.9001  -0.2985
 [30,] STON1        -0.3679 -0.2052 0.8928 
 [31,] ZNF827       0.4448  -0.8885 0      
 [32,] NAP1L3       -0.2966 -0.3359 0.8851 
 [33,] PMEPA1       0.2579  -0.8834 0.2945 
 [34,] PPP1R14C     0.7227  -0.8824 -0.4442
 [35,] CCDC80       -0.4042 -0.1226 0.8821 
 [36,] ISM1         -0.3012 -0.3197 0.8785 
 [37,] PLN          -0.351  -0.216  0.8725 
 [38,] PCDH7        -0.2792 -0.3416 0.8592 
 [39,] MSRB3        -0.3264 -0.2454 0.8556 
 [40,] CXCL12       -0.3595 -0.1778 0.8528 
 [41,] ZFPM2        -0.3839 -0.1239 0.8472 
 [42,] ZNF529       0.2799  -0.8471 0.2222 
 [43,] VGLL3        -0.5663 0.1416  0.8418 
 [44,] NAA15        -0.1388 0.8365  -0.4641
 [45,] PTGIS        -0.2711 -0.3322 0.8363 
 [46,] GPR126       -0.3222 0.8362  -0.1369
 [47,] COLEC12      -0.5427 0.1018  0.8361 
 [48,] HSD17B6      -0.2136 -0.4419 0.8338 
 [49,] SYK          0.3061  -0.8311 0.1608 
 [50,] PDGFC        -0.2845 -0.2864 0.8183 
 [51,] VMP1         0.2327  -0.8178 0.2795 
 [52,] SET          -0.3025 0.8161  -0.1535
 [53,] HOPX         -0.4253 -0.0069 0.8141 
 [54,] SEC22B       0.2418  -0.8111 0.2572 
 [55,] HPSE         -0.4525 0.8097  0.0289 
 [56,] CYR61        -0.4098 -0.0305 0.8081 
 [57,] ALYREF       -0.082  0.8062  -0.5377
 [58,] TXNDC9       0.3141  -0.8046 0.1224 
 [59,] EPM2AIP1     0.3301  -0.8038 0.0932 
 [60,] KIAA1967     -0.1583 0.8031  -0.3989
 [61,] C1orf174     -0.1848 0.8031  -0.3515
 [62,] FAP          -0.5284 0.1114  0.8018 
 [63,] DOK5         -0.3549 -0.1309 0.8018 
 [64,] PRRX1        -0.5416 0.1379  0.8012 
 [65,] CAB39L       0.3124  -0.7987 0.1201 
 [66,] C10orf99     0.7279  -0.795  -0.5332
 [67,] BHLHE41      -0.4135 -0.0078 0.7938 
 [68,] F13A1        -0.3695 -0.0929 0.7932 
 [69,] TYMS         -0.2483 0.7926  -0.2287
 [70,] FERMT2       -0.3307 -0.1678 0.7923 
 [71,] CBX5         0.2114  -0.7923 0.2942 
 [72,] AMACR        0.6015  -0.7903 -0.3123
 [73,] DACT1        -0.3127 -0.1989 0.7887 
 [74,] KANSL1L      0.3223  -0.7864 0.0911 
 [75,] ARL4C        -0.4749 0.0283  0.7823 
 [76,] SSPN         -0.2501 -0.313  0.7812 
 [77,] NR1I2        0.5314  -0.7802 -0.1965
 [78,] RPL22L1      -0.2309 0.7787  -0.2471
 [79,] LOC100130275 -0.3149 0.7778  -0.0965
 [80,] ZNF573       0.2758  -0.7777 0.1662 
 [81,] INHBA        -0.4616 0.008   0.7773 
 [82,] VCAN         -0.3535 -0.1039 0.7746 
 [83,] LINC00094    0.3038  -0.7738 0.1127 
 [84,] UQCRC2       0.2979  -0.7731 0.1227 
 [85,] NNMT         -0.4423 0       0.7722 
 [86,] PLAGL2       0.6969  -0.7645 -0.5059
 [87,] ATP9A        0.4544  -0.7643 -0.0739
 [88,] FRMD6        -0.4315 0       0.7629 
 [89,] PEG3         -0.3019 -0.1889 0.7604 
 [90,] PHACTR2      0.2847  -0.7603 0.1344 
 [91,] SYNC         -0.3383 -0.1176 0.7601 
 [92,] ULBP2        -0.5459 0.7596  0.2413 
 [93,] PRKD1        -0.3218 -0.1447 0.7555 
 [94,] LMCD1        -0.4321 0       0.7542 
 [95,] RNF43        0.6393  -0.754  -0.4127
 [96,] PDLIM3       -0.2674 -0.2491 0.7538 
 [97,] C20orf112    0.4585  -0.7513 -0.093 
 [98,] PRR15        0.5758  -0.7509 -0.3025
 [99,] DUSP4        -0.5655 0.7454  0.2892 
[100,] SAMD4B       0.3489  -0.7409 0.0022 
[101,] ZHX1         0.2408  -0.7376 0.192  
[102,] BAG4         -0.2777 0.7372  -0.1258
[103,] TMEM245      0.2378  -0.7352 0.195  
[104,] ANGPTL1      -0.3244 -0.1175 0.7351 
[105,] MAP1B        -0.3426 -0.0814 0.7347 
[106,] UBE2QL1      -0.3409 -0.0809 0.7312 
[107,] SRGAP2C      -0.4105 0       0.731  
[108,] CYBRD1       -0.2657 -0.2234 0.7274 
[109,] DFNA5        -0.4282 1e-04   0.7248 
[110,] INO80D       0.3159  -0.7245 0.0461 
[111,] MUM1         0.243   -0.7244 0.176  
[112,] ASCL2        0.6299  -0.7233 -0.4242
[113,] RAB31        -0.4087 0       0.722  
[114,] PLXDC2       -0.4831 0.1119  0.7206 
[115,] LOC100509635 -0.3779 0       0.7205 
[116,] EFEMP1       -0.2144 -0.316  0.7205 
[117,] PGGT1B       0.2818  -0.72   0.1027 
[118,] DUSP18       0.4774  -0.7191 -0.156 
[119,] FBN1         -0.3193 -0.1091 0.7185 
[120,] IL1R1        -0.3292 -0.0854 0.7145 
[121,] TAGLN        -0.3003 -0.1414 0.7141 
[122,] AKAP12       -0.2857 -0.1677 0.7121 
[123,] NLGN4X       -0.2737 -0.1911 0.7121 
[124,] PLA2G5       -0.2983 -0.1424 0.7114 
[125,] CDH11        -0.2913 -0.156  0.7113 
[126,] TMEM45A      -0.5829 0.3179  0.7104 
[127,] SKA1         -0.1243 0.7098  -0.3742
[128,] ZNF165       -0.2373 0.7097  -0.1727
[129,] CEP68        0.2803  -0.7089 0.0953 
[130,] RNLS         0.3727  -0.7079 0      
[131,] HSPA4L       -0.2633 0.7078  -0.1245
[132,] C5orf46      -0.5082 0.1751  0.7076 
[133,] TMEM106B     0.2455  -0.707  0.1557 
[134,] XRCC5        0.2871  -0.7068 0.0812 
[135,] MEOX2        -0.3681 0       0.7054 
[136,] DCAKD        -0.1575 0.7052  -0.3108
[137,] CDHR1        0.6064  -0.7051 -0.3989
[138,] TSPAN6       0.5612  -0.7044 -0.3189
[139,] GLT8D2       -0.2481 -0.2323 0.7042 
[140,] FRZB         0.2031  -0.7035 0.2279 
[141,] MXRA7        -0.3257 -0.0801 0.7034 
[142,] MARCH6       0.2628  -0.7026 0.1208 
[143,] DPYSL3       -0.2854 -0.1572 0.7019 
[144,] SPP1         -0.6995 0.5645  0.6932 
[145,] GPC6         -0.3111 -0.1037 0.699  
[146,] ANTXR1       -0.2939 -0.1369 0.6985 
[147,] TUG1         0.3736  -0.6985 0      
[148,] HOXC6        -0.6867 0.6965  0.5498 
[149,] KLHL3        0.3392  -0.6965 0      
[150,] ZNF521       -0.2493 -0.2191 0.6941 
[151,] RNF19B       -0.1955 0.6919  -0.2309
[152,] SLC38A1      0.3657  -0.6918 0      
[153,] C5orf4       0.1171  -0.6913 0.3701 
[154,] LAYN         -0.325  -0.0682 0.6913 
[155,] PPP1CB       0.2706  -0.6907 0.0959 
[156,] CNRIP1       -0.2622 -0.1893 0.6899 
[157,] HNRNPH1      0.2673  -0.6897 0.1008 
[158,] CACNA2D1     -0.3036 -0.107  0.6885 
[159,] DCN          -0.2712 -0.1662 0.6848 
[160,] MORC4        -0.2352 0.6813  -0.1504
[161,] LHFP         -0.245  -0.2114 0.6794 
[162,] DDR2         -0.3177 -0.0608 0.6715 
[163,] DSE          -0.4928 0.1855  0.6708 
[164,] CRYAB        -0.2609 -0.1692 0.6693 
[165,] ENGASE       0.4556  -0.668  -0.164 
[166,] ETV5         -0.5374 0.667   0.3106 
[167,] OXCT1        -0.3313 0.6648  0      
[168,] RECK         -0.2176 -0.247  0.6632 
[169,] SESN1        0.3522  -0.663  0      
[170,] SGCE         -0.284  -0.117  0.6627 
[171,] FITM2        0.6331  -0.6626 -0.4853
[172,] MAGI2-AS3    -0.2731 -0.135  0.6598 
[173,] ZMYND8       0.3931  -0.6552 -0.0642
[174,] SLC5A3       0.2604  -0.6551 0.0816 
[175,] ZNF148       0.2148  -0.6526 0.1607 
[176,] HCG11        0.3279  -0.6519 0      
[177,] RAB32        0.3028  -0.6499 0.0013 
[178,] MEIS2        -0.5731 0.3654  0.6496 
[179,] BMPR1B       -0.1982 -0.268  0.6477 
[180,] PMP22        -0.3898 0.0113  0.6461 
[181,] FUT8         -0.2382 0.6461  -0.113 
[182,] BOC          -0.1879 -0.2848 0.6447 
[183,] NPIPL3       0.2172  -0.643  0.1476 
[184,] PRLR         0.5572  -0.6427 -0.3681
[185,] AKT3         -0.3065 -0.0493 0.641  
[186,] ACTA2        -0.2119 -0.2308 0.6382 
[187,] C20orf194    -0.2552 -0.1459 0.6378 
[188,] CYB5D1       -0.2405 0.6364  -0.1   
[189,] MPDZ         -0.2688 -0.1178 0.6364 
[190,] PPP1R14D     0.5817  -0.6363 -0.4177
[191,] CDCA2        -0.096  0.6358  -0.3571
[192,] E2F7         -0.1413