Methods and molecular pharmacodynamic biomarkers for multiple signaling pathways in response to carboxyamidotriazole orotate

A method for quantifying the response to carboxyamidotriazole orotate (CTO) on more than one signature pathway wherein said signature pathways are RAS, GFS, MEKi, HDAC, NOTCH, WNTβ-catenin, HSP90, EGFR, p53, EGR1, CEACAMI, TGFβ or Dystonin and on pharmacodynamic biomarkers for each of said signature pathways, said method comprising:

• a) obtaining a cell sample obtained from a subject and treating cultures of the cell sample with varying doses of CTO alone, and maintaining the cultures for different time periods;
• b) isolating the mRNA from the treated cultures of the cell sample obtained in step a), and preparing representative cDNA therefrom, and measuring the transcriptional alteration in expression in the treated cultures of the cell sample;
• c) calculating a signature score for each of the pharmacodynamics biomarkers of each of said signature pathways using the Ingenuity Pathway Analysis (IPA) System and quantitating the response to the varying doses of CTO, and selecting a list of overlapping genes expressing after 8 hours and 24 hours of exposure to CTO based on the calculated signature scores, from the list consisting of:
• Probeset ID
• Entrez Gene
• Gene Symbol
• 222450_at
• 56937
• PMEPA1
• 233565_s_at
• 100528031///27111
• FKBP1A-SDCBP2///
• SDCBP2
• 242832_at
• 5187
• PER1
• 240463_at
• —
• —
• 213039_at
• 23370
• ARHGEF18
• 235072_s_at
• 63971
• KIF13A
• 208926_at
• 4758
• NEU1
• 237444_at
• —
• —
• 239451_at
• —
• —
• 222288_at
• —
• —
• 227579_at
• 2241
• FER
• 212717_at
• 9842
• PLEKHM1
• 226853_at
• 55589
• BMP2K
• 214112_s_at
• 541578///91966
• CXorf40A///
• CXorf40B
• 209012_at
• 7204
• TRIO
• 219476_at
• 79098
• C1orf116
• 238086_at
• 100129617
• LOC100129617
• 230721_at
• 730094
• C16orf52
• 1566079_at
• 647190
• RPS16P5
• 223839_s_at
• 6319
• SCD
• 225671_at
• 124976
• SPNS2
• 212961_x_at
• 541578
• CXorf40B
• 223659_at
• 84000
• TMPRSS13
• 229909_at
• 283358
• B4GALNT3
• 223467_at
• 51655
• RASD1
• 235146_at
• 57458
• TMCC3
• 235548_at
• 164284
• APCDD1L
• 206816_s_at
• 26206
• SPAG8
• 242323_at
• 81579
• PLA2G12A
• 224579_at
• 81539
• SLC38A1
• 213315_x_at
• 91966
• CXorf40A
• 227314_at
• 3673
• ITGA2
• 227093_at
• 57602
• USP36
• 200760_s_at
• 10550
• ARL6IP5
• 201790_s_at
• 1717
• DHCR7
• 1554980_a_at
• 467
• ATF3
• 242255_at
• 22884
• WDR37
• 219267_at
• 51228
• GLTP
• 1555786_s_at
• 645687
• LINC00520
• 229734_at
• 283174
• LOC283174
• 242856_at
• —
• —
• 201037_at
• 5214
• PFKP
• 1562970_at
• —
• —
• 201465_s_at
• 3725
• JUN
• 202067_s_at
• 3949
• LDLR
• 223679_at
• 1499
• CTNNB1
• 201235_s_at
• 7832
• BTG2
• 225662_at
• 51776
• ZAK
• 204401_at
• 3783
• KCNN4
• 222906_at
• 28982
• FLVCR1
• 238613_at
• 51776
• ZAK
• 206414_s_at
• 8853
• ASAP2
• 210794_s_at
• 55384
• MEG3
• 226621_at
• 9180
• OSMR
• 230682_x_at
• 8714
• ABCC3
• 235668_at
• 639
• PRDM1
• 205483_s_at
• 9636
• ISG15
• 215808_at
• 5655
• KLK10
• 212281_s_at
• 27346
• TMEM97
• 212282_at
• 27346
• TMEM97
• 226287_at
• 91057
• CCDC34
• 213618_at
• 116984
• ARAP2
• 231089_at
• 100505664
• LOC100505664
• 227140_at
• 3624
• INHBA
• 231467_at
• —
• —
• 202967_at
• 2941
• GSTA4
• 230323_s_at
• 120224
• TMEM45B
• 224471_s_at
• 8945
• BTRC
• 202708_s_at
• 8349
• HIST2H2BE
• 242871_at
• 54852
• PAQR5
• 205627_at
• 978
• CDA
• 235542_at
• 200424
• TET3
• 240410_at
• —
• —
• 236656_s_at
• 100288911
• LOC100288911
• 206164_at
• 9635
• CLCA2
• 203159_at
• 2744
• GLS
• 224991_at
• 80790
• CMIP
• 204258_at
• 1105
• CHD1
• 228249_at
• 119710
• C11orf74
• 229013_at
• 145783
• LOC145783
• 211547_s_at
• 5048
• PAFAH1B1
• 226863_at
• 642273
• FAM110C
• 208161_s_at
• 8714
• ABCC3
• 214805_at
• 1973
• ElF4A1
• 229429_x_at
• 728855///728875
• LOC728855///
• LOC728875
• 202720_at
• 26136
• TES
• 224995_at
• 56907
• SPIRE1
• 214771_x_at
• 23164
• MPRIP
• 201939_at
• 10769
• PLK2
• 238587_at
• 84959
• UBASH3B
• 232113_at
• —
• —
• 208690_s_at
• 9124
• PDLIM1
• 201464_x_at
• 3725
• JUN
• 236657_at
• 100288911
• LOC100288911
• 215541_s_at
• 1729
• DIAPH1
• 238028_at
• 647024
• C6orf132
• 226893_at
• 27
• ABL2
• 237576_x_at
• 100506480
• LOC100506480
• 1552256_a_at
• 949
• SCARB1
• 215255_at
• 22997
• IGSF9B
• 1557258_a_at
• 8915
• BCL10
• 240623_at
• —
• —
• 228754_at
• 6533
• SLC6A6
• 217257_at
• 6452
• SH3BP2
• 241036_at
• —
• —
• 242553_at
• 8714
• ABCC3
• 239358_at
• —
• —
• 210868_s_at
• 79071
• ELOVL6
• 200815_s_at
• 5048
• PAFAH1B1
• 208436_s_at
• 3665
• IRF7
• 208138_at
• 2520
• GAST
• 241780_at
• —
• —
• 200730_s_at
• 7803
• PTP4A1
• 219697_at
• 9956
• HS3ST2
• 201693_s_at
• 1958
• EGR1
• 218847_at
• 10644
• IGF2BP2
• 230469_at
• 219790
• RTKN2
• 209917_s_at
• 11257
• TP53TG1
• 224329_s_at
• 84518
• CNFN
• 212253_x_at
• 100652766///667
• DST///
• LOC100652766
• 238058_at
• 150381
• LOC150381
• 239334_at
• 57488
• ESYT2
• 222271_at
• —
• —
• 216718_at
• 388699
• LINC00302
• 219076_s_at
• 5827
• PXMP2
• 204475_at
• 4312
• MMP1
• 221185_s_at
• 84223
• IQCG
• 203586_s_at
• 379
• ARL4D
• 217802_s_at
• 64710
• NUCKS1
• 205767_at
• 2069
• EREG
• 228360_at
• 130576
• LYPD6B
• 228917_at
• —
• —
• 228748_at
• 966
• CD59
• 219632_s_at
• 23729///7442
• SHPK///TRPV1
• 238715_at
• 646014
• LOC646014
• 218810_at
• 80149
• ZC3H12A
• 225177_at
• 80223
• RAB11FIP1
• 224454_at
• 55500
• ETNK1
• 209498_at
• 634
• CEACAM1
• 1557257_at
• 8915
• BCL10
• 225133_at
• 51274
• KLF3
• 202340_x_at
• 3164
• NR4A1
• 1556545_at
• —
• —
• 212474_at
• 23080
• AVL9
• 210241_s_at
• 11257
• TP53TG1
• 243543_at
• —
• —
• 239132_at
• 4842
• NOS1
• 222757_s_at
• 51776
• ZAK
• 201194_at
• 6415
• SEPW1
• 229874_x_at
• 100506687
• LOC100506687
• 202557_at
• 6782
• HSPA13
• 239669_at
• —
• —
• 231907_at
• 27
• ABL2
• 229074_at
• 30844
• EHD4
• 205428_s_at
• 794
• CALB2
• 205822_s_at
• 3157
• HMGCS1
• 210869_s_at
• 4162
• MCAM
• 225665_at
• 51776
• ZAK
• 212781_at
• 5930
• RBBP6
• 232355_at
• 767579
• SNORD114-3
• 213288_at
• 129642
• MBOAT2
• 221666_s_at
• 29108
• PYCARD
• 203072_at
• 4643
• MYO1E
• 215465_at
• 26154
• ABCA12
• 224453_s_at
• 55500
• ETNK1
• 216935_at
• 388699
• LINC00302
• 209086_x_at
• 4162
• MCAM
• 218833_at
• 51776
• ZAK
• 209377_s_at
• 9324
• HMGN3
• 223519_at
• 51776
• ZAK
• 210138_at
• 8601
• RGS20
• 1558845_at
• 100506089
• LOC100506089
• 201819_at
• 949
• SCARB1
• 204310_s_at
• 4882
• NPR2
• 239377_at
• 84285
• EIF1AD
• 224611_s_at
• 80331
• DNAJC5
• 219155_at
• 26207
• PITPNC1
• 227163_at
• 119391
• GSTO2
• 209633_at
• 5523
• PPP2R3A
• 219681_s_at
• 80223
• RAB11FIP1
• 221860_at
• 3191
• HNRNPL
• 243296_at
• 10135
• NAMPT
• 237133_at
• —
• —
• 1556000_s_at
• 55727
• BTBD7
• 204681_s_at
• 9771
• RAPGEF5
• 215726_s_at
• 1528
• CYB5A
• 210886_x_at
• 11257
• TP53TG1
• 226597_at
• 92840
• REEP6
• 204995_at
• 8851
• CDK5R1
• 236119_s_at
• 6706
• SPRR2G
• 219228_at
• 55422
• ZNF331
• 234971_x_at
• 113026
• PLCD3
• 201127_s_at
• 47
• ACLY
• 226880_at
• 64710
• NUCKS1
• 209383_at
• 1649
• DDIT3
• 204168_at
• 4258
• MGST2
• 239670_at
• 65268
• WNK2
• 208512_s_at
• 4301
• MLLT4
• 213281_at
• 3725
• JUN
• 218310_at
• 154881///27342
• KCTD7///RABGEF1
• 205151_s_at
• 9865
• TRIL
• 218217_at
• 59342
• SCPEP1
• 205055_at
• 3682
• ITGAE
• 215009_s_at
• 100499177
• THAP9-AS1
• 227484_at
• 57522
• SRGAP1
• 239769_at
• 1009
• CDH11
• 230360_at
• 342035
• GLDN
• 227112_at
• 23023
• TMCC1
• 201482_at
• 5768
• QS0X1
• 210337_s_at
• 47
• ACLY
• 203911_at
• 5909
• RAP1GAP
• 206683_at
• 7718
• ZNF165
• 202935_s_at
• 6662
• SOX9
• 218951_s_at
• 55344
• PLCXD1
• 233488_at
• 84659
• RNASE7
• 202562_s_at
• 11161
• C14orf1
• 208745_at
• 10632
• ATP5L
• 236078_at
• 57707
• KIAA1609
• 226226_at
• 120224
• TMEM45B
• 213854_at
• 9145
• SYNGR1
• 243955_at
• —
• —
• 222111_at
• 54629
• FAM63B
• 1560296_at
• —
• —
• 240038_at
• —
• —
• 211372_s_at
• 7850
• IL1R2
• 202672_s_at
• 467
• ATF3
• 218717_s_at
• 55214
• LEPREL1
• 228366_at
• —
• —
• 230516_at
• 115416
• MALSU1
• 201920_at
• 6574
• SLC20A1
• 209632_at
• 5523
• PPP2R3A
• 207367_at
• 479
• ATP12A
• 1557256_a_at
• —
• —
• 200811_at
• 1153
• CIRBP
• 205201_at
• 2737
• GLI3
• 227724_at
• 728190
• LOC728190
• 205403_at
• 7850
• IL1R2
• 242827_x_at
• —
• —
• 228084_at
• 81579
• PLA2G12A
• 209365_s_at
• 1893
• ECM1
• 243279_at
• —
• —
• 224946_s_at
• 84317
• CCDC115
• 218708_at
• 29107
• NXT1
• 1560531_at
• 353132
• LCE1B
• 207761_s_at
• 25840
• METTL7A
• 206011_at
• 834
• CASP1
• 213703_at
• 150759
• LINC00342
• 224595_at
• 23446
• SLC44A1
• 224613_s_at
• 80331
• DNAJC5
• 212504_at
• 22982
• DIP2C
• 213682_at
• 10762
• NUP50
• 205247_at
• 4855
• NOTCH4
• 228235_at
• 84848
• MGC16121
• 242873_at
• —
• —
• 205960_at
• 5166
• PDK4
• 230494_at
• 6574
• SLC20A1
• 221260_s_at
• 81566
• CSRNP2
• 224480_s_at
• 84803
• AGPAT9
• 210180_s_at
• 6434
• TRA2B
• 204621_s_at
• 4929
• NR4A2
• 217863_at
• 8554
• PIAS1
• 236423_at
• —
• —
• 223421_at
• 50626
• CYHR1
• 220272_at
• 54796
• BNC2
• 201791_s_at
• 1717
• DHCR7
• 215574_at
• —
• —
• 224328_s_at
• 84648
• LCE3D
• 211828_s_at
• 23043
• TNIK
• 58367_s_at
• 79744
• ZNF419
• 218950_at
• 64411
• ARAP3
• 1552703_s_at
• 114769///834
• CARD16///CASP1
• 219687_at
• 55733
• HHAT
• 232127_at
• 1184
• CLCN5
• 218377_s_at
• 10069
• RWDD2B
• 210335_at
• 9182
• RASSF9
• 227927_at
• —
• —
• 227224_at
• 55103
• RALGPS2
• 224778_s_at
• 57551
• TAOK1
• 229566_at
• 645638
• LOC645638
• 202734_at
• 9322
• TRIP10
• 201851_at
• 6455
• SH3GL1
• 237337_at
• —
• —
• 37152_at
• 5467
• PPARD
• 209687_at
• 6387
• CXCL12
• 203152_at
• 64976
• MRPL40
• 201627_s_at
• 3638
• INSIG1
• 232593_at
• 93082
• NEURL3
• 224769_at
• 57551
• TAOK1
• 209702_at
• 79068
• FTO
• 204546_at
• 9764
• KIAA0513
• 232224_at
• 5648
• MASP1
• 239930_at
• 2590
• GALNT2
• 203178_at
• 2628
• GATM
• 235782_at
• —
• —
• 218181_s_at
• 9448
• MAP4K4
• 233520_s_at
• 202333
• CMYA5
• 213456_at
• 25928
• SOSTDC1
• 219528_s_at
• 64919
• BCL11B
• 224945_at
• 55727
• BTBD7
• 214866_at
• 5329
• PLAUR
• 209941_at
• 8737
• RIPK1
• 226029_at
• 57216
• VANGL2
• 212596_s_at
• 10042
• HMGXB4
• 229873_at
• 283219
• KCTD21
• 226392_at
• 5922
• RASA2
• 226005_at
• 7326
• UBE2G1
• 214445_at
• 22936
• ELL2
• 227680_at
• 284695
• ZNF326
• 227786_at
• 90390
• MED30
• 222067_x_at
• 3017
• HIST1H2BD
• 1569106_s_at
• 55209
• SETD5
• 231785_at
• 4909
• NTF4
• 223937_at
• 27086
• FOXP1
• 1558685_a_at
• 158960
• LOC158960
• 211965_at
• 677
• ZFP36L1
• 39549_at
• 4862
• NPAS2
• 203800_s_at
• 63931
• MRPS14
• 1556321_a_at
• —
• —
• 212321_at
• 8879
• SGPL1
• 222154_s_at
• 26010
• SPATS2L
• 218774_at
• 28960
• DCPS
• 212268_at
• 1992
• SERPINB1
• 213134_x_at
• 10950
• BTG3
• 230669_at
• 5922
• RASA2
• 1559901_s_at
• 388815
• LINC00478
• 225298_at
• 25953
• PNKD
• 242558_at
• —
• —
• 226043_at
• 26086
• GPSM1
• 210236_at
• 8500
• PPFIA1
• 214066_x_at
• 4882
• NPR2
• 240024_at
• 23541
• SEC14L2
• 235462_at
• 132864
• CPEB2
• 1554015_a_at
• 1106
• CHD2
• 235347_at
• 84859
• LRCH3
• 230847_at
• 56897
• WRNIP1
• 201427_s_at
• 6414
• SEPP1
• 1557905_s_at
• 960
• CD44
• 219084_at
• 64324
• NSD1
• 206176_at
• 654
• BMP6
• 219826_at
• 79744
• ZNF419
• 212356_at
• 23351
• KHNYN
• 218909_at
• 26750
• RPS6KC1
• 230555_s_at
• 90390
• MED30
• 212687_at
• 3987
• LIMS1
• 203098_at
• 9425
• CDYL
• 229054_at
• 677
• ZFP36L1
• 236039_at
• 284348
• LYPD5
• 209661_at
• 3801
• KIFC3
• 209560_s_at
• 8788
• DLK1
• 225812_at
• 619208
• C6orf225
• 227829_at
• 120071
• GYLTL1B
• 238623_at
• —
• —
• 229415_at
• 54205
• CYCS
• 209222_s_at
• 9885
• OSBPL2
• 1555809_at
• 83716
• CRISPLD2
• 204567_s_at
• 9619
• ABCG1
• 232277_at
• 64078
• SLC28A3
• 237197_at
• —
• —
• 225209_s_at
• 118424
• UBE2J2
• 231916_at
• 4842
• NOS1
• 212279_at
• 27346
• TMEM97
• 204862_s_at
• 4832
• NME3
• 230483_at
• —
• —
• 212856_at
• 23151
• GRAMD4
• 224650_at
• 114569
• MAL2
• 202963_at
• 5993
• RFX5
• 225320_at
• 90550
• MCU
• 236274_at
• 8662
• ElF3B
• 209780_at
• 57157
• PHTF2
• 218823_s_at
• 54793
• KCTD9
• 227787_s_at
• 90390
• MED30
• 230296_at
• 730094
• C16orf52
• 222892_s_at
• 55287
• TMEM40
• 210610_at
• 634
• CEACAM1
• 230031_at
• 3309
• HSPA5
• 238477_at
• 10749
• KIF1C
• 209409_at
• 2887
• GRB10
• 217995_at
• 58472
• SQRDL
• 226873_at
• 54629
• FAM63B
• 1553722_s_at
• 220441
• RNF152
• 204710_s_at
• 26100
• WIPI2
• 212653_s_at
• 23301
• EHBP1
• 203979_at
• 1593
• CYP27A1
• 244350_at
• 4651
• MYO10
• 223233_s_at
• 57530
• CGN
• 1555967_at
• —
• —
• 214355_x_at
• 100128553///
• CTAGE15P///
• 100142659///340307///
• CTAGE4///
• 441294///643854
• CTAGE6P///
• CTAGE8///CTAGE9
• 214469_at
• 3012///8335
• HIST1H2AB///
• HIST1H2AE
• 212472_at
• 9645
• MICAL2
• 228115_at
• 64762
• FAM59A
• 228964_at
• 639
• PRDM1
• 230027_s_at
• 84545
• MRPL43
• 207318_s_at
• 8621
• CDK13
• 221689_s_at
• 51227
• PIGP
• 219270_at
• 79094
• CHAC1
• 225299_at
• 4645
• MYO5B
• 239770_at
• 83850
• ESYT3
• 226399_at
• 79982
• DNAJB14
• 226656_at
• 10491
• CRTAP
• 228852_at
• 2029
• ENSA
• 206239_s_at
• 6690
• SPINK1
• 210993_s_at
• 4086
• SMAD1
• 238462_at
• 84959
• UBASH3B
• 211962_s_at
• 677
• ZFP36L1
• 224666_at
• 197370
• NSMCE1
• 239028_at
• 130574
• LYPD6
• 213577_at
• 6713
• SQLE
• 202011_at
• 7082
• TJP1
• 212254_s_at
• 100652766///667
• DST///
• LOC100652766
• 221701_s_at
• 64220
• STRA6
• 239576_at
• 57509
• MTUS1
• 234418_x_at
• 960
• CD44
• 227985_at
• 100506098
• LOC100506098
• 213462_at
• 4862
• NPAS2
• 224975_at
• 4774
• NFIA
• 225990_at
• 91653
• BOC
• 240616_at
• —
• —
• 219911_s_at
• 28231
• SLCO4A1
• 224970_at
• 4774
• NFIA
• 214623_at
• 26226
• FBXW4P1
• 239478_x_at
• 55668
• C14orf118
• 226909_at
• 85460
• ZNF518B
• 208670_s_at
• 23741
• EID1
• 206192_at
• 1041
• CDSN
• 222173_s_at
• 55357
• TBC1D2
• 228450_at
• 144100
• PLEKHA7
• 1558097_at
• 253143
• PRR14L
• 219373_at
• 54344
• DPM3
• 230388_s_at
• 644246
• KANSL1-AS1
• 207098_s_at
• 55669
• MFN1
• 223484_at
• 84419
• C15orf48
• 244804_at
• 8878
• SQSTM1
• 229679_at
• 400073
• C12orf76
• 225826_at
• 326625
• MMAB
• 213352_at
• 23023
• TMCC1
• 211883_x_at
• 634
• CEACAM1
• 210387_at
• 8339///8343///8344///
• HIST1H2BC///
• 8346///8347
• HIST1H2BE///
• HIST1H2BF///
• HIST1H2BG///
• HIST1H2BI
• 210916_s_at
• 960
• CD44
• 221432_s_at
• 81894
• SLC25A28
• 218487_at
• 210
• ALAD
• 223264_at
• 59274
• MESDC1
• 206356_s_at
• 2774
• GNAL
• 218097_s_at
• 79004
• CUEDC2
• 228001_at
• 757
• TMEM5OB
• 212441_at
• 9778
• K1AA0232
• 201854_s_at
• 23300
• ATMIN
• 121_at
• 7849
• PAX8
• 222143_s_at
• 64419
• MTMR14
• 1558002_at
• 11171
• STRAP
• 226040_at
• —
• —
• 226141_at
• 91050
• CCDC149
• 1556567_at
• 4676
• NAP1L4
• 226263_at
• 154007
• SNRNP48
• 212074_at
• 23353
• SUN1
• 227387_at
• 54780
• NSMCE4A
• 232795_at
• —
• —
• 203936_s_at
• 4318
• MMP9
• 225033_at
• 6482
• ST3GAL1
• 209109_s_at
• 7105
• TSPAN6
• 213351_s_at
• 23023
• TMCC1
• 203047_at
• 6793
• STK10
• 220721_at
• 80110
• ZNF614
• 1556127_at
• 23181
• DIP2A
• 215016_x_at
• 100652766///667
• DST///
• LOC100652766
• 206576_s_at
• 634
• CEACAM1
• 240674_at
• 3720
• JARID2
• 225646_at
• 1075
• CTSC
• 1554010_at
• 3340
• NDST1
• 204100_at
• 7067
• THRA
• 221840_at
• 5791
• PTPRE
• 209078_s_at
• 25828
• TXN2
• 218530_at
• 29109
• FHOD1
• 235434_at
• —
• —
• 230063_at
• 9422
• ZNF264
• 40420_at
• 6793
• STK10
• 221027_s_at
• 81579
• PLA2G12A
• 244202_at
• —
• —
• 212108_at
• 23197
• FAF2
• 204294_at
• 275
• AMT
• 225503_at
• 207063
• DHRSX
• 212810_s_at
• 6509
• SLC1A4
• 214814_at
• 91746
• YTHDC1
• 228468_at
• 84930
• MASTL
• 209108_at
• 7105
• TSPAN6
• 220444_at
• 79230
• ZNF557
• 206172_at
• 3598
• IL13RA2
• 225002_s_at
• 25870
• SUMF2
• 212205_at
• 94239
• H2AFV
• 228851_s_at
• 2029
• ENSA
• 209048_s_at
• 23613
• ZMYND8
• 211846_s_at
• 5818
• PVRL1
• 238909_at
• 6281
• S100A10
• 205503_at
• 5784
• PTPN14
• 243829_at
• 673
• BRAF
• 244379_at
• —
• —
• 223251_s_at
• 55608
• ANKRD10
• 202633_at
• 11073
• TOPBP1
• 214502_at
• 8970
• HIST1H2BJ
• 221773_at
• 2004
• ELK3
• 41858_at
• 27315
• PGAP2
• 212850_s_at
• 4038
• LRP4
• 223408_s_at
• —
• —
• 214472_at
• 3013///8350///8351///
• HIST1H2AD///
• 8352///8353///8354///
• HIST1H3A///
• 8355///8356///8357
• HIST1H3B///
• 8358/
• HIST1H3C///
• HIST1H3D///
• HIST1H3E///
• HIST1H3F///
• HIST1H3G///
• HIST1H3H///
• HIST1H3I///
• HIST1H3J
• 225647_s_at
• 1075
• CTSC
• 1559977_a_at
• 284723
• SLC25A34
• 211347_at
• 8555
• CDC14B
• 1558208_at
• —
• —
• 227570_at
• 144110
• TMEM86A
• 227492_at
• 100506658///647859
• LOC647859///OCLN
• 1558778_s_at
• 57496
• MKL2
• 31637_s_at
• 7067///9572
• NR1D1///THRA
• 229190_at
• 100507376
• LOC100507376
• 236188_s_at
• 4676
• NAP1L4
• 212503_s_at
• 22982
• DIP2C
• 204760_s_at
• 7067///9572
• NR1D1///THRA
• 212099_at
• 388
• RHOB
• 214873_at
• 91355
• LRP5L
• 228181_at
• 7779
• SLC30A1
• 212763_at
• 23271
• CAMSAP2
• 226285_at
• 4076
• CAPRIN1
• 213567_at
• 3840
• KPNA4
• 203927_at
• 4794
• NFKBIE
• 208523_x_at
• 8339///8343///8344///
• HIST1H2BC///
• 8346///8347
• HIST1H2BE///
• HIST1H2BF///
• HIST1H2BG///
• HIST1H2BI
• 219389_at
• 55061
• SUSD4
• 202329_at
• 1445
• CSK
• 238523_at
• 79786
• KLHL36
• 1565016_at
• 3276
• PRMT1
• 226409_at
• 128637
• TBC1D20
• 229926_at
• 100500850
• MIR3682
• 208527_x_at
• 8339///8343///8344///
• HIST1H2BC///
• 8346///8347
• HIST1H2BE///
• HIST1H2BF///
• HIST1H2BG///
• HIST1H2BI
• 223598_at
• 5887
• RAD23B
• 243797_at
• 9262
• STK17B
• 203317_at
• 23550
• PSD4
• 230965_at
• 9099
• USP2
• 208490_x_at
• 8339///8343///8344///
• HIST1H2BC///
• 8346///8347
• HIST1H2BE///
• HIST1H2BF///
• HIST1H2BG///
• HIST1H2BI
• 235514_at
• 151516
• ASPRV1
• 209098_s_at
• 182
• JAG1
• 1554229_at
• 153222
• CREBRF
• 209398_at
• 3006
• HIST1H1C
• 202629_at
• 10513
• APPBP2
• 203428_s_at
• 25842
• ASF1A
• 238005_s_at
• 25942
• SIN3A
• 214455_at
• 8339///8343///8344///
• HIST1H2BC///
• 8346///8347
• HIST1H2BE///
• HIST1H2BF///
• HIST1H2BG///
• HIST1H2BI
• 214073_at
• 2017
• CTTN
• 203140_at
• 604
• BCL6
• 232150_at
• —
• —
• 208546_x_at
• 8345
• HIST1H2BH
• 243446_at
• 84962
• AJUBA
• 236207_at
• 6744
• SSFA2
• 212016_s_at
• 5725
• PTBP1
• 232311_at
• 567
• B2M
• 219711_at
• 54807
• ZNF586
• 208579_x_at
• 54145///85236
• H2BFS///
• HIST1H2BK
• 239493_at
• 6129
• RPL7
• 214074_s_at
• 2017
• CTTN
• 228091_at
• 55014
• STX17
• 234331_s_at
• 151354
• FAM84A
• 212372_at
• 4628
• MYH10
• Probeset ID
• Gene Title
• 222450_at
• prostate transmembrane
• protein, androgen induced 1
• 233565_s_at
• FKBP1A-SDCBP2 readthrough
• (non-protein coding)///
• syndecan binding protein
• (syntenin)
• 242832_at
• period homolog 1 (Drosophila)
• 240463_at
• —
• 213039_at
• Rho/Rac guanine nucleotide
• exchange factor (GEF) 18
• 235072_s_at
• kinesin family member 13A
• 208926_at
• sialidase 1 (lysosomal
• sialidase)
• 237444_at
• —
• 239451_at
• —
• 222288_at
• —
• 227579_at
• fer (fps/fes related) tyrosine
• kinase
• 212717_at
• pleckstrin homology domain
• containing, family M (with RUN
• domain) member 1
• 226853_at
• BMP2 inducible kinase
• 214112_s_at
• chromosome X open reading
• frame 40A///chromosome X
• open reading frame 40B
• 209012_at
• triple functional domain (PTPRF
• interacting)
• 219476_at
• chromosome 1 open reading
• frame 116
• 238086_at
• uncharacterized
• LOC100129617
• 230721_at
• chromosome 16 open reading
• frame 52
• 1566079_at
• ribosomal protein S16
• pseudogene 5
• 223839_s_at
• stearoyl-CoA desaturase (delta-
• 9-desaturase)
• 225671_at
• spinster homolog 2 (Drosophila)
• 212961_x_at
• chromosome X open reading
• frame 40B
• 223659_at
• transmembrane protease,
• serine 13
• 229909_at
• beta-1,4-N-acetyl-galactosaminyl
• 223467_at
• transferase 3 RAS, dexamethasone-
• induced 1
• 235146_at
• transmembrane and coiled-coil
• domain family 3
• 235548_at
• adenomatosis polyposis coli
• down-regulated 1-like
• 206816_s_at
• sperm associated antigen 8
• 242323_at
• phospholipase A2, group XIIA
• 224579_at
• solute carrier family 38,
• member 1
• 213315_x_at
• chromosome X open reading
• frame 40A
• 227314_at
• integrin, alpha 2 (CD49B, alpha
• 2 subunit of VLA-2 receptor)
• 227093_at
• Ubiquitin specific peptidase 36
• 200760_s_at
• ADP-ribosylation-like factor 6
• interacting protein 5
• 201790_s_at
• 7-dehydrocholesterol reductase
• 1554980_a_at
• activating transcription factor 3
• 242255_at
• WD repeat domain 37
• 219267_at
• glycolipid transfer protein
• 1555786_s_at
• long intergenic non-protein
• coding RNA 520
• 229734_at
• uncharacterized LOC283174
• 242856_at
• —
• 201037_at
• phosphofructokinase, platelet
• 1562970_at
• —
• 201465_s_at
• jun proto-oncogene
• 202067_s_at
• low density lipoprotein receptor
• 223679_at
• catenin (cadherin-associated
• protein), beta 1, 88kDa
• 201235_s_at
• BTG family, member 2
• 225662_at
• sterile alpha motif and leucine
• zipper containing kinase AZK
• potassium intermediate/small
• 204401_at
• conductance calcium-activated
• channel, subfamily N, member
• 222906_at
• feline leukemia virus subgroup
• C cellular receptor 1
• 238613_at
• sterile alpha motif and leucine
• zipper containing kinase AZK
• ArfGAP with SH3 domain,
• 206414_s_at
• ankyrin repeat and PH domain
• 2
• 210794_s_at
• maternally expressed 3 (non-protein
• coding)
• 226621_at
• oncostatin M receptor
• 230682_x_at
• ATP-binding cassette, sub-family C
• (CFTR/MRP), member3
• 235668_at
• PR domain containing 1, with
• ZNF domain
• 205483_s_at
• ISG15 ubiquitin-like modifier
• 215808_at
• kallikrein-related peptidase 10
• 212281_s_at
• transmembrane protein 97
• 212282_at
• transmembrane protein 97
• 226287_at
• coiled-coil domain containing 34
• 213618_at
• ArfGAP with RhoGAP domain,
• ankyrin repeat and PH domain
• 2
• 231089_at
• uncharacterized
• LOC100505664
• 227140_at
• inhibin, beta A
• 231467_at
• —
• 202967_at
• glutathione S-transferase alpha
• 4
• 230323_s_at
• transmembrane protein 45B
• 224471_s_at
• beta-transducin repeat
• containing E3 ubiquitin protein
• ligase
• 202708_s_at
• histone cluster 2, H2be
• 242871_at
• progestin and adipoQ receptor
• family member V
• 205627_at
• cytidine deaminase
• 235542_at
• tet methylcytosine dioxygenase
• 3
• 240410_at
• —
• 236656_s_at
• uncharacterized
• LOC100288911
• 206164_at
• chloride channel accessory 2
• 203159_at
• glutaminase
• 224991_at
• c-Maf inducing protein
• 204258_at
• chromodomain helicase DNA
• binding protein 1
• 228249_at
• chromosome 11 open reading
• frame 74
• 229013_at
• uncharacterized LOC145783
• platelet-activating factor
• 211547_s_at
• acetylhydrolase lb, regulatory
• subunit 1 (45kDa)
• 226863_at
• family with sequence similarity
• 110, member C
• 208161_s_at
• ATP-binding cassette, sub-
• family C (CFTR/MRP), member 3
• 214805_at
• eukaryotic translation initiation
• factor 4A1
• 229429_x_at
• uncharacterized LOC728855///
• uncharacterized LOC728875
• 202720_at
• testis derived transcript (3 LIM
• domains)
• 224995_at
• spire homolog 1 (Drosophila)
• 214771_x_at
• myosin phosphatase Rho
• interacting protein
• 201939_at
• polo-like kinase 2
• 238587_at
• ubiquitin associated and SH3
• domain containing B
• 232113_at
• —
• 208690_s_at
• PDZ and LIM domain 1
• 201464_x_at
• jun proto-oncogene
• 236657_at
• uncharacterized
• LOC100288911
• 215541_s_at
• diaphanous homolog 1
• (Drosophila)
• 238028_at
• chromosome 6 open reading
• frame 132
• 226893_at
• v-abl Abelson murine leukemia
• viral oncogene homolog 2
• 237576_x_at
• uncharacterized
• LOC100506480
• 1552256_a_at
• scavenger receptor class B,
• member 1
• 215255_at
• immunoglobulin superfamily,
• member 9B
• 1557258_a_at
• B-cell CLL/lymphoma 10
• 240623_at
• —
• solute carrier family 6
• 228754_at
• (neurotransmitter transporter,
• taurine), member 6
• 217257_at
• SH3-domain binding protein 2
• 241036_at
• —
• 242553_at
• ATP-binding cassette, sub-
• family C (CFTR/MRP), member 3
• 239358_at
• —
• 210868_s_at
• ELOVL fatty acid elongase 6
• platelet-activating factor
• 200815_s_at
• acetylhydrolase lb, regulatory
• subunit 1 (45kDa)
• 208436_s_at
• interferon regulatory factor 7
• 208138_at
• gastrin
• 241780_at
• —
• 200730_s_at
• protein tyrosine phosphatase
• type IVA, member 1
• 219697_at
• heparan sulfate (glucosamine)
• 3-0-sulfotransferase 2
• 201693_s_at
• early growth response 1
• 218847_at
• insulin-like growth factor 2
• mRNA binding protein 2
• 230469_at
• rhotekin 2
• 209917_s_at
• TP53 target 1 (non-protein
• coding)
• 224329_s_at
• cornifelin
• 212253_x_at
• dystonin///dystonin-like
• 238058_at
• uncharacterized LOC150381
• 239334_at
• Extended synaptotagmin-like
• protein 2
• 222271_at
• —
• 216718_at
• long intergenic non-protein
• coding RNA 302
• 219076_s_at
• peroxisomal membrane protein
• 2, 22kDa
• 204475_at
• matrix metallopeptidase 1
• (interstitial collagenase)
• 221185_s_at
• IQ motif containing G
• 203586_s_at
• ADP-ribosylation factor-like 4D
• nuclear casein kinase and
• 217802_s_at
• cyclin-dependent kinase
• substrate 1
• 205767_at
• epiregulin
• 228360_at
• LY6/PLAUR domain containing
• 6B
• 228917_at
• —
• 228748_at
• CD59 molecule, complement
• regulatory protein
• 219632_s_at
• sedoheptulokinase///transient
• receptor potential cation
• channel, subfamily V, member
• 238715_at
• Uncharacterized LOC646014
• 218810_at
• zinc finger CCCH-type
• containing 12A
• 225177_at
• RAB11 family interacting
• protein 1 (class I)
• 224454_at
• ethanolamine kinase 1
• 209498_at
• carcinoembryonic antigen-
• related cell adhesion molecule
• 1 (biliary glycoprotein)
• 1557257_at
• B-cell CLL/lymphoma 10
• 225133_at
• Kruppel-like factor 3 (basic)
• 202340_x_at
• nuclear receptor subfamily 4,
• group A, member 1
• 1556545_at
• —
• 212474_at
• AVL9 homolog (S. cerevisiase)
• 210241_s_at
• TP53 target 1 (non-protein
• coding)
• 243543_at
• —
• 239132_at
• nitric oxide synthase 1
• (neuronal)
• 222757_s_at
• sterile alpha motif and leucine
• zipper containing kinase AZK
• 201194_at
• selenoprotein W, 1
• 229874_x_at
• uncharacterized
• LOC100506687
• 202557_at
• heat shock protein 70kDa
• family, member 13
• 239669_at
• —
• 231907_at
• v-abl Abelson murine leukemia
• viral oncogene homolog 2
• 229074_at
• EH-domain containing 4
• 205428_s_at
• calbindin 2
• 205822_s_at
• 3-hydroxy-3-methylglutaryl-CoA
• synthase 1 (soluble)
• 210869_s_at
• melanoma cell adhesion
• molecule
• 225665_at
• sterile alpha motif and leucine
• zipper containing kinase AZK
• 212781_at
• retinoblastoma binding protein
• 6
• 232355_at
• small nucleolar RNA, C/D box
• 114-3
• 213288_at
• membrane bound 0-acyltransferase
• domain containing 2
• 221666_s_at
• PYD and CARD domain
• containing
• 203072_at
• myosin IE
• 215465_at
• ATP-binding cassette, sub-family A
• (ABC1), member 12
• 224453_s_at
• ethanolamine kinase 1
• 216935_at
• long intergenic non-protein
• coding RNA 302
• 209086_x_at
• melanoma cell adhesion
• molecule
• 218833_at
• sterile alpha motif and leucine
• zipper containing kinase AZK
• 209377_s_at
• high mobility group
• nucleosomal binding domain 3
• 223519_at
• sterile alpha motif and leucine
• zipper containing kinase AZK
• 210138_at
• regulator of G-protein signaling
• 20
• 1558845_at
• uncharacterized
• LOC100506089
• 201819_at
• scavenger receptor class B,
• member 1
• 204310_s_at
• natriuretic peptide receptor
• B/guanylate cyclase B
• (atrionatriuretic peptide
• receptor B
• 239377_at
• eukaryotic translation initiation
• factor 1A domain containing
• 224611_s_at
• DnaJ (Hsp40) homolog,
• subfamily C, member 5
• 219155_at
• phosphatidylinositol transfer
• protein, cytoplasmic 1
• 227163_at
• glutathione S-transferase
• omega 2
• 209633_at
• protein phosphatase 2,
• regulatory subunit B″, alpha
• 219681_s_at
• RAB11 family interacting
• protein 1 (class I)
• 221860_at
• heterogeneous nuclear
• ribonucleoprotein L
• 243296_at
• Nicotinamide
• phosphoribosyltransferase
• 237133_at
• —
• 1556000_s_at
• BTB (POZ) domain containing 7
• 204681_s_at
• Rap guanine nucleotide
• exchange factor (GEF) 5
• 215726_s_at
• cytochrome b5 type A
• (microsomal)
• 210886_x_at
• TP53 target 1 (non-protein
• coding)
• 226597_at
• receptor accessory protein 6
• 204995_at
• cyclin-dependent kinase 5,
• regulatory subunit 1 (p35)
• 236119_s_at
• small proline-rich protein 2G
• 219228_at
• zinc finger protein 331
• 234971_x_at
• phospholipase C, delta 3
• 201127_s_at
• ATP citrate lyase
• 226880_at
• Nuclear casein kinase and
• cyclin-dependent kinase
• substrate 1
• 209383_at
• DNA-damage-inducible
• transcript 3
• 204168_at
• microsomal glutathione S-
• transferase 2
• 239670_at
• WNK lysine deficient protein
• kinase 2
• 208512_s_at
• myeloid/lymphoid or mixed-
• lineage leukemia (trithorax homolog,
• Drosophila);
• translocate
• 213281_at
• Jun proto-oncogene
• 218310_at
• potassium channel
• tetramerisation domain
• containing 7//I RAB guanine
• nucleotide exchan
• 205151_s_at
• TLR4 interactor with leucine-rich
• repeats
• 218217_at
• serine carboxypeptidase 1
• 205055_at
• integrin, alpha E (antigen
• CD103, human mucosal
• lymphocyte antigen 1;
• alpha
• polypeptide
• 215009_s_at
• THAP9 antisense RNA 1 (non-
• protein coding)
• 227484_at
• SLIT-ROBO Rho GTPase
• activating protein 1
• 239769_at
• Cadherin 11, type 2, OB-cadherin
• 230360_at
• (osteoblast) gliomedin
• 227112_at
• transmembrane and coiled-coil
• domain family 1
• 201482_at
• quiescin 06 sulfhydryl oxidase
• 1
• 210337_s_at
• ATP citrate lyase
• 203911_at
• RAP1 GTPase activating
• protein
• 206683_at
• zinc finger protein 165
• 202935_s_at
• SRY (sex determining region
• Y)-box 9
• 218951_s_at
• phosphatidylinositol-specific
• phospholipase C, X domain
• containing 1
• 233488_at
• ribonuclease, RNase A family, 7
• 202562_s_at
• chromosome 14 open reading
• frame 1
• 208745_at
• ATP synthase, H+ transporting,
• mitochondrial Fo complex,
• subunit G
• 236078_at
• KIAA1609
• 226226_at
• transmembrane protein 45B
• 213854_at
• synaptogyrin 1
• 243955_at
• —
• 222111_at
• family with sequence similarity
• 63, member B
• 1560296_at
• —
• 240038_at
• —
• 211372_s_at
• interleukin 1 receptor, type II
• 202672_s_at
• activating transcription factor 3
• 218717_s_at
• leprecan-like 1
• 228366_at
• —
• 230516_at
• Mitochondrial assembly of
• ribosomal large subunit 1
• 201920_at
• solute carrier family 20
• (phosphate transporter),
• member 1
• 209632_at
• protein phosphatase 2,
• regulatory subunit B″, alpha
• 207367_at
• ATPase, H+/K+ transporting,
• nongastric, alpha polypeptide
• 1557256_a_at
• —
• 200811_at
• cold inducible RNA binding
• protein
• 205201_at
• GLI family zinc finger 3
• 227724_at
• uncharacterized LOC0728190
• 205403_at
• interleukin 1 receptor, type II
• 242827_x_at
• —
• 228084_at
• phospholipase A2, group XIIA
• 209365_s_at
• extracellular matrix protein 1
• 243279_at
• —
• 224946_s_at
• coiled-coil domain containing
• 115
• 218708_at
• NTF2-like export factor 1
• 1560531_at
• late cornified envelope 1B
• 207761_s_at
• methyltransferase like 7A
• 206011_at
• caspase 1, apoptosis-related
• cysteine peptidase
• 213703_at
• long intergenic non-protein
• coding RNA 342
• 224595_at
• solute carrier family 44,
• member 1
• 224613_s_at
• DnaJ (Hsp40) homolog,
• subfamily C, member 5
• 212504_at
• DIP2 disco-interacting protein 2
• homolog C (Drosophila)
• 213682_at
• nucleoporin 50kDa
• 205247_at
• notch 4
• 228235_at
• uncharacterized protein
• MGC16121
• 242873_at
• —
• 205960_at
• pyruvate dehydrogenase
• kinase, isozyme 4
• 230494_at
• solute carrier family 20
• (phosphate transporter),
• member 1
• 221260_s_at
• cysteine-serine-rich nuclear
• protein 2
• 224480_s_at
• 1-acylglycerol-3-phosphate 0-
• acyltransferase 9
• 210180_s_at
• transformer 2 beta homolog
• (Drosophila)
• 204621_s_at
• nuclear receptor subfamily 4,
• group A, member 2
• 217863_at
• protein inhibitor of activated
• STAT, 1
• 236423_at
• —
• 223421_at
• cysteine/histidine-rich 1
• 220272_at
• basonuclin 2
• 201791_s_at
• 7-dehydrocholesterol reductase
• 215574_at
• —
• 224328_s_at
• late cornified envelope 3D
• 211828_s_at
• TRAF2 and NCK interacting
• kinase
• 58367_s_at
• zinc finger protein 419
• 218950_at
• ArfGAP with RhoGAP domain,
• ankyrin repeat and PH domain
• 3
• 1552703_s_at
• caspase recruitment domain
• family, member 16///caspase
• 1, apoptosis-related cysteine
• 219687_at
• hedgehog acyltransferase
• 232127_at
• chloride channel, voltage-sensitive 5
• 218377_s_at
• RWD domain containing 2B
• 210335_at
• Ras association (RaIGDS/AF-6)
• domain family (N-terminal)
• member 9
• 227927_at
• —
• 227224_at
• Ral GEF with PH domain and
• SH3 binding motif 2
• 224778_s_at
• TAO kinase 1
• 229566_at
• WDNM1-like pseudogene
• 202734_at
• thyroid hormone receptor
• interactor 10
• 201851_at
• SH3-domain GRB2-like 1
• 237337_at
• —
• 37152_at
• peroxisome proliferator-activated receptor
• delta
• 209687_at
• chemokine (C-X-C motif) ligand 12
• 203152_at
• mitochondrial ribosomal protein
• L40
• 201627_s_at
• insulin induced gene 1
• 232593_at
• neuralized homolog 3
• (Drosophila) pseudogene
• 224769_at
• TAO kinase 1
• 209702_at
• fat mass and obesity associated
• 204546_at
• KIAA0513
• 232224_at
• mannan-binding lectin serine
• peptidase 1 (C4/C2 activating
• component of Ra-reactive fac
• 239930_at
• UDP-N-acetyl-alpha-D-galactosamine:
• polypeptide N-acetylgalactosaminyl-
• transferase 2 (Gal
• 203178_at
• glycine amidinotransferase (L-arginine:
• glycine amidinotransferase)
• 235782_at
• —
• 218181_s_at
• mitogen-activated protein
• kinase kinase kinase kinase 4
• 233520_s_at
• cardiomyopathy associated 5
• 213456_at
• sclerostin domain containing 1
• 219528_s_at
• B-cell CLL/lymphoma 11B (zinc
• finger protein)
• 224945_at
• BTB (POZ) domain containing 7
• 214866_at
• plasminogen activator,
• urokinase receptor
• 209941_at
• receptor (TNFRSF)-interacting
• serine-threonine kinase 1
• 226029_at
• yang-like 2 (van gogh,
• Drosophila)
• 212596_s_at
• HMG box domain containing 4
• 229873_at
• potassium channel
• tetramerisation domain
• containing 21
• 226392_at
• RAS p21 protein activator 2
• 226005_at
• ubiquitin-conjugating enzyme
• E2G 1
• 214445_at
• elongation factor, RNA
• polymerase II, 2
• 227680_at
• zinc finger protein 326
• 227786_at
• mediator complex subunit 30
• 222067_x_at
• histone cluster 1, H2bd
• 1569106_s_at
• SET domain containing 5
• 231785_at
• neurotrophin 4
• 223937_at
• forkhead box P1
• 1558685_a_at
• uncharacterized protein
• BC009467
• 211965_at
• zinc finger protein 36, C3H
• type-like 1
• 39549_at
• neuronal PAS domain protein 2
• 203800_s_at
• mitochondrial ribosomal protein
• S14
• 1556321_a_at
• —
• 212321_at
• sphingosine-1-phosphate lyase
• 1
• 222154_s_at
• spermatogenesis associated,
• serine-rich 2-like
• 218774_at
• decapping enzyme, scavenger
• 212268_at
• serpin peptidase inhibitor, clade
• B (ovalbumin), member 1
• 213134_x_at
• BTG family, member 3
• 230669_at
• RAS p21 protein activator 2
• 1559901_s_at
• long intergenic non-protein
• coding RNA 478
• 225298_at
• paroxysmal nonkinesigenic
• dyskinesia
• 242558_at
• —
• 226043_at
• G-protein signaling modulator 1
• 210236_at
• protein tyrosine phosphatase,
• receptor type, f polypeptide
• (PTPRF), interacting protein
• 214066_x_at
• natriuretic peptide receptor
• B/guanylate cyclase B
• (atrionatriuretic peptide receptor
• B
• 240024_at
• SEC14-like 2 (S. cerevisiae)
• 235462_at
• Cytoplasmic polyadenylation
• element binding protein 2
• 1554015_a_at
• chromodomain helicase DNA
• binding protein 2
• 235347_at
• leucine-rich repeats and
• calponin homology (CH)
• domain containing 3
• 230847_at
• Werner helicase interacting
• protein 1
• 201427_s_at
• selenoprotein P, plasma, 1
• 1557905_s_at
• CD44 molecule (Indian blood
• group)
• 219084_at
• nuclear receptor binding SET
• domain protein 1
• 206176_at
• bone morphogenetic protein 6
• 219826_at
• zinc finger protein 419
• 212356_at
• KH and NYN domain containing
• 218909_at
• ribosomal protein S6 kinase,
• 52kDa, polypeptide 1
• 230555_s_at
• Mediator complex subunit 30
• 212687_at
• LIM and senescent cell antigen-
• like domains 1
• 203098_at
• chromodomain protein, Y-like
• 229054_at
• zinc finger protein 36, C3H
• type-like 1
• 236039_at
• LY6/PLAUR domain containing
• 5
• 209661_at
• kinesin family member C3
• 209560_s_at
• delta-like 1 homolog
• (Drosophila)
• 225812_at
• chromosome 6 open reading
• frame 225
• 227829_at
• glycosyltransferase-like 1B
• 238623_at
• —
• 229415_at
• cytochrome c, somatic
• 209222_s_at
• oxysterol binding protein-like 2
• 1555809_at
• cysteine-rich secretory protein
• LCCL domain containing 2
• 204567_s_at
• ATP-binding cassette, sub-family
• G (WHITE), member 1
• 232277_at
• solute carrier family 28 (sodium-
• coupled nucleoside
• transporter), member 3
• 237197_at
• —
• 225209_s_at
• ubiquitin-conjugating enzyme
• E2, J2
• 231916_at
• nitric oxide synthase 1
• (neuronal)
• 212279_at
• transmembrane protein 97
• 204862_s_at
• NME/NM23 nucleoside
• diphosphate kinase 3
• 230483_at
• —
• 212856_at
• GRAM domain containing 4
• 224650_at
• mal, T-cell differentiation protein
• 2 (gene/pseudogene)
• 202963_at
• regulatory factor X, 5
• (influences HLA class II
• expression)
• 225320_at
• mitochondrial calcium uniporter
• 236274_at
• eukaryotic translation initiation
• factor 3, subunit B
• 209780_at
• putative homeodomain
• transcription factor 2
• potassium channel
• 218823_s_at
• tetramerisation domain
• containing 9
• 227787_s_at
• mediator complex subunit 30
• 230296_at
• chromosome 16 open reading
• frame 52
• 222892_s_at
• transmembrane protein 40
• 210610_at
• carcinoembryonic antigen-related
• cell adhesion molecule1 (biliary
• glycoprotein)
• 230031_at
• heat shock 70kDa protein 5
• (glucose-regulated protein,
• 78kDa)
• 238477_at
• kinesin family member 1C
• 209409_at
• growth factor receptor-bound
• protein 10
• 217995_at
• sulfide quinone reductase-like
• (yeast)
• 226873_at
• family with sequence similarity
• 63, member B
• 1553722_s_at
• ring finger protein 152
• 204710_s_at
• WD repeat domain,
• phosphoinositide interacting 2
• 212653_s_at
• EH domain binding protein 1
• 203979_at
• cytochrome P450, family 27,
• subfamily A, polypeptide 1
• 244350_at
• myosin X
• 223233_s_at
• cingulin
• 1555967_at
• —
• 214355_x_at
• CTAGE family, member 15,
• pseudogene///CTAGE family,
• member 4///CTAGE family,
• member
• 214469_at
• histone cluster 1, H2ab///
• histone cluster 1, H2ae
• 212472_at
• microtubule associated
• monoxygenase, calponin and
• LIM domain containing 2
• 228115_at
• family with sequence similarity
• 59, member A
• 228964_at
• PR domain containing 1, with
• ZNF domain
• 230027_s_at
• mitochondrial ribosomal protein
• L43
• 207318_s_at
• cyclin-dependent kinase 13
• 221689_s_at
• phosphatidylinositol glycan
• anchor biosynthesis, class P
• 219270_at
• ChaC, cation transport regulator
• homolog 1 (E. coli)
• 225299_at
• myosin VB
• 239770_at
• extended synaptotagmin-like
• protein 3
• 226399_at
• DnaJ (Hsp40) homolog,
• subfamily B, member 14
• 226656_at
• cartilage associated protein
• 228852_at
• endosulfine alpha
• 206239_s_at
• serine peptidase inhibitor, Kazal
• type 1
• 210993_s_at
• SMAD family member 1
• 238462_at
• ubiquitin associated and SH3
• domain containing B
• 211962_s_at
• zinc finger protein 36, C3H
• type-like 1
• 224666_at
• non-SMC element 1 homolog
• (S. cerevisiae)
• 239028_at
• LY6/PLAUR domain containing
• 6
• 213577_at
• squalene epoxidase
• 202011_at
• tight junction protein 1 (zona
• occludens 1)
• 212254_s_at
• dystonin///dystonin-like
• 221701_s_at
• stimulated by retinoic acid gene
• 6 homolog (mouse)
• 239576_at
• microtubule associated tumor
• suppressor 1
• 234418_x_at
• CD44 molecule (Indian blood
• group)
• 227985_at
• uncharacterized
• LOC100506098
• 213462_at
• neuronal PAS domain protein 2
• 224975_at
• nuclear factor I/A
• 225990_at
• Boc homolog (mouse)
• 240616_at
• —
• 219911_s_at
• solute carrier organic anion
• transporter family, member 4A1
• 224970_at
• nuclear factor I/A
• 214623_at
• F-box and WD repeat domain
• containing 4 pseudogene 1
• 239478_x_at
• chromosome 14 open reading
• frame 118
• 226909_at
• zinc finger protein 518B
• 208670_s_at
• EP300 interacting inhibitor of
• differentiation 1
• 206192_at
• corneodesmosin
• 222173_s_at
• TBC1 domain family, member 2
• 228450_at
• pleckstrin homology domain
• containing, family A member 7
• 1558097_at
• proline rich 14-like
• 219373_at
• dolichyl-phosphate
• mannosyltransferase
• polypeptide 3
• 230388_s_at
• KANSL1 antisense RNA 1 (non-
• protein coding)
• 207098_s_at
• mitofusin 1
• 223484_at
• chromosome 15 open reading
• frame 48
• 244804_at
• sequestosome 1
• 229679_at
• chromosome 12 open reading
• frame 76
• 225826_at
• methylmalonic aciduria
• (cobalamin deficiency) cbIB
• type
• 213352_at
• transmembrane and coiled-coil
• domain family 1
• 211883_x_at
• carcinoembryonic antigen-related
• cell adhesion molecule 1 (biliary
• glycoprotein)
• 210387_at
• histone cluster 1, H2bc///
• histone cluster 1, H2be///
• histone cluster 1, H2bf///his
• 210916_s_at
• CD44 molecule (Indian blood
• group)
• 221432_s_at
• solute carrier family 25
• (mitochondrial iron transporter),
• member 28
• 218487_at
• aminolevulinate dehydratase
• 223264_at
• mesoderm development
• candidate 1
• 206356_s_at
• guanine nucleotide binding
• protein (G protein), alpha
• activating activity polypeptide,
• 218097_s_at
• CUE domain containing 2
• 228001_at
• transmembrane protein 50B
• 212441_at
• K1AA0232
• 201854_s_at
• ATM interactor
• 121_at
• paired box 8
• 222143_s_at
• myotubularin related protein 14
• 1558002_at
• Serine/threonine kinase
• receptor associated protein
• 226040_at
• —
• 226141_at
• coiled-coil domain containing
• 149
• 1556567_at
• nucleosome assembly protein
• 1-like 4
• 226263_at
• small nuclear ribonucleoprotein
• 48kDa (U11/U12)
• 212074_at
• Sad1 and UNC84 domain
• containing 1
• 227387_at
• Non-SMC element 4 homolog A
• (S. cerevisiae)
• 232795_at
• —
• 203936_s_at
• matrix metallopeptidase 9
• (gelatinase B, 92kDa
• gelatinase, 92kDa type IV
• collagenase)
• 225033_at
• ST3 beta-galactoside alpha-2,3-
• sialyltransferase 1
• 209109_s_at
• tetraspanin 6
• 213351_s_at
• transmembrane and coiled-coil
• domain family 1
• 203047_at
• serine/threonine kinase 10
• 220721_at
• zinc finger protein 614
• 1556127_at
• DIP2 disco-interacting protein 2
• homolog A (Drosophila)
• 215016_x_at
• dystonin///dystonin-like
• 206576_s_at
• carcinoembryonic antigen-related
• cell adhesion molecule
• 1 (biliary glycoprotein)
• 240674_at
• jumonji, AT rich interactive
• domain 2
• 225646_at
• cathepsin C
• 1554010_at
• N-deacetylase/N-sulfotransferase
• (heparan glucosaminyl) 1
• 204100_at
• thyroid hormone receptor, alpha
• 221840_at
• protein tyrosine phosphatase,
• receptor type, E
• 209078_s_at
• thioredoxin 2
• 218530_at
• formin homology 2 domain
• containing 1
• 235434_at
• —
• 230063_at
• zinc finger protein 264
• 40420_at
• serine/threonine kinase 10
• 221027_s_at
• phospholipase A2, group XIIA
• 244202_at
• —
• 212108_at
• Fas associated factor family
• member 2
• 204294_at
• aminomethyltransferase
• 225503_at
• dehydrogenase/reductase
• (SDR family) X-linked
• 212810_s_at
• solute carrier family 1
• (glutamate/neutral amino acid
• transporter), member 4
• 214814_at
• YTH domain containing 1
• 228468_at
• microtubule associated
• serine/threonine kinase-like
• 209108_at
• tetraspanin 6
• 220444_at
• zinc finger protein 557
• 206172_at
• interleukin 13 receptor, alpha 2
• 225002_s_at
• sulfatase modifying factor 2
• 212205_at
• H2A histone family, member V
• 228851_s_at
• endosulfine alpha
• 209048_s_at
• zinc finger, MYND-type
• containing 8
• 211846_s_at
• poliovirus receptor-related 1
• (herpesvirus entry mediator C)
• 238909_at
• S100 calcium binding protein
• A10
• 205503_at
• protein tyrosine phosphatase,
• non-receptor type 14
• 243829_at
• v-raf murine sarcoma viral
• oncogene homolog B1
• 244379_at
• —
• 223251_s_at
• ankyrin repeat domain 10
• 202633_at
• topoisomerase (DNA) II binding
• protein 1
• 214502_at
• histone cluster 1, H2bj
• 221773_at
• ELK3, ETS-domain protein
• (SRF accessory protein 2)
• 41858_at
• post-GPI attachment to proteins
• 2
• 212850_s_at
• low density lipoprotein receptor-
• related protein 4
• 223408_s_at
• —
• 214472_at
• histone cluster 1, H2ad///
• histone cluster 1, H3a///
• histone cluster 1, H3b///histo
• 225647_s_at
• cathepsin C
• 1559977_a_at
• solute carrier family 25,
• member 34
• 211347_at
• CDC14
• homolog B (S. cerevisiae)
• 1558208_at
• —
• 227570_at
• transmembrane protein 86A
• 227492_at
• occludin pseudogene///
• occludin
• 1558778_s_at
• MKL/myocardin-like 2
• 31637_s_at
• nuclear receptor subfamily 1,
• group D, member 1///thyroid
• hormone receptor, alpha
• 229190_at
• uncharacterized
• LOC100507376
• 236188_s_at
• Nucleosome assembly protein
• 1-like 4
• 212503_s_at
• DIP2 disco-interacting protein 2
• homolog C (Drosophila)
• 204760_s_at
• nuclear receptor subfamily 1,
• group D, member 1///thyroid
• hormone receptor, alpha
• 212099_at
• ras homolog family member B
• 214873_at
• low density lipoprotein receptor-
• related protein 5-like
• 228181_at
• solute carrier family 30 (zinc
• transporter), member 1
• 212763_at
• calmodulin regulated spectrin-
• associated protein family,
• member 2
• 226285_at
• cell cycle associated protein 1
• 213567_at
• karyopherin alpha 4 (importin
• alpha 3)
• 203927_at
• nuclear factor of kappa light
• polypeptide gene enhancer in
• B-cells inhibitor, epsilon
• 208523_x_at
• histone cluster 1, H2bc///
• histone cluster 1, H2be///
• histone cluster 1, H2bf///his
• 219389_at
• sushi domain containing 4
• 202329_at
• c-src tyrosine kinase
• 238523_at
• kelch-like 36 (Drosophila)
• 1565016_at
• protein arginine
• methyltransferase 1
• 226409_at
• TBC1 domain family, member
• 20
• 229926_at
• microRNA 3682
• 208527_x_at
• histone cluster 1, H2bc///
• histone cluster 1, H2be///
• histone cluster 1, H2bf///his
• 223598_at
• RAD23 homolog B (S.
• cerevisiae)
• 243797_at
• serine/threonine kinase 17b
• 203317_at
• pleckstrin and Sec7 domain
• containing 4
• 230965_at
• ubiquitin specific peptidase 2
• 208490_x_at
• histone cluster 1, H2bc///
• histone cluster 1, H2be///
• histone cluster 1, H2bf///his
• 235514_at
• aspartic peptidase, retroviral-
• like 1
• 209098_s_at
• jagged 1
• 1554229_at
• CREB3 regulatory factor
• 209398_at
• histone cluster 1, H1c
• 202629_at
• amyloid beta precursor protein
• (cytoplasmic tail) binding
• protein 2
• 203428_s_at
• ASF1 anti-silencing function 1
• homolog A (S. cerevisiae)
• 238005_s_at
• SIN3 transcription regulator
• homolog A (yeast)
• 214455_at
• histone cluster 1, H2bc///
• histone cluster 1, H2be///
• histone cluster 1, H2bf///his
• 214073_at
• cortactin
• 203140_at
• B-cell CLL/lymphoma 6
• 232150_at
• —
• 208546_x_at
• histone cluster 1, H2bh
• 243446_at
• ajuba LIM protein
• 236207_at
• sperm specific antigen 2
• 212016_s_at
• polypyrimidine tract binding
• protein 1
• 232311_at
• Beta-2-microglobulin
• 219711_at
• zinc finger protein 586
• 208579_x_at
• H2B histone family, member S
• (pseudogene)///histone cluster
• 1, H2bk
• 239493_at
• ribosomal protein L7
• 214074_s_at
• cortactin
• 228091_at
• syntaxin 17
• 234331_s_at
• family with sequence similarity
• 84, member A
• 212372_at
• myosin, heavy chain 10, non-muscle
• Or, from genes for each of the pharmacodynamic biomarkers from the list further consisting of:
• MMP2
• ESR1
• FOS
• PCLG2
• MAPK6
• JUN
• COND1
• PPAR1
• MAPK1
• MAPK7
• CEBPA
• MAPK3
• PCLG1
• MAPK4
• MAPK12
• AKT2
• CASP3
• FOS
• HSP90AB1
• JUN
• BAG3
• CCND1
• HASP90AA1
• HSP90B1
• AKT1
• ARG2
• CCNA1
• CCND2
• CCNE2
• TNF
• BDNF
• CCNA2
• CCNE1
• CTF1
• BRAF
• ARG2
• CCND2
• TNF
• PPP3R1
• CALM3
• BDNF
• CCNE1
• PPP3CA
• PPP3R2
• CAMK1
• CCNA1
• CCNE2
• PPP3CB
• CALM1
• CAMK1D
• CCNA2
• CTF1
• PPP3CC
• CALM2
• CAMK1G
• BDNF
• CCNE1
• PPP3CC
• ORAI3
• TNF
• CCNA1
• PPP3CB
• CAMK2D
• CCND2
• CALM3
• PPP3CA
• CACNA2D4
• CHRNB3
• HDAC10
• PPP3CB
• CACNB1
• CHRNB4
• HDAC11
• PPP3CC
• CACNB2
• CHRND
• HDAC2
• PPP3R1
• CACNB3
• CHRNE
• HDAC3
• PPP3R2
• CACNB4
• CHRNG
• HDAC4
• ATP2C1
• CACNG1
• GRIA1
• HDAC5
• CACNA1A
• CHRFAM7A
• GRIA2
• HDAC6
• CACNA1B
• CHRNA1
• GRIA3
• HDAC7
• CACNA1C
• CHRNA10
• GRIA4
• HDAC8
• CACNA1D
• CHRNA2
• GRIK1
• HDAC9
• CACNA1F
• CHRNA3
• GRIN1
• HTR3A
• CACNA1H
• CHRNAS
• GRIN2B
• SLC8A1
• CACNA2I
• CHRNA6
• GRIN2C
• TNNC1
• CACNA1G
• CHRNA4
• GRIN2A
• RYR1
• CACNA1S
• CHRNA7
• GRIN2D
• CACNA2D1
• CHRNA9
• GRIN3A
• CACNA2D2
• CHRNB1
• GRIN3B
• CACNA2D3
• CHRNB2
• HDAC1
• CACNA2D1
• CHRNA9
• GRIN3A
• CACNA2D2
• CHRNB1
• GRIN3B
• CACNA2D3
• CHRNB2
• HDACC1
• MAP15
• AKT1
• MOS3
• HSP90B1
• CASP3
• AKT2
• HSP90AA1
• Hsp84-2
• HSPA8
• AKT3
• HSP90AB1
• Hsp84-3
• BAG3
• CEBPA
• MAPK3
• MAPK1
• MAPK7
• CA9
• CALR
• CAMK2A
• CAMK4
• ORAI3
• TRPC3
• TRPC7
• CAMK2B
• NOS2
• STIM1
• TRPC4
• BRAF
• CAMK2D
• ORAI2
• STIM2
• TRPC5
• CA9
• CAMK2G
• ORAI2
• TRPC1
• TRPC6
• CALR
• CAMK1
• ORAI2
• BRAF
• CAMK2G
• STIM2
• CALR
• Or, from genes for each of the pharmacodynamic biomarkers from the list further consisting of:
• ABCC5
• CYHR1
• HIST3H2A
• POU2F3
• ATP6V1B1
• DEPTOR
• HOXB13
• RAMP1
• ATXN3
• DNAL4
• ING4
• SEMA3G
• BCAS1
• EIF4A2
• OVGP1
• SEPP1
• BCL2L11
• EPHX2
• PCMTD1
• SIDT2
• CALCOCO1
• ERBB3
• PCMTD2
• AREG
• CAPN13
• HIST1H2AC
• PDIA4
• BTG3
• CRBN
• HIST1H2BD
• PLEKHG4
• CEBPG
• CORO1C
• IFRD1
• PFKP
• DLEU2
• IMPAD1
• PNPT1
• DPH3
• KLK6
• PSMC4
• EIF5
• KPNA4
• RPS6KA3
• ENO2
• LRP8
• S100A2
• HN1
• MALL
• SERPINB5
• HSP90AA1
• MTHFD1L
• SERPINB8
• HSPA4L
• PADI1
• SLC7A1
• SRXN1
• TIPIN;
• and
• d) identifying, using the calculated signature scores and quantitated responses, each of the pharmacodynamics biomarkers of each of the signature pathways by at least 3 or more genes listed in 1c).