Biomarker identification and trans-regulatory network analyses in esophageal adenocarcinoma and Barrett’s esophagus

Table 1 Differentially expressed transcription factors in the comparison groups in the GSE1420 dataset

Comparison group	Up-regulated TFs	Down-regulated TFs
EAC vs NE	ATF3, ATF5, CEBPB, E2F31, EGR1, EGR3, EGR4, FOXA21, HOXA10, HOXB71, MYBL2, NFIB, PPARG, RELB, SMAD6, SP3, STAT1	PAX91, RARG, SMAD2, TFAP2A, TFAP2B, TFAP2C1, FOXE1, HLF, HOXA4, HOXB2
BE vs NE	ATF3, E2F31, EPAS1, ETS2, FOS, FOSB, FOXA21, HOXB71, NFIB, PPARG, STAT1	PAX91, TFAP2B, TFAP2C1, HLF, HOXA1, HOXA4
EAC vs BE	E2F31, EGR4, FOXA21, HOXA10, HOXB71, MYBL2	PAX91, PPARD, RARG, TFAP2C1, ELK3, ETS2, FOXE1

¹Differentially expressed transcription factors, which displayed the same expression tendency among all the three comparison groups. TF: Transcription factor; EAC: Esophageal adenocarcinoma; NE: Normal esophagus; BE: Barrett's esophagus.

Table 2 Differentially expressed genes in the trans-regulatory networks existed in both GSE1420 and GSE26886 datasets

Comparison group	Up-regulated DEGs	Down-regulated DEGs
EAC vs NE	UCP2, TOP1, TIMP1, TAP1, STAT11, ST6GAL1, SOCS1, SMURF2, SLC19A1, SKIL, SERPINE1, SDC4, RELB1, RARRES3, PTPN6, PSMB9, PRKCA, PPARG1, PLAUR, PLAU, PECAM1, PDGFA, ODC1, NT5E, NR1H3, NQO1, MYBL21, MUC5AC, MTRR, MMP9, MMP7, MET, MAN2B1, LAMB1, ITGB1, ITGAV, IRF3, IRF1, IGFBP3, ICAM1, HSD17B2, HOXB71, HMGA2, HFE, HEXB, HEXA, GUSB, GBP1, GALC, F2R, ENG, EGR11, DSG2, CXCL1, COL5A2, COL1A2, COL1A1, CFTR, CD14, ATP2A3, APOE, ADAM28, A2M	TOM1, TGM1, TGFA, TFAP2C1, TFAP2A1, TALDO1, SRPX2, SNAI2, SMARCA2, SMAD21, SLC6A4, SLC13A4, SERPINB2, RORA1, RARG1, PRNP, PPL, PIM1, PEX3, PBX1, OAT, MAPT, MAPK1, LMO2, KRT5, KRT4, KRT16, KRT14, IMPA2, HSPB1, HRAS, HOXA41, HMOX1, HLF1, GSTP1, GM2A, GLUD1, FLG, FGFR3, FCER1A, ETF1, DSG3, DSG1, DBI, CYP11A1, CSTA, CRABP2, CEACAM1, CALB2, BCKDHA, ATP12A, ALDH3A2, AKR1C1, AGA, ADIPOR1, ACOX1, ACAA1
BE vs NE	UCP2, TIMP1, TGFBR2, SOCS3, REG1A, PPARG1, PLAUR, NR1H3, NQO1, MMP1, KRT18, GDF15, GBP1, FOS1, CA2, ANPEP, A2M	RORA, HOXA11, FCER1A, CYP11A1, BMP7

¹Differentially expressed transcription factors. DEGs: Differentially expressed genes; EAC: Esophageal adenocarcinoma; NE: Normal esophagus; BE: Barrett's esophagus.