Table 3 Pathway analysis.

From: Forkhead box F1 induces columnar phenotype and epithelial-to-mesenchymal transition in esophageal squamous cells to initiate Barrett’s like metaplasia

Top network

Score

Focus molecules

Moleculesa

Cell Cycle, Cell-To-Cell Signaling and Interaction, Gene Expression

22

10

6beta-hydroxytestosterone, ABCC8, Akt, BPHL, CROT, CSHL1, CUX2, Cyp2a1, Cyp2a12/Cyp2a22, Cyp2d9 (includes others), DCAF8, EPO, GCC2, GH1, GNAQ, HNF4A, HSD11B1, IGFALS, Insulin, LOC299282, LTA4H, MT-CYB, MYH7, NHLRC3, NRF1, Proinsulin, RIMS2, SERP1, SLC16A14, Slco1a1, TEF, TMEM260, TOX, UQCRHL, ZNF701

Cellular Function and Maintenance, Developmental Disorder, Neurological Disease

21

10

ADRM1, AKT1S1, APLP1, APP, BCYRN1, Beta Tubulin, CAD, CALB1, CAST, CC2D2A, CTH, DAP, DDX21, DEF6, DOCK10, EEF1D, EMB, FMR1, FOS, GRID1, MMP13, MT-CYB, PARVA, PFDN4, POTEE/POTEF, RAC1, RELA, SEPT2, STAU1, TAF11, TFF3, TPR, UBA7, ZNF268, ZNF449

Cancer, Cellular Assembly and Organization, DNA Replication, Recombination, and Repair

21

10

AKT1S1, ASPM, ATRX, BCKDHA, CALB1, CHN1, COMT, CPE, DBP, DUT, EDA2R, ESR1, HDAC1, HDAC4, HIST1H4J, HSPA13, mir-183, MTHFD1, MYC, NCOA5, NDRG2, NFkB (complex), PAX8, PHLDB2, PSMB3, RNF4, TAF1D, TLE4, TP53, TRIM28, TWIST2, USP7, VEZF1, ZNF10, ZNF594

  1. aGenes in bold were upregulated and genes in italics were downregulated. Focus molecules are the “seed” molecules that are predicted to have the most interactions with other genes. The score refers to the total number of molecules that associate with focus molecules in that network.
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