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Table 2 Highly enriched gene sets in specific combinations of signaling networks and leukemia subtypes, with the nominal p values produced by GSEA for these sets in their respective combinations

From: Computing interaction probabilities in signaling networks

Subtype Network p value Gene set
Hyperdiploid Apoptosis 0.0083 NFKB1, RELA, BCL2, PPP3CA, PPP3CB, PPP3CC, IL3RA, TNF, BAD,
    PPP3R1, AKT3, AKT1, AKT2, CHUK, TNFRSF1A, CASP7, DFFA,
    IKBKB, IKBKG, CASP3, IL3, CASP10, CSF2RB
ETV6_RUNX1 Cell cycle 0.0151 TFDP1, TFDP2, E2F1, RBP3, E2F2, E2F3, CCND3, RBL1, PRB1, RBL2,
    CCNE1, CCNE2, CDK4, CDK6, CCND1, CCND2, CCNA1, CDK2, CCNA2
T-ALL Apoptosis 0.0162 BIRC2, BIRC3, XIAP, BIRC7, CASP7, NFKB1, IL1RAP, TRADD, FASLG,
    RELA, CASP3, DFFA, FADD, CASP8, IL1R1, FAS
TCF3-PBX1 Apoptosis 0.0167 PRKACA, PRKACB, PRKACG, PRKAR1A, PRKAR1B, IL1RAP, FADD,
    PRKAR2A, PRKAR2B, PRKX, BAD, IL1A, IL1B, IL1R1, TNFRSF10B,
    TNFRSF10C, TNFRSF10D
Hypo Apoptosis 0.0484 CAPN1, CAPN2, IRAK3, IRAK1, IRAK4, MAP3K14, BCL2, TP53,
    NGF, NTRK1
Ph Cell cycle 0.088 BUB1, BUB3, CDKN2A, CDK4, CDK6, CCND1, GADD45A, GADD45B
    CCND2, CCND3, RB1, CDC45L, MCM7, MCM2, CDC25A, CDKN1A,
    MCM6, MCM5, MCM4, MCM3, CCNL1, LAT, CCNE1, CCNE2, CDK2,
    ORC3L, ORC5L, ORC4L, ORC2L, ORC1L, ORC6L, TP53, GADD45G,
    CDC2, CCNA2, CCNA1, CDKN1B, CDKN1C