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

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