Node-Structured Integrative Gaussian Graphical Model Guided by Pathway Information

Table 3

The pathway sets from the Molecular Signatures Database (MSigDB) analyzed in the nsiGGM. (Note: asterisks represent pathway genes identified by only the nsiGGM not by JGGM.)

Pathway 1: extracellular region (11 genes)
SERPINA5  MMP13, EREG  HAPLN1  CP  S100A7, CRISP3, SCGB1D2, COL11A1, TFPI2  MSMB
Pathway 2: membrane part (11 genes)
EREG  PTPRN2, CLCA2, NPY1R, TRPA1, TNFRSF17, AGTR1, CEACAM6, SLC1A1  PROM1, HSD17B2
Pathway 3: membrane (14 genes)
EREG  PTPRN2, STEAP4  GRIA2, CLCA2, NPY1R, TRPA1, TNFRSF17, AGTR1, SERPINA5  CEACAM6, SLC1A1  PROM1, HSD17B2
Pathway 4: cytoplasm (13 genes)
OGN, CA2, MYBPC1, NLRP2, MAOB, UGT2B28, S100A7, CRISP3, PEG10, S100P, FABP4, CLGN, HSD17B2
Pathway 5: plasma membrane (12 genes)
AGTR1, CEACAM6, EREG  PTPRN2, SLC1A1  STEAP4  PROM1, GRIA2, CLCA2, NPY1R, TRPA1, TNFRSF17
Pathway 6: system development (12 genes)
EREG  TFAP2B, CALML5, KRT15, KRT14, DLX2  BMPR1B, MSTN, S100A7, NKX2-2, COL11A1, COL2A1
Pathway 7: signal transduction (15 genes)
EREG  CALML5 , GRIA2, TRH  PGR, NPY1R, CGA  CRABP1  TNFRSF17, AGTR1, CEACAM6, PEG10, GRB14  STC2  NMU
Pathway 8: multicellular organismal development (15 genes)
EREG  TFAP2B, CALML5, KRT15, KRT14, DLX2, BMPR1B, MSTN, S100A7, NKX2-2, COL11A1, EHF, COL2A1  CRABP1  TNFRSF17
Pathway 9: cell signaling (11 genes)
PGR, CEACAM6, EREG  PCSK1  CXCL13, SLC1A1  CGA  STC2  GAD1  GRIA2, TRH
Pathway 10: anatomical structure development (13 genes)
EREG  TFAP2B, CALML5, KRT15, KRT14, DLX2  BMPR1B, MSTN, S100A7, NKX2-2, COL11A1  COL2A1, EHF
Pathway 11: organ development (11 genes)
MSTN, EREG  CALML5, S100A7, KRT15, KRT14, NKX2-2, DLX2  COL11A1, COL2A1  BMPR1B