Table 4

Significant pathways (FDR < 0.01) detected by the Plink set-based test.

Pathway (KEGG ID)

P

FDR


Jak-STAT signaling pathway (hsa04630)*

0.001

0.043

Chronic myeloid leukemia (hsa05220)

0.001

0.043

Small cell lung cancer (hsa05222)

0.001

0.043

TGF-beta signaling pathway (hsa04350)

0.002

0.043

Endometrial cancer (hsa05213)

0.002

0.043

Thyroid cancer (hsa05216)*

0.002

0.043

Bladder cancer (hsa05219)

0.002

0.043

Acute myeloid leukemia (hsa05221)

0.002

0.043

Cell cycle (hsa04110)

0.003

0.043

Wnt signaling pathway (hsa04310)

0.003

0.043

Fc gamma R-mediated phagocytosis (hsa04666)

0.003

0.043

Regulation of actin cytoskeleton (hsa04810)

0.003

0.043

Colorectal cancer (hsa05210)

0.003

0.043

The PGDB gene set

0.004

0.053

ErbB signaling pathway (hsa04012)

0.008

0.099


*Overlap with SRT.

Overlap with GSEA.

Jia et al. BMC Systems Biology 2012 6(Suppl 3):S13   doi:10.1186/1752-0509-6-S3-S13

Open Data