Investigating the effect of paralogs on microarray gene-set analysis

BMC Bioinformatics

Table 3 SAM-GS GSA results

Original dataset: unique GSA results	Reduced dataset: unique GSA results
APOPTOSIS	ADIP_VS_FIBRO_DN
APOPTOSIS-GENMAPP	BCNU_GLIOMA_MGMT_48HRS_UP
APOPTOSIS_KEGG	BRCA1_SW480_DN
CELLCYCLEPATHWAY	BREAST_CANCER_ESTROGEN_SIGNALING
CHEMICALPATHWAY	DAC_PANC50_UP
FSH_HUMAN_GRANULOSA_UP	DNA_DAMAGE_SIGNALING
G1PATHWAY	DRUG_RESISTANCE_AND_METABOLISM
HSA05219_BLADDER_CANCER	G2PATHWAY
HSP27PATHWAY	HSA05040_HUNTINGTONS_DISEASE
IL4PATHWAY	OXSTRES_BREASTCA_UP
P53_BRCA1_UP	PARP_KO_UP
RACCYCDPATHWAY	PASSERINI_APOPTOSIS
SA_FAS_SIGNALING	SA_DIACYLGLYCEROL_SIGNALING SHEPARD_NEG_REG_OF_CELL_PROLIFERATION

SAM-GS results indicating functional gene sets (MSigDB:C2) significantly enriched in the expression patterns of NCI-60 cancer cell lines with wild-type p53, compared to those of p53 mutants. Only those terms exclusive to the results obtained from either the original or paralog-reduced list are shown. A threshold of FDR ≤ 0.001 was used to determine significance.

ISSN: 1471-2105