Table 4

GSEA tests for enrichment of HCC- and hepatitis-associated gene sets

Gene Set Name

Size

ES

NES

NOM p-value

Up-regulated in acute liver treatment

KUROKAWA_5FU_IFN_SENSITIVE_VS_RESISTANT_DN

25

0.585

1.642

0.025

WONG_IFNA_HCC_RESISTANT_VS_SENSITIVE_UP

10

0.507

1.407

0.046

Down-regulated in acute liver treatment

HBX_HEP_UP

12

-0.540

-1.460

0.038

Up-regulated in chronic liver treatment

HCC_SURVIVAL_GOOD_VS_POOR_DN

112

0.452

1.549

0.000

Down-regulated in chronic liver treatment

None

Results for gene sets representing Hepatocellular carcinoma (HCC) and hepatitis, tested for enrichment by GSEA following methylmercury treatment. Here, we test whether liver-associated sets are enriched following methylmercury exposure. Size refers to the number of genes in the set; ES and NES are the enrichment scores and normalized enrichment scores (respectively) for the set; NOM p-value is the nominal p-value for the NES. Descriptions of each set (and lists of constituent genes) can be found by searching for set names at the MSigDB [8].

Thomas et al. BMC Genomics 2011 12:66   doi:10.1186/1471-2164-12-66