TABLE 1.

Data Sets A and F Contain Similar Patterns of Gene Expression by GSEA

Ranked Gene Subsets from Data Set A Are Enriched in Data Set F
Gene SubsetESNESNOM PFDR qFWER PNo. Enriched Genes
Down_100−0.76−1.620.0090.0090.02063
Down_200−0.73−1.590.0280.0170.036116
Down_500−0.65−1.500.0810.0520.115234
Up_1000.771.510.050.0460.10677
Up_2000.781.610.0090.0130.028141
Up_5000.721.600.0240.0130.033339
Ranked Gene Subsets from Data Set F Are Enriched in Data Set A
Gene Subset
ES
NES
NOM P
FDR q
FWER P
No. Enriched Genes
Down_100−0.71−1.640.0080.0070.01864
Down_200−0.72−1.670.0050.0080.015131
Down_500−0.69−1.650.0050.0080.012296
Up_1000.811.790.0020.0030.00462
Up_2000.711.70.0170.0050.01194
Up_5000.691.660.0270.0050.011227
  • NOTE: GSEA (see Materials and Methods) shows that the top-ranked subsets of genes in set A are significantly enriched in samples from metastatic variants from set F, and vice versa. Number of enriched genes refers to the number of genes in one gene subset that contribute positively to its enrichment in the other expression data set. Gene subsets analyzed are as follows: Up_100, Up_200, or Up_500, top 100, 200, or 500 up-regulated genes in samples from highly metastatic variants; Down_100, Down_200, or Down_500, top 100, 200, or 500 down-regulated genes in samples from highly metastatic variants. P < 0.05 and FDR score <0.25 are considered to reflect relatedness between a gene set and the comparison gene list. Note that all but one of the comparisons meet these criteria.

  • Abbreviations: ES, enrichment score; NES, normalized enrichment score; nom P, nominal P value; FDR, false discovery rate; FWER, family-wise error rate.