Comparison of GSEA and GFA for miR-1 and miR-124 transfection data. GSEA ( A ) and GFA ( B ) were performed for the microarray data of HeLa cells transfected with miR-1, miR-124, mutant miR-124 (124mut5-6 and 124mut9-10) and chimeric miRNAs (chimiR-1/124 and chimiR-124/1) for 12 or 24 h. In GFA, we ran FAME for the two collection of leading-edge subsets, which were down-regulated (left panel) and up-regulated (right panel) in the cells transfected with miRNA relative to controls, in an enrichment direction of over-representation (enrichment, left panel) and under-representation (depletion, right panel), respectively. The distribution of GSEA normalized enrichment scores (NES) and GFA ranking [−log10( P -value)] are shown. GSEA NES and GFA ranking for miR-1 and miR-124 are indicated by red diamonds and blue circles, respectively.