Comparison of Genes Ranked by Network Connectivity and Differential Expression in the Ivanova et al data set. Ingenuity Pathway Analysis of functional enrichments in the set of genes ranked within the top 1000 by Student's t-test and k
and yet do not overlap with each other. Venn diagrams show the amount of gene overlap between the top 1000 black (pluripotency) module genes and the top 1000 genes most significantly down-regulated upon Oct4 RNAi (left); gene overlap between the top 1000 blue (differentiation) module genes and the 1000 genes most significantly up-regulated with Oct4 RNAi (right). Significance of differential expression was determined using Student's t-statistic. p-values have been corrected for multiple hypothesis tests (Benjamini-Hochberg). Only significantly enriched functional groups are shown.