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Table 2 Functional correlations between overall differential expression and noncoding adaptation

From: Gene expression and adaptive noncoding changes during human evolution

Collection # sets r_r p(r_r) q(r_r)
C3:TFT (transcription factor targets) 472 0.35 < 0.0001 < 0.0005
C2:CGP (chemical and genetic perturbations) 645 0.28 < 0.0001 < 0.0005
C7:All (immunologic signatures) 1723 0.14 < 0.0001 < 0.0005
C4:CGN (cancer gene neighborhoods) 88 0.5 0.012 0.045
C6:All (oncogenic signatures) 109 0.22 0.019 0.057
C4:CM (cancer modules) 87 0.29 0.036 0.09
C5:CC (GO cellular components) 37 0.33 0.14 0.27
C3:MIR (microRNA targets) 109 0.11 0.14 0.27
C1:All (positional gene sets) 9 0.17 0.34 0.53
H:All (hallmark gene sets) 25 0.089 0.35 0.53
C2:CP:Reactome (Reactome gene sets) 39 0.058 0.4 0.55
C2:CP:KEGG (KEGG gene sets) 11 −0.17 0.7 0.88
C2:CP:Other (other canonical pathways) 6 −0.49 0.8 0.93
C5:BP (GO biological processes) 123 −0.28 0.95 0.96
C5:MF (GO molecular functions) 44 −0.41 0.96 0.96
  1. All MSigDB collections we considered are listed except for C2:CP:BioCarta, in which no gene set contained at least 50 genes analyzed in a previous study of adaptive noncoding changes. # sets is the number of gene sets we considered in the collection. r r is the rank correlation between rank-biserial correlations for enrichment with differential expression (each of which is a rank-biserial correlation as in Table 1) and rank-biserial correlations for enrichment with noncoding adaptation (each of which is likewise a rank-biserial correlation). p(r r) is the one-tailed p-value of r r via permutation test with 10,000 permutations; collections are ordered by increasing p(r r), which reflects r r, # sets, and patterns of overlap among gene sets in the collection