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Table 2 Genes showing developmental changes are enriched for genes altered by liver-specific deletion of HNF4α

From: Sex-specific mouse liver gene expression: genome-wide analysis of developmental changes from pre-pubertal period to young adulthood

A. Background: All genes (22,831) Genes up regulated in male HNF4α- deficient liver (2,619 genes) Genes down regulated in male HNF4α- deficient liver (2,712 genes)
  # of overlapping genes Fold enrichment Fisher Test p -value # of overlapping genes Fold enrichment Fisher Test p - value
All genes up regulated in male liver 3-8 wk (1,550 genes) 127 0.71 4.61E-05 537 2.92 3.87E-110
All genes down regulated in male liver 3-8 wk (1,791 genes) 486 2.37 1.15E-66 131 0.62 9.10E-10
B. Background: All genes (22,831) Genes up regulated in female HNF4α- deficient liver (2,227 genes) Genes down regulated in female HNF4α- deficient liver (2,255 genes)
  # of overlapping genes Fold enrichment Fisher Test p-value # of overlapping genes Fold enrichment Fisher Test p- value
All genes up regulated in female liver 3-8 wk (1,087 genes) 93 0.88 0.208 337 3.14 2.43E-77
All genes down regulated in female liver 3-8 wk (1,360 genes) 366 2.76 6.39E-67 85 0.63 4.35E-06
  1. Genes identified in the present microarray study were grouped based on their regulation from 3 wk to 8 wk and compared to genes from a previous microarray study [24] grouped by their response to liver-specific HNF4α-deficiency. All of the genes used to calculate the enrichment scores shown in this Table were represented on both microarray platforms. Total numbers of genes comprising each group are shown in parenthesis. Sample enrichment score calculation: [% of the genes down regulated in male liver from 3 wk to 8 wk that are up-regulated in male HNF4α-knockout mouse liver]/[% of all genes that are up-regulated in male HNF4α-knockout mouse liver], i.e., (486/1,791)/(2,619/22,831) = 2.37 fold enrichment. Bold text indicates enrichment with a highly significant p-value (p < 0.0001, Fisher's exact test), and italic text indicates depletion with a highly significant p-value (p < 0.0001, Fisher's exact test).