Skip to main content

Table 1 Genomic regions with enriched gene expression changes

From: Impairment of organ-specific T cell negative selection by diabetes susceptibility genes: genomic analysis by mRNA profiling

Cytogenetic band Size* NES NOM p val FDR q val§
Regions enriched for gene expression changes during positive selection (B10k)     
   Decreased in positive selection     
chr12 F 69 1.8 0.002 0.05
chr3 B 29 1.5 0.035 0.24
chr2 F 100 1.5 0.009 0.24
Regions enriched for gene expression changes during negative selection (B10k)     
   Increased in negative selection     
chr2 F 100 1.7 0.002 0.08
   Decreased in negative selection     
chr11 E 206 -1.7 0.000 0.06
chr6 B 138 -1.5 0.000 0.24
Regions enriched for expression differences between strains in pre-selection thymocytes     
   Increased in B10k     
chr8 E 110 1.6 0.003 0.17
chr7 E 103 1.6 0.000 0.13
chr18 E 91 1.6 0.008 0.13
chr12 F 69 1.5 0.012 0.14
chr6 C 101 1.5 0.010 0.12
chr1 B 48 1.5 0.030 0.16
chr15 D 99 1.5 0.011 0.14
chr5 F 175 1.4 0.018 0.22
chr10 C 204 1.4 0.007 0.22
chr19 A 199 1.4 0.009 0.21
chr4 E 126 1.4 0.030 0.25
   Decreased in B10k     
chrX F 109 -2.4 0.000 0.00
chr3 E 43 -1.9 0.003 0.01
chrX D 25 -1.8 0.004 0.01
chr3 H 76 -1.8 0.003 0.01
chr5 C 66 -1.7 0.000 0.03
chr12 C 101 -1.5 0.008 0.09
chr1 A 39 -1.5 0.017 0.09
chrX A 207 -1.5 0.010 0.13
Regions with enriched strain expression differences during negative selection     
   Increased in B10k     
chr2 F 100 1.8 0.002 0.05
chr3 A 61 1.6 0.008 0.19
  1. *Size: number of genes in the cytogenetic band represented by Affymetrix probesets. NES: normalized (multiplicative rescaling) enrichment score. NOM p val: nominal p value from the null distribution of the gene set. §FDR q val: false discovery rate q values (only false discovery rate < 0.25 have been included).