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

Table 1 Genomic regions with enriched gene expression changes

Cytogenetic band	Size*	NES^†	NOM p val^‡	FDR q val^§
Regions enriched for gene expression changes during positive selection (B10^k)
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 (B10^k)
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 B10^k
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 B10^k
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 B10^k
chr2 F	100	1.8	0.002	0.05
chr3 A	61	1.6	0.008	0.19

*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).

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