Exploring the relationship between polymorphic (TG/CA)n repeats RESEARCH Table 2. Summary of the (TG/CA)n repeats in intron 1 regions (version hg 16) Number of repeats Number of genes aAll intron 1 regions. bIntron 1 regions larger than 2.5 kb. (n All 6)a 1137 839 (6 Short n < 12)a 704 536 Long 12)a (n 433 388 Long 12)b (n 371 330 Long (50 windowb) 205 187 Long (30 windowa) 194 187 chromosomes were found to be either over- represented or under-represented relative to the human genome reference. also enriched among these genes. Table 3 lists these enriched biological processes and pathways (FDR , 0.05). Enriched biological processes and pathways Using the DAVID web application,29,30 four GO23 and 17 PANTHER31 biological processes were found to be enriched among the 330 gene- containing long I1 (TG/CA)n repeats. The most signiﬁcant enriched biological process was the PANTHER31 term for cation transport (97 genes; p ¼ 6.20 10211; pc ¼ 1.40 1028). One KEGG24 pathway — the calcium signalling pathway (16 genes; p ¼ 2.1 10211, FDR ¼ 0.041) — was Genotyping of the I1 repeats in the CEU samples Ten I1-repeats-containing genes (the genes encod- ing runt-related transcription factor [RUNX], CD38 molecule [CD38], CLMN, very low – density lipoprotein receptor [VLDLR], calcium channel, voltage-dependent, R type, alpha 1E subunit [CACNA1E], aryl hydrocarbon receptor [AHR], neuregulin 2 [NRG2], par-3 partitioning defective 3 homolog [PARD3], INSR and Figure 2. Chromosomal distribution of genes containing long (TG/CA)n repeats (where n 12). In total, 330 genes containing long repeats were identiﬁed in the 50 and/or 30 2.5 kb windows of the intron 1 regions in the human genome. Chromosome 11 was under-represented relative to the human genome reference (version hg16). # HENRY STEWART PUBLICATIONS 1479–7364. HUMAN GENOMICS. VOL 3. NO 3. 236–245 APRIL 2009 241