Results from gene expression analysis of 34 candidate genes.

Expression (e.g. mRNA levels) of these genes was either up- or down-regulated in small intestinal biopsies from CD cases compared with control patients. Effect direction is presented for cases with control group as a reference. The selection column indicates if the gene was selected due to its presence in two-locus or pathway analyses. “Top” indicates top SNP in the present GWAS and “top previous” indicates that it was present in the GWAS by Dubois et al.
All the gene assays (primers and probes) were predesigned and ordered from Life technologies (CA, USA).
Reference genes tested were: ACTB (Hs00357333_g1), B2M (Hs99999907_m1), EPCAM (Hs00158980_m1), GUSB (Hs99999908_m1), HPRT1 (Hs99999909_m1), MUC1 (Hs00159357_m1), PGK1 (Hs99999906_m1). For the results a combined value of ACTB, EPCAM, and PGK1 showed to be optimal when analysed by GeNorm and were selected as reference.
aGene not included in the gene list used for pathway analyses due to recombination between associated SNP and gene promotor: rs10861406.
(APPL2), rs882820 (ADCY9). However, possible regulatory site could be close to associated SNP and influence gene expression.
bP-values corrected using Bonferroni correction.