Fig. 1

Impact of IBD gene candidate ORFs on the HT-29 transcriptome. A Selected examples illustrating the impacts observed on the transcriptome of HT-29 cells following the expression of different ORFs for IBD gene candidates. HITS are identified as genes with probes from either microarray platform showing detectable expression in HT-29 (endogenously or following ORF expression) for which the fold effect in response to the expression of a given ORF is greater than two compared to the baseline and shows expression outside the expected range. As examples, FUT2 (left), a terminal enzyme in a metabolic pathway, had no impact on the transcriptome (0 HITS); NOD2 (middle), an intracellular PAMP receptor, had only marginal impact on the transcriptome (28 HITS) in the absence of its ligand, and HNF4A, a transcription factor known to have a central role in intestinal epithelial cells, had the strongest effect (1123 HITS). Each dot represents a single detectable probe from the genome-wide array tagging a specific gene in the HT-29 transcriptome. The x-axis shows the log₂-transformed median expression across all conditions (baseline). The y-axis represents the effect of transduction of a given ORF, as the log₂-transformed fold-induction compared to baseline. Sky blue dots are probes with expression value within expected range of variation ( |Z| ≤ 2), orange dots represent probes suggestively outside the range ( |Z| > 2), and red dots represent probes outside the range ( |Z| > 4). Grey dots are probes with expression value below detection threshold. B Impact of the expression of all IBD gene candidates on the transcriptome of HT-29 cells. ORFs are ordered along the x-axis by increasing total number of HITs (see Additional file 1: Table S5), with number of upregulated and downregulated HITs gene shown along the y-axis. Starred ORFs are previously reported IBD candidate causal genes and ORFs listed in red indicate known transcription factors (as defined by Lambert et al. [38])