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Fig. 2 | Genome Biology

Fig. 2

From: Systematic analysis of chromatin interactions at disease associated loci links novel candidate genes to inflammatory bowel disease

Fig. 2

Candidate gene characteristics. a Flowchart of filtering steps that were performed to identify IBD candidate genes (4C interactions with p > 10–8; locus activity based on the co-localization of the associated variant or a variant in LD with H3K27Ac; gene expression: log2(RPKM) > –0.5). The number of remaining genes after each step is depicted in the corresponding arrow. b A Venn diagram of the candidate genes (that meet all three criteria) identified in the three separate cell types. The surface of the circles corresponds with the numbers of genes that are unique for one cell type and with the genes that where only two cell types overlap. The number of genes shared by all three cell types is depicted in the center of the diagram. The differences between DLDs and the immune cells is not solely due to shared active enhancers between monocytes and lymphocytes that are inactive in DLDs. To address this, Additional file 2: Figure S5 depicts a Venn diagram of all genes interacting with one of all (92) assayed viewpoints. These results confirm the ability of 4C-seq to detect cell type specific chromatin-chromatin interactions. c Distribution of the distance between the reported candidate genes and the viewpoints. The majority of the genes is located several hundreds of kilobases away from the susceptibility locus

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