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Fig. 2 | Genome Biology

Fig. 2

From: Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data

Fig. 2

A downregulated gene set from a GATA6 knockdown experiment in gastric cancer KATO-III cells is used as a case study to demonstrate the Lisa framework. a Heatmap of regulatory potentials used to discriminate downregulated genes from non-regulated background genes. b In silico deletion analysis using GATA6 and CTCF cistromes to probe chromatin landscape models near an illustrative downregulated gene, LINC01133, and a background gene, ZC3H12A. Only the H3K27ac ChIP-seq and DNase-seq chromatin profiles with the largest positive coefficients are shown, although other samples contribute to the respective H3K27ac ChIP-seq and DNase-seq chromatin models. c Comparison of ΔRPs indicates GATA6 and GATA4 cistromes have a large impact on the chromatin landscapes near downregulated genes and are therefore likely to be regulators of the query gene set. CTCF does not influence the chromatin landscape of the downregulated genes and is not likely to regulate the query gene set. d The rank statistics for the Lisa analysis of the downregulated gene set in the GATA6 knockdown experiment were combined to get overall TR ranks. The top eight and the bottom eight TRs for all TR ChIP-seq samples are shown

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