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Fig. 3 | BMC Bioinformatics

Fig. 3

From: CAGEfightR: analysis of 5′-end data using R/Bioconductor

Fig. 3

Analysis of enhancer candidates. a: Chromatin modifications at TCs and enhancer candidates from the Hela set. X-axis shows distance to TC peak or enhancer candidate midpoint. Y-axis are average signal of respective DNase-Seq or ChIP-Seq data in the given panel. Color indicates whether signals are centered on TC peaks or enhancer candidate midpoints. b: Example of predicted enhancer candidate-TC links in the ulcerative colitis set. Plot shows a genome-browser style visualization of correlations between TCs and enhancer candidates around the TNFRSF1A gene (central group of transcripts, highlighted). Bottom track shows UCSC transcript models and middle track shows clusters, as in Fig. 1b-c. Top track shows predicted TC-enhancer candidate links, where higher arches correspond to more significant correlations. Light grey links indicate that only one part of the pair is within the visualized region. c: Example of predicted enhancer stretch in the ulcerative colitis set. Bottom track shows UCSC transcript models and lower-middle track shows clusters, as in Fig. 1b-c. Upper-middle track shows the identified stretch of enhancer candidates. Top track shows correlations between enhancer candidates as in B

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