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Fig. 3 | Epigenetics & Chromatin

Fig. 3

From: A computational approach for the functional classification of the epigenome

Fig. 3

Enrichment of chromatin profiles with respect to genomic features. The heatmap represents the enrichment of each chromatin profile (rows) compared to different regions of the gene and distinct types of genomic features in the genome (columns). The enrichment is defined as a log-odd ratio as described in “Methods”. Positive associations (odd-ratio >1) are colored from green/yellow to brown whereas negative associations (odd-ratio <1) are indicated in blue. As shown in the heatmap, each combinatorial profile reveals a distinct pattern of enrichment, thus demonstrating the usefulness of the NMF-approach in the biological interpretation of the different chromatin functions. In this heatmap, each profile is associated to a specific biological label in order to facilitate the mnemonic association between the profile and its functional role on the basis of the observed enrichment (top-bottom): ActProm = Active Promoter (profile 1), TxInit = Transcription Initiation (profile 3), RepReg = Repressed Regulatory Regions (profile 4), Ehn = Enhancer Regions (profile 6), RegEl = Regulatory Elements (profile 7), GenBd = Gene Body Transcription (profile 5), RepChr = Repressed Chromatin (profile 2). Genomic features indicated in the columns are: CAGE = hESC-H1 CAGE clusters from ENCODE; RfTSS = Refseq Transcription Start Sites; RfTES = Refseq Transcription End Sites; 5UTR=Refseq 5’untranslated region; 3UTR = Refseq 3’unstranslated regions; H1 Enhancers = Superenhancer regions from hESC; CpG = CpG islands; Upstream = 1Kb upstream regions from Refseq TSSs; DNase1 = hESC DNase1 Hypersensitive sites from ENCODE; TFBS = Conserved transcription factor binding sites from the Transfac Matrix Database; 5C = Chromatin conformation capture carbon copy data from hESC; EnhancersDB = experimentally validated enhancer elements from the VistaEnhancer Dabatabse; Rf = Refseq genes; Int = intronic sequences from Refseq genes; Ex = exonic sequences from Refseq genes; PolyA = predicted poly-adenylation sites; sRNA = small RNAs; HMMhetero = predicted heterochromatin regions in hESC

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