Gene communities in co-expression networks across different tissues
Fig 5
Expression and co-expression analysis of a cluster of genes in community 5 on chromosome 17.
The co-expression matrices for these genes in (A) skin and in (B) pancreas are shown. The average expression for each gene in these tissues is shown in the bar graphs. The location of these genes on chromosome 17 is shown in (C), with arrows (colored according to the associated tissue) pointing from putative regulatory elements to highly co-expressed genes. (D) The panel shows different measures of the regulatory potential of this genome section. From top to bottom: 1. H3K27AC modification to histone H3 within the region, which often correlates with activation of transcription and is associated with active enhancers in a given tissue available through ENCODE database [119]. 2. DNAse1 hypersensitivity sites. They are sections of the genome that are cut by DNAse1 enzyme. Given that the chromatin has to be “open” for the DNAse to access the sequence, the sequences that are cut by DNAse indicate open chromatin, which is in turn associated with regulatory activity. Data are available through ENCODE database [119]. 3. Enhancer/promoters. These are sequences that are predicted as enhancers (gray) and promoters (red) from the GeneHancer database [120]. 4. Established interactions between regulatory regions and genes as documented by GeneHancer database [120]. These data sets combined with our co-expression analysis provide a novel outlook into potential topologically associated domains that may be regulated by specific sequences in a tissue-specific manner.