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Owsing through all the genes in a list. However CState also
Owsing through all the genes in a list. However CState also provides for gene-specific views across the chosen cell types and features. Clicking on any plot in the display opens a modal for the gene (Fig. 4), where the data representing that gene in multiple cell-types is stacked vertically for closer inspection; the larger aspect ratio of a landscape layout allows focusing on an expanded viewpoint anywhere along the entire locus. The plots are interactive, and support panning as well as zooming (using either the mouse scroll or the zoom controls provided at the top of the modal), with the scaleThe Author(s) BMC Bioinformatics 2017, 18(Suppl 10):Page 18 ofFig. 3 Open View accordion of C-State displaying gene data of a) two cell types and b) six cell types. Screenshot shows 3 of the 330 genes in the View pane. Blue rectangle indicates the folded Files accordionautomatically adjusting to the zoom level. PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28607003 The zoom is linked to all the data tracks and cell types for a seamless comparison, and can be reset to the original state with the “Reset zoom” button. In addition, certain context specific information is displayed in the modal view such as the genomic coordinates and orientation of the gene (top left), exon information (alternating thick and thin bars to represent exons and introns respectively), peak intensity information and gene expression score or value (below cell type name).Case study Overview of datasetsAddressing biologically relevant questions often involves analyzing sets of genes belonging to particular pathways or regulating distinct cellular processes. However, extracting chromatin peak information of selected genes of interest from genome-wide datasets is a cumbersometask. The following use cases demonstrate the utility of C-State in the analysis of 16 epigenetic (4 histone marks across 4 different cell types) and 4 RNA-Seq datasets from the ENCODE project [12]. We have focused on data from multiple human cell lines ?K562, HeLa, and GM12878 ?for comparison with H1 embryonic stem cells (H1-hESC) to examine changes in histone modification profiles. Whole genome ChIP-seq datasets are downloaded for H3K4me3 and H3K9ac (associated with gene activation), H3K36me3 (active transcription) and H3K27me3 (repression). The downloaded BED files are loaded directly into C-State as feature files in the Files accordion. The FPKM values of all genes derived from RNA-seq datasets of these cell types are loaded as expression data files (See Tutorial in the website for details and formats). To Nutlin-3a chiral site identify enrichment patterns at a selected subset of genes in these differentiated versus pluripotent cell states,The Author(s) BMC Bioinformatics 2017, 18(Suppl 10):Page 19 ofFig. 4 Expanded gene modal showing peak features (colored tracks) and expression values (heatmap scale on left, value in parenthesis) of a single gene (thick bars represent exons, thin bars introns) across 5 cell types stacked verticallywe created a list of `stemness’ genes potentially important for regulating the ES cell state from published datasets analyzing the hESC transcriptome [13] and pluripotency factor bound gene networks in hESCs [14]. A subset of 330 genes, shortlisted based on their change in expression profile upon ESC differentiation, is loaded into the Files accordion for comparative analysis. Gene expression patterns along with associated histone marks are analyzed across the group of 330 target genes and 20 KB of their flanking upstream and downstream regions. The.

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