Identifying and Mapping Cell-type Specific Chromatin Programming of Gene Expression

This web service allows for computation of local ARS profiles of all genes across cell-types as outlined in our publication.

We calculated ARS across 20 different cell-types, considering different genomic segments of DHS volume. These results are searchable via the main interface. It is possible to search by gene-name (HGNC), cell-type and significance thresholds.

Each gene in each genomic segment is represented by a single row containing the following: Gene-name, the actual ARS statistics, angle, cell-type, p-value and q-value. Next to each gene are two options: Plot and Calculate track.

Plot will display the 2D projection of all cell-types, scaled and median centered; with gene expression on the x-axis, and DHS volume on the y-axis. Distinct outlying points are scaled relative to the maximum ARS, thereby indicating the ordering of the genes in terms of likely outliers.

Calculate track will generate a wiggle-track of the local ARS profile. The user is to select which cell-types should be present in the wig-file, but all are used in calculating the actual local ARS values. The generated wig-track can either be downloaded or directly displayed in the UCSC genome browser.