Developing a web-based tool for analysing cell type-specificity of genomic variation data

Abstract

The majority of trait associated variants found in GWAS studies lie within non coding sequences. This suggests that a large proportion of variants alter regulatory regions. Certain genomic features has been shown useful as marks of cell type specific activity of genomic regions. Analyzing such genomic features against variant regions may therefore be used to find previously unknown links between trait and cell type. Although there have been done several investigations of this type, no easily accessible tools for this type of research exists. This makes reproduction of such results difficult and time consuming, hindering confirmation and updates of such results

Such an accessible tool for studying cell-type specificity of genomic regions is presented here, created in a Galaxy-based web interface at the Genomic HyperBrowser server. It allows the user to run a selection of analyses on their own genomic variation data against genomic tracks of cell-type specific marks. A table presenting the main results provides a broad overview of the most relevant cell types, while links to further details behind each main result allows for deeper investigations.

The tool here presented allows anyone to run such analyses without deep knowledge of statistics and informatics, as most parameters and variables are set automatically by the system. Combined with the graphical interface in the HyperBrowser, this makes it easy to specify and reproduce analyses.