cGRNexp: a web platform for building combinatorial gene regulation networks based on user-uploaded gene expression datasets

Abstract

While we witness rapid progresses in development of methodologies/algorithms for constructing and analyzing the combinatorial regulation network which includes both TF regulators and miRNA regulators, we find a lack of tools or servers available for facilitating related works. A web service is especially needed that allows user to upload their own expression datasets and mine the combinatorial gene reglatory networks regarding the particular experimental context. Herein we report cGRNexp, a web platform for building combinatorial gene regulation networks based on user-uploaded gene expression datasets. In cGRNexp, we deposit three types of sequence-matching-based regulatory relationships and implement two functional modules for processing microRNA-perturbed gene expression datasets and parallel miRNA/mRNA expression datasets. With the microarrays and next-generation sequencing platforms being increasingly accessible, a large amount of miRNA or mRNA expression datasets will be attainable in the near future, and thus, our web platform cGRNexp will be very useful for helping people mine the conditional combinatorial regulatory networks from their own expression datasets. cGRNexp is accessible at http://www.scbit.org/cgrnexp/.