Deciphering transcriptional regulations coordinating the response to environmental changes.

ABSTRACT:

Background

Gene co-expression evidenced as a response to environmental changes has shown that transcriptional activity is coordinated, which pinpoints the role of transcriptional regulatory networks (TRNs). Nevertheless, the prediction of TRNs based on the affinity of transcription factors (TFs) with binding sites (BSs) generally produces an over-estimation of the observable TF/BS relations within the network and therefore many of the predicted relations are spurious.

Results

We present LOMBARDE, a bioinformatics method that extracts from a TRN determined from a set of predicted TF/BS affinities a subnetwork explaining a given set of observed co-expressions by choosing the TFs and BSs most likely to be involved in the co-regulation. LOMBARDE solves an optimization problem wh

SUBMITTER: Acuna V 

PROVIDER: S-EPMC4715341 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature