Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites.

ABSTRACT:

Background

From initial seed germination through reproduction, plants continuously reprogram their transcriptional repertoire to facilitate growth and development. This dynamic is mediated by a diverse but inextricably-linked catalog of regulatory proteins called transcription factors (TFs). Statistically quantifying TF binding site (TFBS) abundance in promoters of differentially expressed genes can be used to identify binding site patterns in promoters that are closely related to stress-response. Output from today's transcriptomic assays necessitates statistically-oriented software to handle large promoter-sequence sets in a computationally tractable fashion.

Results

We present Marina, an open-source software for identifying over-represented TFBSs from amongst large sets of

SUBMITTER: Hosseini P 

PROVIDER: S-EPMC3639912 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature