Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors.

ABSTRACT:

Background

We address the issue of explaining the presence or absence of phase-specific transcription in budding yeast cultures under different conditions. To this end we use a model-based detector of gene expression periodicity to divide genes into classes depending on their behavior in experiments using different synchronization methods. While computational inference of gene regulatory circuits typically relies on expression similarity (clustering) in order to find classes of potentially co-regulated genes, this method instead takes advantage of known time profile signatures related to the studied process.

Results

We explain the regulatory mechanisms of the inferred periodic classes with cis-regulatory descriptors that combine upstream sequence motifs with experimentally d

SUBMITTER: Andersson CR 

PROVIDER: S-EPMC2200664 | biostudies-literature | 2007 Oct

REPOSITORIES: biostudies-literature