Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire.

ABSTRACT: We constructed and applied an open source informatic framework called Cistematic in an effort to predict the target gene repertoire for transcription factors with large binding sites. Cistematic uses two different evolutionary conservation-filtering algorithms in conjunction with several analysis modules. Beginning with a single conserved and biologically tested site for the neuronal repressor NRSF/REST, Cistematic generated a refined PSFM (position specific frequency matrix) based on conserved site occurrences in mouse, human, and dog genomes. Predictions from this model were validated by chromatin immunoprecipitation (ChIP) followed by quantitative PCR. The combination of transfection assays and ChIP enrichment data provided an objective basis for setting a threshold for membership and r

SUBMITTER: Mortazavi A 

PROVIDER: S-EPMC1581430 | biostudies-literature | 2006 Oct

REPOSITORIES: biostudies-literature