Using potential master regulator sites and paralogous expansion to construct tissue-specific transcriptional networks.

ABSTRACT:

Background

Transcriptional networks of higher eukaryotes are difficult to obtain. Available experimental data from conventional approaches are sporadic, while those generated with modern high-throughput technologies are biased. Computational predictions are generally perceived as being flooded with high rates of false positives. New concepts about the structure of regulatory regions and the function of master regulator sites may provide a way out of this dilemma.

Methods

We combined promoter scanning with positional weight matrices with a 4-genome conservativity analysis to predict high-affinity, highly conserved transcription factor (TF) binding sites and to infer TF-target gene relations. They were expanded to paralogous TFs and filtered for tissue-specific expression patt

SUBMITTER: Haubrock M 

PROVIDER: S-EPMC3521180 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature