LLM3D: a log-linear modeling-based method to predict functional gene regulatory interactions from genome-wide expression data.

ABSTRACT: All cellular processes are regulated by condition-specific and time-dependent interactions between transcription factors and their target genes. While in simple organisms, e.g. bacteria and yeast, a large amount of experimental data is available to support functional transcription regulatory interactions, in mammalian systems reconstruction of gene regulatory networks still heavily depends on the accurate prediction of transcription factor binding sites. Here, we present a new method, log-linear modeling of 3D contingency tables (LLM3D), to predict functional transcription factor binding sites. LLM3D combines gene expression data, gene ontology annotation and computationally predicted transcription factor binding sites in a single statistical analysis, and offers a methodological improveme

SUBMITTER: Geeven G 

PROVIDER: S-EPMC3141251 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature