Transcription factor binding profiles reveal cyclic expression of human protein-coding genes and non-coding RNAs.

ABSTRACT: Cell cycle is a complex and highly supervised process that must proceed with regulatory precision to achieve successful cellular division. Despite the wide application, microarray time course experiments have several limitations in identifying cell cycle genes. We thus propose a computational model to predict human cell cycle genes based on transcription factor (TF) binding and regulatory motif information in their promoters. We utilize ENCODE ChIP-seq data and motif information as predictors to discriminate cell cycle against non-cell cycle genes. Our results show that both the trans- TF features and the cis- motif features are predictive of cell cycle genes, and a combination of the two types of features can further improve prediction accuracy. We apply our model to a complete list of GE

SUBMITTER: Cheng C 

PROVIDER: S-EPMC3708869 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature