Transcription Factor Binding Profiles Reveal Cyclic Expression of Human Protein-coding Genes and Non-coding RNAs

Institute for Quantitative Biomedical Sciences, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America.
PLoS Computational Biology (Impact Factor: 4.62). 07/2013; 9(7):e1003132. DOI: 10.1371/journal.pcbi.1003132
Source: PubMed


Author Summary
Cell cycle is a complex and highly supervised process that must proceed with regulatory precision to achieve successful cellular division. Microarray time course experiments have been successfully used to identify cell cycle regulated genes but with several limitations, e.g. less effective in identifying genes with low expression. We propose a computational approach to predict cell cycle genes based on TF binding data and motif information in their promoters. Specifically, we take advantage of ChIP-seq TF binding data generated by the ENCODE project and the TF binding motif information available from public databases. These data were processed and utilized as predictor for predicting cell cycle genes using the Random Forest method. Our results show that both the trans- TF features and the cis- motif features are predictive to cell cycle genes, and a combination of the two types features can further improve prediction accuracy. We apply our model to a complete list of GENCODE promoters to predict novel cell cycle driving promoters for both protein-coding genes and non-coding RNAs such as lincRNAs. We find that a similar percentage of lincRNAs are cell cycle regulated as protein-coding genes, suggesting the importance of non-coding RNAs in cell cycle division.

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Available from: Matthew Ung, Jan 07, 2014
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    • "Hence, it is very timely crucial to comprehensively review existing methods with pros and cons and guide future direction on analytical strategy and application of methods in static and temporal dynamics. Timeseries experiment is largely composed of three different settings, (I) a single-series time course to study a developmental transient pattern (Pauli et al., 2012), (II) a multi-series or factorial time course that interrogates multiple biological reactions to specific external stimuli at each time point (Jager et al., 2011; Sivriver et al., 2011), and (III) a periodical time course in cell-cycle or circadian rhythmic data (Bar-Joseph et al., 2012; Cheng et al., 2013; Lokody, 2014). "
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