A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation.

ABSTRACT: Much has been learned about transcriptional cascades and networks from large-scale systems analyses of high-throughput datasets. However, analysis methods that optimize statistical power through simultaneous evaluation of thousands of ChIP-seq peaks or differentially expressed genes possess substantial limitations in their ability to uncover mechanistic principles of transcriptional control. By examining nascent transcript RNA-seq, ChIP-seq, and binding motif datasets from lipid A-stimulated macrophages with increased attention to the quantitative distribution of signals, we identified unexpected relationships between the in vivo binding properties of inducible transcription factors, motif strength, and transcription. Furthermore, rather than emphasizing common features of large clusters o

SUBMITTER: Tong AJ 

PROVIDER: S-EPMC4808443 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature