Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities
[2];
- Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093,
- Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093,, Bioinformatics and Systems Biology Program, University of California at San Diego, La Jolla, CA 92093,
- Department of Genetic Engineering, Kyung Hee University, Yongin 17104, South Korea,
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093,
- Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093,, Bioinformatics and Systems Biology Program, University of California at San Diego, La Jolla, CA 92093,, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Horsholm, Denmark,, Department of Pediatrics, University of California at San Diego, La Jolla, CA 92093
Significance While the transcriptional regulatory network (TRN) of Escherichia coli has expanded considerably in recent years through new chromatin immunoprecipitation (ChIP) data, an open question remains: Does the global TRN, reconstructed by combining ChIP data for individual transcriptions factors, consistently explain observed differential gene expression? We have reconstructed a high-confidence TRN, determined its consistency with transcriptomics and predictive capabilities across multiple conditions, extracted 10 functional regulatory modules, and characterized this network at the sequence and structural levels. Our multiomics algorithmic pipeline is expected to facilitate rigorous validation and prioritization of experiments to elucidate TRNs in other bacteria.
- Sponsoring Organization:
- USDOE
- Grant/Contract Number:
- SC0008701
- OSTI ID:
- 1378781
- Alternate ID(s):
- OSTI ID: 1465783
- Journal Information:
- Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Issue: 38 Vol. 114; ISSN 0027-8424
- Publisher:
- Proceedings of the National Academy of SciencesCopyright Statement
- Country of Publication:
- United States
- Language:
- English
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