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An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network
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Arrieta‐Ortiz, Mario L, Hafemeister, Christoph, Bate, Ashley Rose, Chu, Timothy, Greenfield, Alex, Shuster, Bentley, Barry, Samantha N, Gallitto, Matthew, Liu, Brian, Kacmarczyk, Thadeous, Santoriello, Francis, Chen, Jie, Rodrigues, Christopher D.A., Sato, Tsutomu, Rudner, David Z, Driks, Adam, Bonneau, Richard and Eichenberger, Patrick (2015) An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network. Molecular Systems Biology, 11 (11). 839. doi:10.15252/msb.20156236 ISSN 1744-4292.
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Official URL: http://dx.doi.org/10.15252/msb.20156236
Abstract
Organisms from all domains of life use gene regulation networks to control cell growth, identity, function, and responses to environmental challenges. Although accurate global regulatory models would provide critical evolutionary and functional insights, they remain incomplete, even for the best studied organisms. Efforts to build comprehensive networks are confounded by challenges including network scale, degree of connectivity, complexity of organism–environment interactions, and difficulty of estimating the activity of regulatory factors. Taking advantage of the large number of known regulatory interactions in Bacillus subtilis and two transcriptomics datasets (including one with 38 separate experiments collected specifically for this study), we use a new combination of network component analysis and model selection to simultaneously estimate transcription factor activities and learn a substantially expanded transcriptional regulatory network for this bacterium. In total, we predict 2,258 novel regulatory interactions and recall 74% of the previously known interactions. We obtained experimental support for 391 (out of 635 evaluated) novel regulatory edges (62% accuracy), thus significantly increasing our understanding of various cell processes, such as spore formation.
Item Type: | Journal Article | ||||||
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||
Journal or Publication Title: | Molecular Systems Biology | ||||||
Publisher: | EMBO | ||||||
ISSN: | 1744-4292 | ||||||
Official Date: | 17 November 2015 | ||||||
Dates: |
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Volume: | 11 | ||||||
Number: | 11 | ||||||
Article Number: | 839 | ||||||
DOI: | 10.15252/msb.20156236 | ||||||
Status: | Peer Reviewed | ||||||
Publication Status: | Published | ||||||
Access rights to Published version: | Open Access (Creative Commons) |
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