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Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions
2010
Database: The Journal of Biological Databases and Curation
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The integrated analysis of the data predicted a new type of bacterial transcriptional regulation involving co-transcription of the intergenic region with the downstream gene and suggested a biological ...
role for co-transcription that likely prevents the binding of a regulator of the upstream gene to the regulator binding site located in the intergenic region. ...
Acknowledgements We thank members of the Shewanella Federation for their contribution in developing the resource and in data submission. We are especially grateful to Jim Conflict of interest. ...
doi:10.1093/database/baq012
pmid:20627862
pmcid:PMC2911847
fatcat:bpto34rdqzc27i63ikcf2mxzzy
Conserved synteny at the protein family level reveals genes underlying Shewanella species' cold tolerance and predicts their novel phenotypes
2009
Functional & Integrative Genomics
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The second, a bottomup approach, predicts novel phenotypes of the species by calculating profiles of each Pfam domain among their genomes and following pair-wise correlation of the profiles and their network ...
Our first approach is top-down and involves experimental evaluation and quantification of the species' cold tolerance followed by identification of the correlated Pfam domains and genes with a conserved ...
Mushegian and other reviewers of the paper for thoughtful suggestions and comments on the study. ...
doi:10.1007/s10142-009-0142-y
pmid:19802638
pmcid:PMC2834769
fatcat:co23bsd3tfbclkvajkk6jih3ga
Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA
2012
Gene Regulation and Systems Biology
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We explore the hypothesis that the number of BMs plays an important role in transcriptional regulation, examining empirical data from transcriptional profiling of the CRP and ArcA regulons. ...
We compare the power of BM counts and of full TFBS characteristics to predict induced transcriptional activity. ...
Acknowledgements The authors would like to thank Tim Gardner and his group for providing unpublished microarray data on crpmutant strain of S. oneidensis MR-1 for the analysis. ...
doi:10.4137/grsb.s9357
pmid:22701314
pmcid:PMC3370831
fatcat:5eli4lf5mjcw7oxzaj5jxkzepq
M. genitalium Whole-cell Model :: Data S1
2012
Figshare
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Supplemental text for Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Assad-Garcia N, Glass JI & Covert MW. A Whole-Cell Computational Model Predicts Phenotype from Genotype. ...
While there is a separate set of data for each of the 5 genes, the Transcription process class requires a single probability of transcription for each transcription unit. ...
For example, the copy number of each gene plays a role in RNA polymerase binding in the Transcription process, and affects the cell's gene expression. ...
doi:10.6084/m9.figshare.93256.v1
fatcat:sy5hfikbgfgovflreompaunamq
A Pan-Genome Guided Metabolic Network Reconstruction of Five Propionibacterium Species Reveals Extensive Metabolic Diversity
2020
Genes
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Overall, the data provide a platform to explore Propionibacterium metabolism and a tool for the rational design of strains. ...
Such data also enable a comparative genomic approach to annotation and provide a new opportunity to revisit our understanding of their metabolism. ...
Acknowledgments: We thank Paul Swanson for his assistance performing and providing the BIOLOG analysis.
Conflicts of Interest: The authors declare that they have no competing interests. ...
doi:10.3390/genes11101115
pmid:32977700
pmcid:PMC7650540
fatcat:x2sf23ze4vdp7a4s3zhn4rqjai