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Volumn 12, Issue 5, 2017, Pages

Validating regulatory predictions from diverse bacteria with mutant fitness data

Author keywords

[No Author keywords available]

Indexed keywords

FUMARATE REDUCTASE; TRANSCRIPTION FACTOR; BACTERIAL PROTEIN; ESCHERICHIA COLI PROTEIN;

EID: 85019872465     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0178258     Document Type: Article
Times cited : (6)

References (25)
  • 1
    • 34548219522 scopus 로고    scopus 로고
    • Comparative genomic reconstruction of transcriptional regulatory networks in bacteria
    • PMID: 17636889
    • Rodionov D. A. (2007). Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chemical reviews, 107(8), 3467-3497. https://doi.org/10.1021/cr068309+ PMID: 17636889
    • (2007) Chemical Reviews , vol.107 , Issue.8 , pp. 3467-3497
    • Rodionov, D.A.1
  • 2
    • 78649874431 scopus 로고    scopus 로고
    • Genomic repertoires of DNA-binding transcription factors across the tree of life
    • PMID: 20675356
    • Charoensawan V., Wilson D., &Teichmann S. A. (2010). Genomic repertoires of DNA-binding transcription factors across the tree of life. Nucleic acids research, 38(21), 7364-7377. https://doi.org/10. 1093/nar/gkq617 PMID: 20675356
    • (2010) Nucleic Acids Research , vol.38 , Issue.21 , pp. 7364-7377
    • Charoensawan, V.1    Wilson, D.2    Teichmann, S.A.3
  • 3
    • 33846400424 scopus 로고    scopus 로고
    • Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
    • PMID: 17214507
    • Faith J. J., Hayete B., Thaden J. T., Mogno I., Wierzbowski J., Cottarel G. et al., (2007). Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS biol, 5(1), e8. https://doi.org/10.1371/journal.pbio.0050008 PMID: 17214507
    • (2007) PLoS Biol , vol.5 , Issue.1 , pp. e8
    • Faith, J.J.1    Hayete, B.2    Thaden, J.T.3    Mogno, I.4    Wierzbowski, J.5    Cottarel, G.6
  • 4
    • 84963800566 scopus 로고    scopus 로고
    • Transcription profile of Escherichia coli: Genomic SELEX search for regulatory targets of transcription factors
    • Ishihama A., Shimada T., & Yamazaki Y. (2016). Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors. Nucleic acids research, gkw051.
    • (2016) Nucleic Acids Research , pp. gkw051
    • Ishihama, A.1    Shimada, T.2    Yamazaki, Y.3
  • 5
    • 34447279700 scopus 로고    scopus 로고
    • Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data
    • Wu W., Li W., & Chen B. (2007). Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. BMC bioinformatics, 8(1), 1.
    • (2007) BMC Bioinformatics , vol.8 , Issue.1 , pp. 1
    • Wu, W.1    Li, W.2    Chen, B.3
  • 7
    • 0041429503 scopus 로고    scopus 로고
    • Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays
    • Wendisch V. F. (2003). Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays. Journal of biotechnology, 104(1), 273-285.
    • (2003) Journal of Biotechnology , vol.104 , Issue.1 , pp. 273-285
    • Wendisch, V.F.1
  • 8
    • 84874886134 scopus 로고    scopus 로고
    • ChIP-Seq and the complexity of bacterial transcriptional regulation
    • Galagan J., Lyubetskaya A., & Gomes A. (2012). ChIP-Seq and the complexity of bacterial transcriptional regulation. Systems Biology, 43-68.
    • (2012) Systems Biology , pp. 43-68
    • Galagan, J.1    Lyubetskaya, A.2    Gomes, A.3
  • 9
    • 80053912671 scopus 로고    scopus 로고
    • Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium
    • PMID: 21992415
    • Rajeev L, Luning E.G., Dehal P. S., Price M. N., Arkin A. P., & Mukhopadhyay A. (2011). Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium. Genome Biol, 12(10), R99. https://doi.org/10.1186/gb-2011-12-10-r99 PMID: 21992415
    • (2011) Genome Biol , vol.12 , Issue.10 , pp. R99
    • Rajeev, L.1    Luning, E.G.2    Dehal, P.S.3    Price, M.N.4    Arkin, A.P.5    Mukhopadhyay, A.6
  • 12
    • 14644388890 scopus 로고    scopus 로고
    • Making connections between novel transcription factors and their DNA motifs
    • PMID: 15653829
    • Tan K., McCue L. A., & Stormo G. D. (2005). Making connections between novel transcription factors and their DNA motifs. Genome research, 15(2), 312-320. https://doi.org/10.1101/gr.3069205 PMID: 15653829
    • (2005) Genome Research , vol.15 , Issue.2 , pp. 312-320
    • Tan, K.1    McCue, L.A.2    Stormo, G.D.3
  • 13
    • 84886739636 scopus 로고    scopus 로고
    • RegPrecise 3.0-a resource for genome-scale exploration of transcriptional regulation in bacteria
    • Novichkov P. S., Kazakov A. E., Ravcheev D. A., Leyn S. A., Kovaleva G. Y., Sutormin R. A., et al. (2013). RegPrecise 3.0-a resource for genome-scale exploration of transcriptional regulation in bacteria. BMC genomics, 14(1), 745.
    • (2013) BMC Genomics , vol.14 , Issue.1 , pp. 745
    • Novichkov, P.S.1    Kazakov, A.E.2    Ravcheev, D.A.3    Leyn, S.A.4    Kovaleva, G.Y.5    Sutormin, R.A.6
  • 15
    • 84936929916 scopus 로고    scopus 로고
    • Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons
    • PMID: 25968644
    • Wetmore K. M., Price M. N., Waters R. J., Lamson J. S., He J., Hoover C. A. et al., (2015). Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. MBio, 6 (3), e00306-15. https://doi.org/10.1128/mBio.00306-15 PMID: 25968644
    • (2015) MBio , vol.6 , Issue.3 , pp. e00306-e00315
    • Wetmore, K.M.1    Price, M.N.2    Waters, R.J.3    Lamson, J.S.4    He, J.5    Hoover, C.A.6
  • 17
    • 81755163097 scopus 로고    scopus 로고
    • Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions
    • PMID: 22125499
    • Deutschbauer A., Price M. N., Wetmore K. M., Shao W., Baumohl J. K., Xu Z. et al., (2011). Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. PLoS Genet, 7(11), e1002385. https://doi.org/10.1371/journal.pgen.1002385 PMID: 22125499
    • (2011) PLoS Genet , vol.7 , Issue.11 , pp. e1002385
    • Deutschbauer, A.1    Price, M.N.2    Wetmore, K.M.3    Shao, W.4    Baumohl, J.K.5    Xu, Z.6
  • 18
    • 0033047695 scopus 로고    scopus 로고
    • The role of the trehalose system in regulating the maltose regulon of Escherichia coli
    • Decker Katja, Gerhardt Friederike, and Boos Winfried. "The role of the trehalose system in regulating the maltose regulon of Escherichia coli." Molecular microbiology 32.4 (1999): 777-788.
    • (1999) Molecular Microbiology , vol.32 , Issue.4 , pp. 777-788
    • Katja, D.1    Friederike, G.2    Winfried, B.3
  • 19
    • 84876543942 scopus 로고    scopus 로고
    • RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
    • Jan 1 Epub 2012 Nov 29
    • Salgado H. et al., (2013). "RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more". Nucleic Acids Research. 2013 Jan 1; 41(D1): D203-D213. Epub 2012 Nov 29.
    • (2013) Nucleic Acids Research , vol.41 , Issue.D1 , pp. D203-D213
    • Salgado, H.1
  • 20
    • 84906309533 scopus 로고    scopus 로고
    • Conservation of transcription start sites within genes across a bacterial genus
    • PMID: 24987095
    • Shao W., Price M. N., Deutschbauer A. M., Romine M. F., & Arkin A. P. (2014). Conservation of transcription start sites within genes across a bacterial genus. MBio, 5(4), e01398-14. https://doi.org/10. 1128/mBio.01398-14 PMID: 24987095
    • (2014) MBio , vol.5 , Issue.4 , pp. e01398-e01414
    • Shao, W.1    Price, M.N.2    Deutschbauer, A.M.3    Romine, M.F.4    Arkin, A.P.5
  • 21
    • 38549134505 scopus 로고    scopus 로고
    • Many Microbe Microarrays Database: Uniformly normalized Affymetrix compendia with structured experimental metadata
    • Faith J. J., Driscoll M. E., Fusaro V. A., Cosgrove E. J., Hayete B., Juhn F. S., et al. (2008). Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic acids research, 36(suppl 1), D866-D870.
    • (2008) Nucleic Acids Research , vol.36 , pp. D866-D870
    • Faith, J.J.1    Driscoll, M.E.2    Fusaro, V.A.3    Cosgrove, E.J.4    Hayete, B.5    Juhn, F.S.6
  • 22
    • 0242386460 scopus 로고    scopus 로고
    • Identifying global regulators in transcriptional regulatory networks in bacteria
    • PMID: 14572541
    • Martinez-Antonio A., & Collado-Vides J. (2003). Identifying global regulators in transcriptional regulatory networks in bacteria. Current opinion in microbiology, 6(5), 482-489. PMID: 14572541
    • (2003) Current Opinion in Microbiology , vol.6 , Issue.5 , pp. 482-489
    • Martinez-Antonio, A.1    Collado-Vides, J.2
  • 23
    • 33748679406 scopus 로고    scopus 로고
    • Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes-a genomic approach
    • Moreno-Campuzano S., Janga S. C, & Perez-Rueda E. (2006). Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes-a genomic approach. BMC genomics, 7(1), 147.
    • (2006) BMC Genomics , vol.7 , Issue.1 , pp. 147
    • Moreno-Campuzano, S.1    Janga, S.C.2    Perez-Rueda, E.3
  • 24
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • PMID: 20709691
    • Edgar R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26 (19), 2460-2461. https://doi.org/10.1093/bioinformatics/btq461 PMID: 20709691
    • (2010) Bioinformatics , vol.26 , Issue.19 , pp. 2460-2461
    • Edgar, R.C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.