메뉴 건너뛰기




Volumn 9, Issue 5, 2012, Pages 1293-1300

How little do we actually know? on the size of gene regulatory networks

Author keywords

Computational biology; network statistics; transcriptional gene regulatory networks

Indexed keywords

BACILLUS SUBTILIS; COMPUTATIONAL BIOLOGY; DNA SEQUENCING; GENE REGULATORY NETWORKS; GENETIC CONTROL; LARGE-SCALE EVOLUTION; LOWER BOUNDS; MODEL ORGANISMS; MOLECULAR CONTROL MECHANISM; NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATIONS; NETWORK STATISTICS; ON-GOING IMPROVEMENT; POPULATION GENETICS; REGULATORY INTERACTIONS; REGULATORY NETWORK; WHOLE GENOME SEQUENCES;

EID: 84864925344     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2012.71     Document Type: Article
Times cited : (27)

References (34)
  • 1
    • 75549088687 scopus 로고    scopus 로고
    • Database resources of the national center for biotechnology information
    • Jan.
    • E.W. Sayers et al., "Database Resources of the National Center for Biotechnology Information," Nucleic Acids Research, vol. 38, pp. D5-D16, Jan. 2010.
    • (2010) Nucleic Acids Research , vol.38
    • Sayers, E.W.1
  • 2
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies-the next generation
    • Jan.
    • M.L. Metzker, "Sequencing Technologies-the Next Generation," Nature Rev. Genetics, vol. 11, pp. 31-46, Jan. 2010.
    • (2010) Nature Rev. Genetics , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 3
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation dna sequencing
    • Oct.
    • J. Shendure and H. Ji, "Next-Generation DNA Sequencing," Nature Biotechnology, vol. 26, pp. 1135-1145, Oct. 2008.
    • (2008) Nature Biotechnology , vol.26 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2
  • 4
    • 69049103184 scopus 로고    scopus 로고
    • Reconstructing prokaryotic transcriptional regulatory networks: Lessons from actinobacter-ia
    • T.M. Venancio and L. Aravind, "Reconstructing Prokaryotic Transcriptional Regulatory Networks: Lessons from Actinobacter-ia," J. Biology, vol. 8, p. 29, 2009.
    • (2009) J. Biology , vol.8 , pp. 29
    • Venancio, T.M.1    Aravind, L.2
  • 5
    • 60749118619 scopus 로고    scopus 로고
    • Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks
    • J. Baumbach et al., "Towards the Integrated Analysis, Visualization and Reconstruction of Microbial Gene Regulatory Networks," Briefings in Bioinformatics, vol. 10, p. 75, 2009.
    • (2009) Briefings in Bioinformatics , vol.10 , pp. 75
    • Baumbach, J.1
  • 6
    • 0026682657 scopus 로고
    • Transcription factors: Structural families and principles of dna recognition
    • C.O. Pabo and R.T. Sauer, "Transcription Factors: Structural Families and Principles of DNA Recognition," Ann. Rev. Biochemistry, vol. 61, pp. 1053-1095, 1992.
    • (1992) Ann. Rev. Biochemistry , vol.61 , pp. 1053-1095
    • Pabo, C.O.1    Sauer, R.T.2
  • 7
    • 30344472977 scopus 로고    scopus 로고
    • Adaptive evolution by optimizing expression levels in different environments
    • DOI 10.1016/j.tim.2005.11.005, PII S0966842X05003100
    • M.M. Babu and L. Aravind, "Adaptive Evolution by Optimizing Expression Levels in Different Environments," Trends in Microbiology, vol. 14, pp. 11-14, Jan. 2006. (Pubitemid 43063186)
    • (2006) Trends in Microbiology , vol.14 , Issue.1 , pp. 11-14
    • Babu, M.M.1    Aravind, L.2
  • 8
    • 67149102196 scopus 로고    scopus 로고
    • Methods to reconstruct and compare transcriptional regulatory networks
    • M.M. Babu et al., "Methods to Reconstruct and Compare Transcriptional Regulatory Networks," Methods in Molecular Biology, vol. 541, pp. 163-180, 2009.
    • (2009) Methods in Molecular Biology , vol.541 , pp. 163-180
    • Babu, M.M.1
  • 10
    • 68149161129 scopus 로고    scopus 로고
    • Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using coryneregnet
    • J. Baumbach et al., "Integrated Analysis and Reconstruction of Microbial Transcriptional Gene Regulatory Networks Using CoryneRegNet," Nature Protocols, vol. 4, pp. 992-1005, 2009.
    • (2009) Nature Protocols , vol.4 , pp. 992-1005
    • Baumbach, J.1
  • 11
    • 70949102952 scopus 로고    scopus 로고
    • Next generation sequencing of microbial transcriptomes: Challenges and opportunities
    • Nov.
    • A.H. van Vliet, "Next Generation Sequencing of Microbial Transcriptomes: Challenges and Opportunities," FEMS Microbiol Letters, vol. 302, pp. 1-7, Nov. 2009.
    • (2009) FEMS Microbiol Letters , vol.302 , pp. 1-7
    • Van Vliet, A.H.1
  • 12
    • 34548169696 scopus 로고    scopus 로고
    • Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions
    • DOI 10.1038/nprot.2007.249, PII NPROT.2007.249
    • L.M. Hellman and M.G. Fried, "Electrophoretic Mobility Shift Assay (EMSA) for Detecting Protein-Nucleic acid Interactions," Nature Protocols, vol. 2, pp. 1849-1861, 2007. (Pubitemid 47308124)
    • (2007) Nature Protocols , vol.2 , Issue.8 , pp. 1849-1861
    • Hellman, L.M.1    Fried, M.G.2
  • 13
    • 0018199224 scopus 로고
    • DNAase footprinting: A simple method for the detection of protein-DNA binding specificity
    • D.J. Galas and A. Schmitz, "DNAse Footprinting: A Simple Method for the Detection of Protein-DNA Binding Specificity," Nucleic Acids Research, vol. 5, pp. 3157-3170, Sept. 1978. (Pubitemid 9016990)
    • (1978) Nucleic Acids Research , vol.5 , Issue.9 , pp. 3157-3170
    • Galas, D.J.1    Schmitz, A.2
  • 15
    • 52649132425 scopus 로고    scopus 로고
    • Genome-wide identification of in vivo proteindna binding sites from chip-seq data
    • Sept.
    • R. Jothi et al., "Genome-Wide Identification of in vivo ProteinDNA Binding Sites from Chip-Seq Data," Nucleic Acids Research, vol. 36, pp. 5221-5231, Sept. 2008.
    • (2008) Nucleic Acids Research , vol.36 , pp. 5221-5231
    • Jothi, R.1
  • 16
    • 54249124501 scopus 로고    scopus 로고
    • Learning biological networks: From modules to dynamics
    • Nov.
    • R. Bonneau, "Learning Biological Networks: From Modules to Dynamics," Nature Chemical Biology, vol. 4, pp. 658-664, Nov. 2008.
    • (2008) Nature Chemical Biology , vol.4 , pp. 658-664
    • Bonneau, R.1
  • 17
    • 1242328740 scopus 로고    scopus 로고
    • Reconstruction of microbial transcriptional regulatory networks
    • DOI 10.1016/j.copbio.2003.11.002
    • M.J. Herrgard et al., "Reconstruction of Microbial Transcriptional Regulatory Networks," Current Opinion in Biotechnology, vol. 15, pp. 70-77, Feb. 2004. (Pubitemid 38224253)
    • (2004) Current Opinion in Biotechnology , vol.15 , Issue.1 , pp. 70-77
    • Herrgard, M.J.1    Covert, M.W.2    Palsson, B.O.3
  • 18
    • 33746887057 scopus 로고    scopus 로고
    • Escalating model sizes and complexities call for standardized forms of representation
    • article 2005.0011
    • M. Hucka and A. Finney, "Escalating Model Sizes and Complexities Call for Standardized Forms of Representation," Molecular Systems Biology, vol. 1, article 2005.0011, 2005.
    • (2005) Molecular Systems Biology , vol.1
    • Hucka, M.1    Finney, A.2
  • 21
    • 58149179979 scopus 로고    scopus 로고
    • EcoCyc: A comprehensive view of escher-ichia coli biology
    • Jan.
    • I.M. Keseler et al., "EcoCyc: A Comprehensive View of Escher-ichia Coli Biology," Nucleic Acids Research, vol. 37, pp. D464-D470, Jan. 2009.
    • (2009) Nucleic Acids Research , vol.37
    • Keseler, I.M.1
  • 22
    • 38549162091 scopus 로고    scopus 로고
    • DBTBS: A database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information
    • DOI 10.1093/nar/gkm910
    • N. Sierro et al., "DBTBS: A Database of Transcriptional Regulation in Bacillus Subtilis Containing Upstream Intergenic Conservation Information," Nucleic Acids Research, vol. 36, pp. D93-D96, 2008. (Pubitemid 351149702)
    • (2008) Nucleic Acids Research , vol.36 , Issue.SUPPL. 1
    • Sierro, N.1    Makita, Y.2    De Hoon, M.3    Nakai, K.4
  • 23
    • 33646907417 scopus 로고    scopus 로고
    • AGRIS and AtRegNet. A platform to link cis-regulatory elements and transcription factors into regulatory networks
    • DOI 10.1104/pp.105.072280
    • S.K. Palaniswamy et al., "AGRIS and AtRegNet. a Platform to Link Cis-Regulatory Elements and Transcription Factors into Regulatory Networks," Plant Physiology, vol. 140, pp. 818-829, 2006. (Pubitemid 43956237)
    • (2006) Plant Physiology , vol.140 , Issue.3 , pp. 818-829
    • Palaniswamy, S.K.1    James, S.2    Sun, H.3    Lamb, R.S.4    Davuluri, R.V.5    Grotewold, E.6
  • 24
    • 33644873438 scopus 로고    scopus 로고
    • RegulonDB (version 5.0): Escherichia coli k-12 transcriptional regulatory network, operon organization, and growth conditions
    • Jan.
    • H. Salgado et al., "RegulonDB (Version 5.0): Escherichia coli K-12 Transcriptional Regulatory Network, Operon Organization, and Growth Conditions," Nucleic Acids Research, vol. 34, pp. D394-D397, Jan. 2006.
    • (2006) Nucleic Acids Research , vol.34
    • Salgado, H.1
  • 26
    • 67651091927 scopus 로고    scopus 로고
    • Evaluation of three automated genome annotations for halorhabdus utahensis
    • P. Bakke et al., "Evaluation of Three Automated Genome Annotations for Halorhabdus Utahensis," PLoS One, vol. 4, p. e6291, 2009.
    • (2009) PLoS One , vol.4
    • Bakke, P.1
  • 27
    • 38549146907 scopus 로고    scopus 로고
    • DBD - Taxonomically broad transcription factor predictions: New content and functionality
    • DOI 10.1093/nar/gkm964
    • D. Wilson et al., "DBD-Taxonomically Broad Transcription Factor Predictions: New Content and Functionality," Nucleic Acids Research, vol. 36, pp. D88-D92, 2008. (Pubitemid 351149701)
    • (2008) Nucleic Acids Research , vol.36 , Issue.SUPPL. 1
    • Wilson, D.1    Charoensawan, V.2    Kummerfeld, S.K.3    Teichmann, S.A.4
  • 28
    • 55549111608 scopus 로고    scopus 로고
    • The temporal response of the mycobacterium tuberculosis gene regulatory network during growth arrest
    • G. Balazsi et al., "The Temporal Response of the Mycobacterium Tuberculosis Gene Regulatory Network During Growth Arrest," Molecular Systems Biology, vol. 4, p. 225, 2008.
    • (2008) Molecular Systems Biology , vol.4 , pp. 225
    • Balazsi, G.1
  • 29
    • 67650082448 scopus 로고    scopus 로고
    • Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system
    • July
    • M. Guo et al., "Dissecting Transcription Regulatory Pathways through a New Bacterial One-Hybrid Reporter System," Genome Research, vol. 19, pp. 1301-1308, July 2009.
    • (2009) Genome Research , vol.19 , pp. 1301-1308
    • Guo, M.1
  • 30
    • 0000713911 scopus 로고    scopus 로고
    • Bootstrap confidence intervals
    • T.J. DiCiccio and B. Efron, "Bootstrap Confidence Intervals," Statistical Science, vol. 11, pp. 189-212, 1996.
    • (1996) Statistical Science , vol.11 , pp. 189-212
    • Diciccio, T.J.1    Efron, B.2
  • 32
    • 65949090511 scopus 로고    scopus 로고
    • Target genes of the mads transcription factor sepallata3: Integration of developmental and hormonal pathways in the arabidopsis flower
    • K. Kaufmann et al., "Target Genes of the MADS Transcription Factor SEPALLATA3: Integration of Developmental and Hormonal Pathways in the Arabidopsis flower," PLoS Biology, vol. 7, p. e1000090, 2009.
    • (2009) PLoS Biology , vol.7
    • Kaufmann, K.1
  • 33
    • 64749089220 scopus 로고    scopus 로고
    • Genome-wide analysis of genes targeted by phytochrome interacting factor 3-like5 during seed germination in arabidopsis
    • E. Oh et al., "Genome-Wide Analysis of Genes Targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during Seed Germination in Arabidopsis," The Plant Cell, vol. 21, pp. 403-419, 2009.
    • (2009) The Plant Cell , vol.21 , pp. 403-419
    • Oh, E.1
  • 34
    • 70849092086 scopus 로고    scopus 로고
    • Global identification of targets of the arabidopsis mads domain protein agamous-like15
    • Y. Zheng et al., "Global Identification of Targets of the Arabidopsis MADS Domain Protein AGamous-Like15," The Plant Cell, vol. 21, pp. 2563-2577, 2009.
    • (2009) The Plant Cell , vol.21 , pp. 2563-2577
    • Zheng, Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.