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Volumn 11, Issue 1, 2010, Pages

Genome-wide inference of regulatory networks in Streptomyces coelicolor

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME; ARGININE;

EID: 77957911046     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-578     Document Type: Article
Times cited : (37)

References (68)
  • 1
    • 0037251368 scopus 로고    scopus 로고
    • Streptomyces genetics: a genomic perspective
    • 10.1080/713609296, 12693442
    • Paradkar A, Trefzer A, Chakraburtty R, Stassi D. Streptomyces genetics: a genomic perspective. Crit Rev Biotechnol 2003, 23(1):1-27. 10.1080/713609296, 12693442.
    • (2003) Crit Rev Biotechnol , vol.23 , Issue.1 , pp. 1-27
    • Paradkar, A.1    Trefzer, A.2    Chakraburtty, R.3    Stassi, D.4
  • 3
    • 28244432190 scopus 로고    scopus 로고
    • Cross-regulation among disparate antibiotic biosynthetic pathways of Streptomyces coelicolor
    • 10.1111/j.1365-2958.2005.04879.x, 16313616
    • Huang J, Shi J, Molle V, Sohlberg B, Weaver D, Bibb MJ, Karoonuthaisiri N, Lih CJ, Kao CM, Buttner MJ, et al. Cross-regulation among disparate antibiotic biosynthetic pathways of Streptomyces coelicolor. Mol Microbiol 2005, 58(5):1276-1287. 10.1111/j.1365-2958.2005.04879.x, 16313616.
    • (2005) Mol Microbiol , vol.58 , Issue.5 , pp. 1276-1287
    • Huang, J.1    Shi, J.2    Molle, V.3    Sohlberg, B.4    Weaver, D.5    Bibb, M.J.6    Karoonuthaisiri, N.7    Lih, C.J.8    Kao, C.M.9    Buttner, M.J.10
  • 4
    • 33846400424 scopus 로고    scopus 로고
    • Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
    • 10.1371/journal.pbio.0050008, 1764438, 17214507
    • Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 2007, 5(1):e8. 10.1371/journal.pbio.0050008, 1764438, 17214507.
    • (2007) PLoS Biol , vol.5 , Issue.1
    • Faith, J.J.1    Hayete, B.2    Thaden, J.T.3    Mogno, I.4    Wierzbowski, J.5    Cottarel, G.6    Kasif, S.7    Collins, J.J.8    Gardner, T.S.9
  • 5
    • 37548999354 scopus 로고    scopus 로고
    • Transcriptome dynamics-based operon prediction and verification in Streptomyces coelicolor
    • 10.1093/nar/gkm501, 2175336, 17959654
    • Charaniya S, Mehra S, Lian W, Jayapal KP, Karypis G, Hu WS. Transcriptome dynamics-based operon prediction and verification in Streptomyces coelicolor. Nucleic Acids Res 2007, 35(21):7222-7236. 10.1093/nar/gkm501, 2175336, 17959654.
    • (2007) Nucleic Acids Res , vol.35 , Issue.21 , pp. 7222-7236
    • Charaniya, S.1    Mehra, S.2    Lian, W.3    Jayapal, K.P.4    Karypis, G.5    Hu, W.S.6
  • 6
    • 0033655775 scopus 로고    scopus 로고
    • Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements
    • Butte AJ, Kohane IS. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput 2000, 418-429.
    • (2000) Pac Symp Biocomput , pp. 418-429
    • Butte, A.J.1    Kohane, I.S.2
  • 7
  • 8
    • 33947305781 scopus 로고    scopus 로고
    • ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
    • 10.1186/1471-2105-7-S1-S7, 1810318, 16723010
    • Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 2006, 7(Suppl 1):S7. 10.1186/1471-2105-7-S1-S7, 1810318, 16723010.
    • (2006) BMC Bioinformatics , vol.7 , Issue.SUPPL 1
    • Margolin, A.A.1    Nemenman, I.2    Basso, K.3    Wiggins, C.4    Stolovitzky, G.5    Dalla Favera, R.6    Califano, A.7
  • 9
    • 36248999573 scopus 로고    scopus 로고
    • Information-theoretic inference of large transcriptional regulatory networks
    • 2267250, 18354736
    • Meyer PE, Kontos K, Lafitte F, Bontempi G. Information-theoretic inference of large transcriptional regulatory networks. EURASIP J Bioinform Syst Biol 2007, 79879. 2267250, 18354736.
    • (2007) EURASIP J Bioinform Syst Biol , pp. 79879
    • Meyer, P.E.1    Kontos, K.2    Lafitte, F.3    Bontempi, G.4
  • 10
    • 62549091023 scopus 로고    scopus 로고
    • Benchmarking regulatory network reconstruction with GRENDEL
    • 10.1093/bioinformatics/btp068, 2732301, 19188190
    • Haynes BC, Brent MR. Benchmarking regulatory network reconstruction with GRENDEL. Bioinformatics 2009, 25(6):801-807. 10.1093/bioinformatics/btp068, 2732301, 19188190.
    • (2009) Bioinformatics , vol.25 , Issue.6 , pp. 801-807
    • Haynes, B.C.1    Brent, M.R.2
  • 11
    • 59849099039 scopus 로고    scopus 로고
    • On the impact of entropy estimation on transcriptional regulatory network inference based on mutual information
    • 2621307, 19148299
    • Olsen C, Meyer PE, Bontempi G. On the impact of entropy estimation on transcriptional regulatory network inference based on mutual information. EURASIP J Bioinform Syst Biol 2009, 308959. 2621307, 19148299.
    • (2009) EURASIP J Bioinform Syst Biol , pp. 308959
    • Olsen, C.1    Meyer, P.E.2    Bontempi, G.3
  • 14
    • 69749086899 scopus 로고    scopus 로고
    • Identification of rare cancer driver mutations by network reconstruction
    • 10.1101/gr.092833.109, 2752121, 19574499
    • Torkamani A, Schork NJ. Identification of rare cancer driver mutations by network reconstruction. Genome Res 2009, 19(9):1570-1578. 10.1101/gr.092833.109, 2752121, 19574499.
    • (2009) Genome Res , vol.19 , Issue.9 , pp. 1570-1578
    • Torkamani, A.1    Schork, N.J.2
  • 15
    • 38349086492 scopus 로고    scopus 로고
    • The global role of ppGpp synthesis in morphological differentiation and antibiotic production in Streptomyces coelicolor A3(2)
    • 10.1186/gb-2007-8-8-r161, 2374992, 17683547
    • Hesketh A, Chen WJ, Ryding J, Chang S, Bibb M. The global role of ppGpp synthesis in morphological differentiation and antibiotic production in Streptomyces coelicolor A3(2). Genome Biol 2007, 8(8):R161. 10.1186/gb-2007-8-8-r161, 2374992, 17683547.
    • (2007) Genome Biol , vol.8 , Issue.8
    • Hesketh, A.1    Chen, W.J.2    Ryding, J.3    Chang, S.4    Bibb, M.5
  • 16
    • 33747063538 scopus 로고    scopus 로고
    • Rag genes: novel components of the RamR regulon that trigger morphological differentiation in Streptomyces coelicolor
    • 10.1111/j.1365-2958.2006.05304.x, 16925552
    • San Paolo S, Huang J, Cohen SN, Thompson CJ. rag genes: novel components of the RamR regulon that trigger morphological differentiation in Streptomyces coelicolor. Mol Microbiol 2006, 61(5):1167-1186. 10.1111/j.1365-2958.2006.05304.x, 16925552.
    • (2006) Mol Microbiol , vol.61 , Issue.5 , pp. 1167-1186
    • San Paolo, S.1    Huang, J.2    Cohen, S.N.3    Thompson, C.J.4
  • 17
    • 0035576880 scopus 로고    scopus 로고
    • Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays
    • 10.1101/gad.943401, 312833, 11731481
    • Huang J, Lih CJ, Pan KH, Cohen SN. Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Genes Dev 2001, 15(23):3183-3192. 10.1101/gad.943401, 312833, 11731481.
    • (2001) Genes Dev , vol.15 , Issue.23 , pp. 3183-3192
    • Huang, J.1    Lih, C.J.2    Pan, K.H.3    Cohen, S.N.4
  • 18
    • 33847212809 scopus 로고    scopus 로고
    • Characterization of a large, stable, high-copy-number Streptomyces plasmid that requires stability and transfer functions for heterologous polyketide overproduction
    • 10.1128/AEM.01888-06, 1828658, 17142363
    • Fong R, Vroom JA, Hu Z, Hutchinson CR, Huang J, Cohen SN, Kao CM. Characterization of a large, stable, high-copy-number Streptomyces plasmid that requires stability and transfer functions for heterologous polyketide overproduction. Appl Environ Microbiol 2007, 73(4):1296-1307. 10.1128/AEM.01888-06, 1828658, 17142363.
    • (2007) Appl Environ Microbiol , vol.73 , Issue.4 , pp. 1296-1307
    • Fong, R.1    Vroom, J.A.2    Hu, Z.3    Hutchinson, C.R.4    Huang, J.5    Cohen, S.N.6    Kao, C.M.7
  • 19
    • 0038681008 scopus 로고    scopus 로고
    • The chaplins: a family of hydrophobic cell-surface proteins involved in aerial mycelium formation in Streptomyces coelicolor
    • 10.1101/gad.264403, 196181, 12832397
    • Elliot MA, Karoonuthaisiri N, Huang J, Bibb MJ, Cohen SN, Kao CM, Buttner MJ. The chaplins: a family of hydrophobic cell-surface proteins involved in aerial mycelium formation in Streptomyces coelicolor. Genes Dev 2003, 17(14):1727-1740. 10.1101/gad.264403, 196181, 12832397.
    • (2003) Genes Dev , vol.17 , Issue.14 , pp. 1727-1740
    • Elliot, M.A.1    Karoonuthaisiri, N.2    Huang, J.3    Bibb, M.J.4    Cohen, S.N.5    Kao, C.M.6    Buttner, M.J.7
  • 20
    • 23844442155 scopus 로고    scopus 로고
    • A master regulator sigmaB governs osmotic and oxidative response as well as differentiation via a network of sigma factors in Streptomyces coelicolor
    • 10.1111/j.1365-2958.2005.04761.x, 16101999
    • Lee EJ, Karoonuthaisiri N, Kim HS, Park JH, Cha CJ, Kao CM, Roe JH. A master regulator sigmaB governs osmotic and oxidative response as well as differentiation via a network of sigma factors in Streptomyces coelicolor. Molecular Microbiology 2005, 57(5):1252-1264. 10.1111/j.1365-2958.2005.04761.x, 16101999.
    • (2005) Molecular Microbiology , vol.57 , Issue.5 , pp. 1252-1264
    • Lee, E.J.1    Karoonuthaisiri, N.2    Kim, H.S.3    Park, J.H.4    Cha, C.J.5    Kao, C.M.6    Roe, J.H.7
  • 21
    • 40949165022 scopus 로고    scopus 로고
    • Genome-wide transcriptome analysis reveals that a pleiotropic antibiotic regulator, AfsS, modulates nutritional stress response in Streptomyces coelicolor A3(2)
    • 10.1186/1471-2164-9-56, 2267785, 18230178
    • Lian W, Jayapal KP, Charaniya S, Mehra S, Glod F, Kyung YS, Sherman DH, Hu WS. Genome-wide transcriptome analysis reveals that a pleiotropic antibiotic regulator, AfsS, modulates nutritional stress response in Streptomyces coelicolor A3(2). BMC Genomics 2008, 9:56. 10.1186/1471-2164-9-56, 2267785, 18230178.
    • (2008) BMC Genomics , vol.9 , pp. 56
    • Lian, W.1    Jayapal, K.P.2    Charaniya, S.3    Mehra, S.4    Glod, F.5    Kyung, Y.S.6    Sherman, D.H.7    Hu, W.S.8
  • 22
    • 34548042564 scopus 로고    scopus 로고
    • Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans
    • 10.1186/1471-2164-8-229, 1934918, 17623098
    • Jayapal KP, Lian W, Glod F, Sherman DH, Hu WS. Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans. BMC Genomics 2007, 8:229. 10.1186/1471-2164-8-229, 1934918, 17623098.
    • (2007) BMC Genomics , vol.8 , pp. 229
    • Jayapal, K.P.1    Lian, W.2    Glod, F.3    Sherman, D.H.4    Hu, W.S.5
  • 23
    • 78149499530 scopus 로고    scopus 로고
    • Genome-wide analysis of regulatory networks controling secondary metabolism in Streptomyces species
    • University of Minnesota, Department of Chemical Engineering and Materials Science
    • Lian W. Genome-wide analysis of regulatory networks controling secondary metabolism in Streptomyces species. PhD thesis 2005, University of Minnesota, Department of Chemical Engineering and Materials Science.
    • (2005) PhD thesis
    • Lian, W.1
  • 24
    • 33745622982 scopus 로고    scopus 로고
    • DNA microarray-based analysis of gene expression in Streptomyces coelicolor A3(2) and Streptomyces lividans
    • University of Manchester, Department of Biomolecular Sciences
    • Mersinias V. DNA microarray-based analysis of gene expression in Streptomyces coelicolor A3(2) and Streptomyces lividans. PhD thesis 2004, University of Manchester, Department of Biomolecular Sciences.
    • (2004) PhD thesis
    • Mersinias, V.1
  • 27
    • 78149497426 scopus 로고    scopus 로고
    • Protein Classification Scheme
    • Protein Classification Scheme. , http://www.sanger.ac.uk/Projects/S_coelicolor/scheme.shtml
  • 28
    • 20444365683 scopus 로고    scopus 로고
    • GOToolBox: functional analysis of gene datasets based on Gene Ontology
    • 10.1186/gb-2004-5-12-r101, 545796, 15575967
    • Martin D, Brun C, Remy E, Mouren P, Thieffry D, Jacq B. GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol 2004, 5(12):R101. 10.1186/gb-2004-5-12-r101, 545796, 15575967.
    • (2004) Genome Biol , vol.5 , Issue.12
    • Martin, D.1    Brun, C.2    Remy, E.3    Mouren, P.4    Thieffry, D.5    Jacq, B.6
  • 29
    • 34250764323 scopus 로고    scopus 로고
    • GOSim--an R-package for computation of information theoretic GO similarities between terms and gene products
    • 10.1186/1471-2105-8-166, 1892785, 17519018
    • Frohlich H, Speer N, Poustka A, Beissbarth T. GOSim--an R-package for computation of information theoretic GO similarities between terms and gene products. BMC Bioinformatics 2007, 8:166. 10.1186/1471-2105-8-166, 1892785, 17519018.
    • (2007) BMC Bioinformatics , vol.8 , pp. 166
    • Frohlich, H.1    Speer, N.2    Poustka, A.3    Beissbarth, T.4
  • 30
    • 58149197596 scopus 로고    scopus 로고
    • OperonDB: a comprehensive database of predicted operons in microbial genomes
    • 10.1093/nar/gkn784, 2686487, 18948284
    • Pertea M, Ayanbule K, Smedinghoff M, Salzberg SL. OperonDB: a comprehensive database of predicted operons in microbial genomes. Nucleic Acids Res 2009, (37 Database):D479-482. 10.1093/nar/gkn784, 2686487, 18948284.
    • (2009) Nucleic Acids Res , Issue.37 DATABASE
    • Pertea, M.1    Ayanbule, K.2    Smedinghoff, M.3    Salzberg, S.L.4
  • 31
    • 0035282698 scopus 로고    scopus 로고
    • Prediction of operons in microbial genomes
    • 10.1093/nar/29.5.1216, 29727, 11222772
    • Ermolaeva MD, White O, Salzberg SL. Prediction of operons in microbial genomes. Nucleic Acids Res 2001, 29(5):1216-1221. 10.1093/nar/29.5.1216, 29727, 11222772.
    • (2001) Nucleic Acids Res , vol.29 , Issue.5 , pp. 1216-1221
    • Ermolaeva, M.D.1    White, O.2    Salzberg, S.L.3
  • 32
    • 78149501333 scopus 로고    scopus 로고
    • StrepDB - The Streptomyces Annotation Server
    • StrepDB - The Streptomyces Annotation Server. , http://strepdb.streptomyces.org.uk/cgi-bin/dc3.pl?accession=AL645882&start=4291472&end=4302043&iorm=map&width=900
  • 33
    • 0002714543 scopus 로고    scopus 로고
    • Making large-scale support vector machine learning practical
    • MIT Press, Scholkofp B, Burges CJC, Mika S
    • Joachims T. Making large-scale support vector machine learning practical. Advances in kernel methods 1999, 169-184. MIT Press, Scholkofp B, Burges CJC, Mika S.
    • (1999) Advances in kernel methods , pp. 169-184
    • Joachims, T.1
  • 34
    • 33645467335 scopus 로고    scopus 로고
    • Nur, a nickel-responsive regulator of the Fur family, regulates superoxide dismutases and nickel transport in Streptomyces coelicolor
    • 10.1111/j.1365-2958.2006.05065.x, 16553888
    • Ahn BE, Cha J, Lee EJ, Han AR, Thompson CJ, Roe JH. Nur, a nickel-responsive regulator of the Fur family, regulates superoxide dismutases and nickel transport in Streptomyces coelicolor. Mol Microbiol 2006, 59(6):1848-1858. 10.1111/j.1365-2958.2006.05065.x, 16553888.
    • (2006) Mol Microbiol , vol.59 , Issue.6 , pp. 1848-1858
    • Ahn, B.E.1    Cha, J.2    Lee, E.J.3    Han, A.R.4    Thompson, C.J.5    Roe, J.H.6
  • 35
    • 33745906951 scopus 로고    scopus 로고
    • DevA, a GntR-like transcriptional regulator required for development in Streptomyces coelicolor
    • 10.1128/JB.00307-06, 1539961, 16816174
    • Hoskisson PA, Rigali S, Fowler K, Findlay KC, Buttner MJ. DevA, a GntR-like transcriptional regulator required for development in Streptomyces coelicolor. J Bacteriol 2006, 188(14):5014-5023. 10.1128/JB.00307-06, 1539961, 16816174.
    • (2006) J Bacteriol , vol.188 , Issue.14 , pp. 5014-5023
    • Hoskisson, P.A.1    Rigali, S.2    Fowler, K.3    Findlay, K.C.4    Buttner, M.J.5
  • 36
    • 33645244512 scopus 로고    scopus 로고
    • Coenzyme B12 controls transcription of the Streptomyces class Ia ribonucleotide reductase nrdABS operon via a riboswitch mechanism
    • 10.1128/JB.188.7.2512-2520.2006, 1428431, 16547038
    • Borovok I, Gorovitz B, Schreiber R, Aharonowitz Y, Cohen G. Coenzyme B12 controls transcription of the Streptomyces class Ia ribonucleotide reductase nrdABS operon via a riboswitch mechanism. J Bacteriol 2006, 188(7):2512-2520. 10.1128/JB.188.7.2512-2520.2006, 1428431, 16547038.
    • (2006) J Bacteriol , vol.188 , Issue.7 , pp. 2512-2520
    • Borovok, I.1    Gorovitz, B.2    Schreiber, R.3    Aharonowitz, Y.4    Cohen, G.5
  • 37
    • 34249806024 scopus 로고    scopus 로고
    • The zinc-responsive regulator Zur controls a zinc uptake system and some ribosomal proteins in Streptomyces coelicolor A3(2)
    • 10.1128/JB.01851-06, 1913400, 17416659
    • Shin JH, Oh SY, Kim SJ, Roe JH. The zinc-responsive regulator Zur controls a zinc uptake system and some ribosomal proteins in Streptomyces coelicolor A3(2). J Bacteriol 2007, 189(11):4070-4077. 10.1128/JB.01851-06, 1913400, 17416659.
    • (2007) J Bacteriol , vol.189 , Issue.11 , pp. 4070-4077
    • Shin, J.H.1    Oh, S.Y.2    Kim, S.J.3    Roe, J.H.4
  • 38
    • 34249811787 scopus 로고    scopus 로고
    • Zinc-responsive regulation of alternative ribosomal protein genes in Streptomyces coelicolor involves zur and sigmaR
    • 10.1128/JB.01901-06, 1913420, 17400736
    • Owen GA, Pascoe B, Kallifidas D, Paget MS. Zinc-responsive regulation of alternative ribosomal protein genes in Streptomyces coelicolor involves zur and sigmaR. J Bacteriol 2007, 189(11):4078-4086. 10.1128/JB.01901-06, 1913420, 17400736.
    • (2007) J Bacteriol , vol.189 , Issue.11 , pp. 4078-4086
    • Owen, G.A.1    Pascoe, B.2    Kallifidas, D.3    Paget, M.S.4
  • 39
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: a software environment for integrated models of biomolecular interaction networks
    • 10.1101/gr.1239303, 403769, 14597658
    • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504. 10.1101/gr.1239303, 403769, 14597658.
    • (2003) Genome Res , vol.13 , Issue.11 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.S.4    Wang, J.T.5    Ramage, D.6    Amin, N.7    Schwikowski, B.8    Ideker, T.9
  • 41
    • 1142273091 scopus 로고    scopus 로고
    • Strong control, conservative point estimation, and simultaneous conservatie consistency of false discovery rates: A unified approach
    • Storey JD, Taylor JE, Siegmund D. Strong control, conservative point estimation, and simultaneous conservatie consistency of false discovery rates: A unified approach. Journal of the Royal Statistical Society, Series B 2004, 66:187-205.
    • (2004) Journal of the Royal Statistical Society, Series B , vol.66 , pp. 187-205
    • Storey, J.D.1    Taylor, J.E.2    Siegmund, D.3
  • 42
    • 33747823564 scopus 로고    scopus 로고
    • MEME: discovering and analyzing DNA and protein sequence motifs
    • 10.1093/nar/gkl198, 1538909, 16845028
    • Bailey TL, Williams N, Misleh C, Li WW. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 2006, (34 Web Server):W369-373. 10.1093/nar/gkl198, 1538909, 16845028.
    • (2006) Nucleic Acids Res , Issue.34 WEB SERVER
    • Bailey, T.L.1    Williams, N.2    Misleh, C.3    Li, W.W.4
  • 43
    • 0031877016 scopus 로고    scopus 로고
    • Combining evidence using p-values: application to sequence homology searches
    • 10.1093/bioinformatics/14.1.48, 9520501
    • Bailey TL, Gribskov M. Combining evidence using p-values: application to sequence homology searches. Bioinformatics 1998, 14(1):48-54. 10.1093/bioinformatics/14.1.48, 9520501.
    • (1998) Bioinformatics , vol.14 , Issue.1 , pp. 48-54
    • Bailey, T.L.1    Gribskov, M.2
  • 44
    • 2142738304 scopus 로고    scopus 로고
    • WebLogo: a sequence logo generator
    • 10.1101/gr.849004, 419797, 15173120
    • Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res 2004, 14(6):1188-1190. 10.1101/gr.849004, 419797, 15173120.
    • (2004) Genome Res , vol.14 , Issue.6 , pp. 1188-1190
    • Crooks, G.E.1    Hon, G.2    Chandonia, J.M.3    Brenner, S.E.4
  • 45
    • 0035133737 scopus 로고    scopus 로고
    • Genetic and transcriptional analysis of absA, an antibiotic gene cluster-linked two-component system that regulates multiple antibiotics in Streptomyces coelicolor
    • 10.1046/j.1365-2958.2001.02240.x, 11169098
    • Anderson TB, Brian P, Champness WC. Genetic and transcriptional analysis of absA, an antibiotic gene cluster-linked two-component system that regulates multiple antibiotics in Streptomyces coelicolor. Mol Microbiol 2001, 39(3):553-566. 10.1046/j.1365-2958.2001.02240.x, 11169098.
    • (2001) Mol Microbiol , vol.39 , Issue.3 , pp. 553-566
    • Anderson, T.B.1    Brian, P.2    Champness, W.C.3
  • 46
    • 0036210082 scopus 로고    scopus 로고
    • Expression, autoregulation, and DNA binding properties of the Mycobacterium tuberculosis TrcR response regulator
    • 10.1128/JB.184.8.2192-2203.2002, 134962, 11914351
    • Haydel SE, Benjamin WH, Dunlap NE, Clark-Curtiss JE. Expression, autoregulation, and DNA binding properties of the Mycobacterium tuberculosis TrcR response regulator. J Bacteriol 2002, 184(8):2192-2203. 10.1128/JB.184.8.2192-2203.2002, 134962, 11914351.
    • (2002) J Bacteriol , vol.184 , Issue.8 , pp. 2192-2203
    • Haydel, S.E.1    Benjamin, W.H.2    Dunlap, N.E.3    Clark-Curtiss, J.E.4
  • 47
    • 0034537103 scopus 로고    scopus 로고
    • Molecular characterization of the mycobacterial SenX3-RegX3 two-component system: evidence for autoregulation
    • Himpens S, Locht C, Supply P. Molecular characterization of the mycobacterial SenX3-RegX3 two-component system: evidence for autoregulation. Microbiology 2000, 146(12):3091-3098.
    • (2000) Microbiology , vol.146 , Issue.12 , pp. 3091-3098
    • Himpens, S.1    Locht, C.2    Supply, P.3
  • 48
    • 1642514522 scopus 로고    scopus 로고
    • Intracellular autoregulation of the Mycobacterium tuberculosis PrrA response regulator
    • 10.1099/mic.0.26516-0, 14702417
    • Ewann F, Locht C, Supply P. Intracellular autoregulation of the Mycobacterium tuberculosis PrrA response regulator. Microbiology 2004, 150(1):241-246. 10.1099/mic.0.26516-0, 14702417.
    • (2004) Microbiology , vol.150 , Issue.1 , pp. 241-246
    • Ewann, F.1    Locht, C.2    Supply, P.3
  • 49
    • 0036176756 scopus 로고    scopus 로고
    • Regulation of the Streptomyces coelicolor calcium-dependent antibiotic by absA, encoding a cluster-linked two-component system
    • 10.1128/JB.184.3.794-805.2002, 139508, 11790750
    • Ryding NJ, Anderson TB, Champness WC. Regulation of the Streptomyces coelicolor calcium-dependent antibiotic by absA, encoding a cluster-linked two-component system. J Bacteriol 2002, 184(3):794-805. 10.1128/JB.184.3.794-805.2002, 139508, 11790750.
    • (2002) J Bacteriol , vol.184 , Issue.3 , pp. 794-805
    • Ryding, N.J.1    Anderson, T.B.2    Champness, W.C.3
  • 51
    • 0025899144 scopus 로고
    • The act cluster contains regulatory and antibiotic export genes, direct targets for translational control by the bldA tRNA gene of Streptomyces
    • 10.1016/0092-8674(91)90120-N, 1878971
    • Fernandez-Moreno MA, Caballero JL, Hopwood DA, Malpartida F. The act cluster contains regulatory and antibiotic export genes, direct targets for translational control by the bldA tRNA gene of Streptomyces. Cell 1991, 66(4):769-780. 10.1016/0092-8674(91)90120-N, 1878971.
    • (1991) Cell , vol.66 , Issue.4 , pp. 769-780
    • Fernandez-Moreno, M.A.1    Caballero, J.L.2    Hopwood, D.A.3    Malpartida, F.4
  • 52
    • 0031016476 scopus 로고    scopus 로고
    • BldA dependence of undecylprodigiosin production in Streptomyces coelicolor A3(2) involves a pathway-specific regulatory cascade
    • 178740, 9006013
    • White J, Bibb M. bldA dependence of undecylprodigiosin production in Streptomyces coelicolor A3(2) involves a pathway-specific regulatory cascade. J Bacteriol 1997, 179(3):627-633. 178740, 9006013.
    • (1997) J Bacteriol , vol.179 , Issue.3 , pp. 627-633
    • White, J.1    Bibb, M.2
  • 53
    • 34447560037 scopus 로고    scopus 로고
    • Phosphorylated AbsA2 negatively regulates antibiotic production in Streptomyces coelicolor through interactions with pathway-specific regulatory gene promoters
    • 10.1128/JB.00305-07, 1951880, 17513473
    • McKenzie NL, Nodwell JR. Phosphorylated AbsA2 negatively regulates antibiotic production in Streptomyces coelicolor through interactions with pathway-specific regulatory gene promoters. J Bacteriol 2007, 189(14):5284-5292. 10.1128/JB.00305-07, 1951880, 17513473.
    • (2007) J Bacteriol , vol.189 , Issue.14 , pp. 5284-5292
    • McKenzie, N.L.1    Nodwell, J.R.2
  • 54
    • 3142743426 scopus 로고    scopus 로고
    • Characterization of an inducible vancomycin resistance system in Streptomyces coelicolor reveals a novel gene (vanK) required for drug resistance
    • 10.1111/j.1365-2958.2004.04032.x, 15130128
    • Hong HJ, Hutchings MI, Neu JM, Wright GD, Paget MSB, Buttner MJ. Characterization of an inducible vancomycin resistance system in Streptomyces coelicolor reveals a novel gene (vanK) required for drug resistance. Molecular Microbiology 2004, 52(4):1107-1121. 10.1111/j.1365-2958.2004.04032.x, 15130128.
    • (2004) Molecular Microbiology , vol.52 , Issue.4 , pp. 1107-1121
    • Hong, H.J.1    Hutchings, M.I.2    Neu, J.M.3    Wright, G.D.4    Paget, M.S.B.5    Buttner, M.J.6
  • 55
    • 0036042516 scopus 로고    scopus 로고
    • The ramC gene is required for morphogenesis in Streptomyces coelicolor and expressed in a cell type-specific manner under the direct control of RamR
    • 10.1046/j.1365-2958.2002.03004.x, 12100547
    • O'Connor TJ, Kanellis P, Nodwell JR. The ramC gene is required for morphogenesis in Streptomyces coelicolor and expressed in a cell type-specific manner under the direct control of RamR. Mol Microbiol 2002, 45(1):45-57. 10.1046/j.1365-2958.2002.03004.x, 12100547.
    • (2002) Mol Microbiol , vol.45 , Issue.1 , pp. 45-57
    • O'Connor, T.J.1    Kanellis, P.2    Nodwell, J.R.3
  • 56
    • 41449117761 scopus 로고    scopus 로고
    • Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor
    • 10.1186/1471-2164-9-79, 2276206, 18269733
    • Laing E, Sidhu K, Hubbard SJ. Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor. BMC Genomics 2008, 9:79. 10.1186/1471-2164-9-79, 2276206, 18269733.
    • (2008) BMC Genomics , vol.9 , pp. 79
    • Laing, E.1    Sidhu, K.2    Hubbard, S.J.3
  • 57
    • 0030855121 scopus 로고    scopus 로고
    • Arginine boxes and the argR gene in Streptomyces clavuligerus: evidence for a clear regulation of the arginine pathway
    • 10.1046/j.1365-2958.1997.4511815.x, 9282734
    • Rodriguez-Garcia A, Ludovice M, Martin JF, Liras P. Arginine boxes and the argR gene in Streptomyces clavuligerus: evidence for a clear regulation of the arginine pathway. Mol Microbiol 1997, 25(2):219-228. 10.1046/j.1365-2958.1997.4511815.x, 9282734.
    • (1997) Mol Microbiol , vol.25 , Issue.2 , pp. 219-228
    • Rodriguez-Garcia, A.1    Ludovice, M.2    Martin, J.F.3    Liras, P.4
  • 58
    • 20244388405 scopus 로고    scopus 로고
    • A bacterial hormone (the SCB1) directly controls the expression of a pathway-specific regulatory gene in the cryptic type I polyketide biosynthetic gene cluster of Streptomyces coelicolor
    • 10.1111/j.1365-2958.2005.04543.x, 15813737
    • Takano E, Kinoshita H, Mersinias V, Bucca G, Hotchkiss G, Nihira T, Smith CP, Bibb M, Wohlleben W, Chater K. A bacterial hormone (the SCB1) directly controls the expression of a pathway-specific regulatory gene in the cryptic type I polyketide biosynthetic gene cluster of Streptomyces coelicolor. Mol Microbiol 2005, 56(2):465-479. 10.1111/j.1365-2958.2005.04543.x, 15813737.
    • (2005) Mol Microbiol , vol.56 , Issue.2 , pp. 465-479
    • Takano, E.1    Kinoshita, H.2    Mersinias, V.3    Bucca, G.4    Hotchkiss, G.5    Nihira, T.6    Smith, C.P.7    Bibb, M.8    Wohlleben, W.9    Chater, K.10
  • 59
    • 38649084424 scopus 로고    scopus 로고
    • Secreted-protein response to sigmaU activity in Streptomyces coelicolor
    • 10.1128/JB.01759-07, 2223559, 18065550
    • Gordon ND, Ottaviano GL, Connell SE, Tobkin GV, Son CH, Shterental S, Gehring AM. Secreted-protein response to sigmaU activity in Streptomyces coelicolor. J Bacteriol 2008, 190(3):894-904. 10.1128/JB.01759-07, 2223559, 18065550.
    • (2008) J Bacteriol , vol.190 , Issue.3 , pp. 894-904
    • Gordon, N.D.1    Ottaviano, G.L.2    Connell, S.E.3    Tobkin, G.V.4    Son, C.H.5    Shterental, S.6    Gehring, A.M.7
  • 60
    • 0035731116 scopus 로고    scopus 로고
    • Negative regulation of the heat shock response in Streptomyces
    • 10.1007/s002030100321, 11685367
    • Servant P, Mazodier P. Negative regulation of the heat shock response in Streptomyces. Arch Microbiol 2001, 176(4):237-242. 10.1007/s002030100321, 11685367.
    • (2001) Arch Microbiol , vol.176 , Issue.4 , pp. 237-242
    • Servant, P.1    Mazodier, P.2
  • 61
    • 34548742517 scopus 로고    scopus 로고
    • Identification of functional modules using network topology and high-throughput data
    • 10.1186/1752-0509-1-8, 1839897, 17408515
    • Ulitsky I, Shamir R. Identification of functional modules using network topology and high-throughput data. BMC Syst Biol 2007, 1:8. 10.1186/1752-0509-1-8, 1839897, 17408515.
    • (2007) BMC Syst Biol , vol.1 , pp. 8
    • Ulitsky, I.1    Shamir, R.2
  • 62
    • 33751363730 scopus 로고    scopus 로고
    • Proteins encoded by the conservon of Streptomyces coelicolor A3(2) comprise a membrane-associated heterocomplex that resembles eukaryotic G protein-coupled regulatory system
    • 10.1111/j.1365-2958.2006.05461.x, 17083469
    • Komatsu M, Takano H, Hiratsuka T, Ishigaki Y, Shimada K, Beppu T, Ueda K. Proteins encoded by the conservon of Streptomyces coelicolor A3(2) comprise a membrane-associated heterocomplex that resembles eukaryotic G protein-coupled regulatory system. Mol Microbiol 2006, 62(6):1534-1546. 10.1111/j.1365-2958.2006.05461.x, 17083469.
    • (2006) Mol Microbiol , vol.62 , Issue.6 , pp. 1534-1546
    • Komatsu, M.1    Takano, H.2    Hiratsuka, T.3    Ishigaki, Y.4    Shimada, K.5    Beppu, T.6    Ueda, K.7
  • 63
    • 0034609791 scopus 로고    scopus 로고
    • The large-scale organization of metabolic networks
    • 10.1038/35036627, 11034217
    • Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL. The large-scale organization of metabolic networks. Nature 2000, 407(6804):651-654. 10.1038/35036627, 11034217.
    • (2000) Nature , vol.407 , Issue.6804 , pp. 651-654
    • Jeong, H.1    Tombor, B.2    Albert, R.3    Oltvai, Z.N.4    Barabasi, A.L.5
  • 64
    • 1842580761 scopus 로고    scopus 로고
    • Functional and topological characterization of protein interaction networks
    • 10.1002/pmic.200300636, 15048975
    • Yook SH, Oltvai ZN, Barabasi AL. Functional and topological characterization of protein interaction networks. Proteomics 2004, 4(4):928-942. 10.1002/pmic.200300636, 15048975.
    • (2004) Proteomics , vol.4 , Issue.4 , pp. 928-942
    • Yook, S.H.1    Oltvai, Z.N.2    Barabasi, A.L.3
  • 65
    • 47749130062 scopus 로고    scopus 로고
    • Uncovering genes with divergent mRNA-protein dynamics in Streptomyces coelicolor
    • 10.1371/journal.pone.0002097, 2367054, 18461186
    • Jayapal KP, Philp RJ, Kok YJ, Yap MG, Sherman DH, Griffin TJ, Hu WS. Uncovering genes with divergent mRNA-protein dynamics in Streptomyces coelicolor. PLoS One 2008, 3(5):e2097. 10.1371/journal.pone.0002097, 2367054, 18461186.
    • (2008) PLoS One , vol.3 , Issue.5
    • Jayapal, K.P.1    Philp, R.J.2    Kok, Y.J.3    Yap, M.G.4    Sherman, D.H.5    Griffin, T.J.6    Hu, W.S.7
  • 66
    • 36248989626 scopus 로고    scopus 로고
    • Theory and limitations of genetic network inference from microarray data
    • 10.1196/annals.1407.019, 17925348
    • Margolin AA, Califano A. Theory and limitations of genetic network inference from microarray data. Ann N Y Acad Sci 2007, 1115:51-72. 10.1196/annals.1407.019, 17925348.
    • (2007) Ann N Y Acad Sci , vol.1115 , pp. 51-72
    • Margolin, A.A.1    Califano, A.2
  • 67
    • 77952663448 scopus 로고    scopus 로고
    • TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach
    • 10.1186/1471-2105-11-154, 2862045, 20338053
    • Zoppoli P, Morganella S, Ceccarelli M. TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach. BMC Bioinformatics 2010, 11(1):154. 10.1186/1471-2105-11-154, 2862045, 20338053.
    • (2010) BMC Bioinformatics , vol.11 , Issue.1 , pp. 154
    • Zoppoli, P.1    Morganella, S.2    Ceccarelli, M.3


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