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Volumn 5, Issue , 2011, Pages

DENSE: Efficient and prior knowledge-driven discovery of phenotype-associated protein functional modules

Author keywords

[No Author keywords available]

Indexed keywords

FIBRONECTIN; NEUROPILIN 1; PANCREATIC ELASTASE; VASCULOTROPIN A; VASCULOTROPIN RECEPTOR;

EID: 82655184662     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-172     Document Type: Article
Times cited : (7)

References (45)
  • 1
    • 35349025902 scopus 로고    scopus 로고
    • Cross-talk between iron and nitrogen regulatory networks in Anabaena (Nostoc) sp. PCC 7120: Identification of overlapping genes in FurA and NtcA regulons
    • 10.1016/j.jmb.2007.09.010, 17920076
    • Lopez-Gomollon S, Hernandez JA, Pellicer S, Angarica VE, Peleato ML, Fillat MF. Cross-talk between iron and nitrogen regulatory networks in Anabaena (Nostoc) sp. PCC 7120: Identification of overlapping genes in FurA and NtcA regulons. J Mol Biol 2007, 374:267-281. 10.1016/j.jmb.2007.09.010, 17920076.
    • (2007) J Mol Biol , vol.374 , pp. 267-281
    • Lopez-Gomollon, S.1    Hernandez, J.A.2    Pellicer, S.3    Angarica, V.E.4    Peleato, M.L.5    Fillat, M.F.6
  • 2
    • 0041365478 scopus 로고    scopus 로고
    • Cross-talk between the L-sorbose and D-sorbitol (D-glucitol) metabolic pathways in Lactobacillus casei
    • Yebra MJ, Perez-Martinez G. Cross-talk between the L-sorbose and D-sorbitol (D-glucitol) metabolic pathways in Lactobacillus casei. Microbiology 2002, 148(8):2351-2359.
    • (2002) Microbiology , vol.148 , Issue.8 , pp. 2351-2359
    • Yebra, M.J.1    Perez-Martinez, G.2
  • 4
    • 32644435068 scopus 로고    scopus 로고
    • Biological hydrogen production by Clostridium acetobutylicum in an unsaturated flow reactor
    • 10.1016/j.watres.2005.11.041, 16427113
    • Zhang H, Bruns MA, Logan BE. Biological hydrogen production by Clostridium acetobutylicum in an unsaturated flow reactor. Water Res 2006, 40(4):728-734. 10.1016/j.watres.2005.11.041, 16427113.
    • (2006) Water Res , vol.40 , Issue.4 , pp. 728-734
    • Zhang, H.1    Bruns, M.A.2    Logan, B.E.3
  • 5
    • 77952245252 scopus 로고    scopus 로고
    • Succesion of the bacterial community and dynamics of hydrogen producers in a hydrogen-producing bioreactor
    • 10.1128/AEM.02444-09, 2869144, 20305018
    • Huang Y, Zong W, Yang X, Wang R, Hemme CL, Zhou J, Zhou Z. Succesion of the bacterial community and dynamics of hydrogen producers in a hydrogen-producing bioreactor. Appl Environ Microbiol 2010, 76(10):3387-3390. 10.1128/AEM.02444-09, 2869144, 20305018.
    • (2010) Appl Environ Microbiol , vol.76 , Issue.10 , pp. 3387-3390
    • Huang, Y.1    Zong, W.2    Yang, X.3    Wang, R.4    Hemme, C.L.5    Zhou, J.6    Zhou, Z.7
  • 6
    • 77950629484 scopus 로고    scopus 로고
    • Metabolite stress and tolerance in the production of biofuels and chemicals: Gene-expression-based systems analysis of butanol, butyrate, and acetate stresses in the anaerobe Clostridium acetobutylicum
    • Alsaker KV, Paredes C, Papoutsakis ET. Metabolite stress and tolerance in the production of biofuels and chemicals: Gene-expression-based systems analysis of butanol, butyrate, and acetate stresses in the anaerobe Clostridium acetobutylicum. Biotechnol Bioeng 2010, 105(6):1131-1147.
    • (2010) Biotechnol Bioeng , vol.105 , Issue.6 , pp. 1131-1147
    • Alsaker, K.V.1    Paredes, C.2    Papoutsakis, E.T.3
  • 7
    • 0022480123 scopus 로고
    • Nutritional Factors Affecting the Ratio of Solvents Produced by Clostridium acetobutylicum
    • 203431, 16347104
    • Bahl H, Gottwald M, Kuhn A, Rale V, Andersch W, Gottschalk G. Nutritional Factors Affecting the Ratio of Solvents Produced by Clostridium acetobutylicum. Appl Environ Microbiol 1986, 52:169-172. 203431, 16347104.
    • (1986) Appl Environ Microbiol , vol.52 , pp. 169-172
    • Bahl, H.1    Gottwald, M.2    Kuhn, A.3    Rale, V.4    Andersch, W.5    Gottschalk, G.6
  • 9
    • 0034886919 scopus 로고    scopus 로고
    • Classification and phylogeny of hydrogenases
    • Vignais PM, Billoud B, Meyer J. Classification and phylogeny of hydrogenases. FEMS Microbiol Rev 2001, 25(4):455-501.
    • (2001) FEMS Microbiol Rev , vol.25 , Issue.4 , pp. 455-501
    • Vignais, P.M.1    Billoud, B.2    Meyer, J.3
  • 10
    • 33947219284 scopus 로고    scopus 로고
    • Redirection of metabolism for biological hydrogen production
    • 10.1128/AEM.02565-06, 1828789, 17220249
    • Rey FE, Heiniger EK, Harwood CS. Redirection of metabolism for biological hydrogen production. Appl Environ Microbiol 2007, 73(5):1665-1671. 10.1128/AEM.02565-06, 1828789, 17220249.
    • (2007) Appl Environ Microbiol , vol.73 , Issue.5 , pp. 1665-1671
    • Rey, F.E.1    Heiniger, E.K.2    Harwood, C.S.3
  • 11
    • 37049036552 scopus 로고    scopus 로고
    • Engineering of a synthetic HydF-HydE-HydG-HydA operon for biohydrogen production
    • 10.1016/j.ab.2007.10.018, 17996187
    • Akhtar MK, Jones PR. Engineering of a synthetic HydF-HydE-HydG-HydA operon for biohydrogen production. Anal Biochem 2008, 373:170-172. 10.1016/j.ab.2007.10.018, 17996187.
    • (2008) Anal Biochem , vol.373 , pp. 170-172
    • Akhtar, M.K.1    Jones, P.R.2
  • 12
    • 34548408733 scopus 로고    scopus 로고
    • Crystal structures of hydrogenase maturation protein HypE in the Apo and ATP-bound forms
    • 10.1016/j.jmb.2007.07.023, 17706667
    • Shomura Y, Komori H, Miyabe N, Tomiyama M, Shibata N, Higuchi Y. Crystal structures of hydrogenase maturation protein HypE in the Apo and ATP-bound forms. J Mol Biol 2007, 372(4):1045-1054. 10.1016/j.jmb.2007.07.023, 17706667.
    • (2007) J Mol Biol , vol.372 , Issue.4 , pp. 1045-1054
    • Shomura, Y.1    Komori, H.2    Miyabe, N.3    Tomiyama, M.4    Shibata, N.5    Higuchi, Y.6
  • 13
    • 7044222771 scopus 로고    scopus 로고
    • The complex between hydrogenase-maturation proteins HypC and HypD is an intermediate in the supply of cyanide to the active site iron of [NiFe]-hydrogenases
    • 10.1016/j.jmb.2004.09.040, 15504408
    • Blokesch M, Albracht SPJ, Matzanke BF, Drapal NM, Jacobi A, Böck A. The complex between hydrogenase-maturation proteins HypC and HypD is an intermediate in the supply of cyanide to the active site iron of [NiFe]-hydrogenases. J Mol Biol 2004, 344:155-167. 10.1016/j.jmb.2004.09.040, 15504408.
    • (2004) J Mol Biol , vol.344 , pp. 155-167
    • Blokesch, M.1    Albracht, S.P.J.2    Matzanke, B.F.3    Drapal, N.M.4    Jacobi, A.5    Böck, A.6
  • 14
    • 0016301451 scopus 로고
    • Phosphoheptose isomerase, first enzyme in the biosynthesis of aldoheptose in Salmonella typhimurium
    • Eidels L, Osborn MJ. Phosphoheptose isomerase, first enzyme in the biosynthesis of aldoheptose in Salmonella typhimurium. J Biol Chem 1974, 249(17):5642-5648.
    • (1974) J Biol Chem , vol.249 , Issue.17 , pp. 5642-5648
    • Eidels, L.1    Osborn, M.J.2
  • 15
    • 0036066728 scopus 로고    scopus 로고
    • Novel pathways for biosynthesis of nucleotide-activated glycero-manno-heptose precursors of bacterial glycoproteins and cell surface polysaccharides
    • Valvano MA, Messner P, Kosma P. Novel pathways for biosynthesis of nucleotide-activated glycero-manno-heptose precursors of bacterial glycoproteins and cell surface polysaccharides. Microbiology 2002, 148(7):1979-1989.
    • (2002) Microbiology , vol.148 , Issue.7 , pp. 1979-1989
    • Valvano, M.A.1    Messner, P.2    Kosma, P.3
  • 16
    • 68349158947 scopus 로고    scopus 로고
    • Metabolic pathway engineering for enhanced biohydrogen production
    • Mathews J, Wang G. Metabolic pathway engineering for enhanced biohydrogen production. Int J Hydrogen Energy 2009, 34(17):7404-7416.
    • (2009) Int J Hydrogen Energy , vol.34 , Issue.17 , pp. 7404-7416
    • Mathews, J.1    Wang, G.2
  • 17
    • 51849115840 scopus 로고    scopus 로고
    • Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network
    • 10.1007/s00253-008-1654-4, 18758767
    • Lee J, Yun H, Feist A, Palsson B, Lee S. Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Appl Microbiol Biotechnol 2008, 80(5):849-862. 10.1007/s00253-008-1654-4, 18758767.
    • (2008) Appl Microbiol Biotechnol , vol.80 , Issue.5 , pp. 849-862
    • Lee, J.1    Yun, H.2    Feist, A.3    Palsson, B.4    Lee, S.5
  • 19
    • 0029882154 scopus 로고    scopus 로고
    • Molecular characterization of the genes encoding pyruvate formate-lyase and its activating enzyme of Clostridium pasteurianum
    • 177960, 8636053
    • Weidner G, Sawers G. Molecular characterization of the genes encoding pyruvate formate-lyase and its activating enzyme of Clostridium pasteurianum. J Bacteriol 1996, 178(8):2440-2444. 177960, 8636053.
    • (1996) J Bacteriol , vol.178 , Issue.8 , pp. 2440-2444
    • Weidner, G.1    Sawers, G.2
  • 21
    • 0024615960 scopus 로고
    • Phosphotransbutyrylase from Clostridium acetobutylicum ATCC 824 and its role in acidogenesis
    • 184108, 2719475
    • Wiesenborn D, Rudolph F, Papoutsakis E. Phosphotransbutyrylase from Clostridium acetobutylicum ATCC 824 and its role in acidogenesis. Appl Environ Microbiol 1989, 55(2):317-322. 184108, 2719475.
    • (1989) Appl Environ Microbiol , vol.55 , Issue.2 , pp. 317-322
    • Wiesenborn, D.1    Rudolph, F.2    Papoutsakis, E.3
  • 22
    • 0021261020 scopus 로고
    • Intermediary metabolism inClostridium acetobutylicum levels of enzymes involved in the formation of acetate and butyrate
    • 240219, 16346566
    • Hartmanis MGN, Gatenbeck S. Intermediary metabolism inClostridium acetobutylicum levels of enzymes involved in the formation of acetate and butyrate. Appl Environ Microbiol 1984, 47(6):1277-1283. 240219, 16346566.
    • (1984) Appl Environ Microbiol , vol.47 , Issue.6 , pp. 1277-1283
    • Hartmanis, M.G.N.1    Gatenbeck, S.2
  • 23
    • 82655161121 scopus 로고    scopus 로고
    • Microbial physiology genetics and ecology
    • Manglam Publications
    • Rathi J. Microbial physiology genetics and ecology. 2009, Manglam Publications.
    • (2009)
    • Rathi, J.1
  • 24
    • 4544319129 scopus 로고    scopus 로고
    • Adaptive acid tolerance response of Streptococcus sobrinus
    • 10.1128/JB.186.19.6383-6390.2004, 516607, 15375118
    • Nascimento MM, Lemos JAC, Abranches J, Goncalves RB, Burne RA. Adaptive acid tolerance response of Streptococcus sobrinus. J Bacteriol 2004, 186(19):6383-6390. 10.1128/JB.186.19.6383-6390.2004, 516607, 15375118.
    • (2004) J Bacteriol , vol.186 , Issue.19 , pp. 6383-6390
    • Nascimento, M.M.1    Lemos, J.A.C.2    Abranches, J.3    Goncalves, R.B.4    Burne, R.A.5
  • 25
    • 0032932220 scopus 로고    scopus 로고
    • Acid- and base-induced proteins during aerobic and anaerobic growth of Escherichia coli revealed by two-dimensional gel electrophoresis
    • 93635, 10094700
    • Blankenhorn D, Phillips J, Slonczewski JL. Acid- and base-induced proteins during aerobic and anaerobic growth of Escherichia coli revealed by two-dimensional gel electrophoresis. J Bacteriol 1999, 181(7):2209-2216. 93635, 10094700.
    • (1999) J Bacteriol , vol.181 , Issue.7 , pp. 2209-2216
    • Blankenhorn, D.1    Phillips, J.2    Slonczewski, J.L.3
  • 27
    • 0035416012 scopus 로고    scopus 로고
    • Low-complexity fuzzy relational clustering algorithms for Web mining
    • Krishnapuram R, Joshi A, Nasraoui O, Yi L. Low-complexity fuzzy relational clustering algorithms for Web mining. IEEE T Fuzzy Syst 2001, 9(4):595-607.
    • (2001) IEEE T Fuzzy Syst , vol.9 , Issue.4 , pp. 595-607
    • Krishnapuram, R.1    Joshi, A.2    Nasraoui, O.3    Yi, L.4
  • 30
    • 0043130664 scopus 로고    scopus 로고
    • Decomposing gene expression into cellular processes
    • E S, A B, D K. Decomposing gene expression into cellular processes. Pac Symp Biocomput 2003, 89-100.
    • (2003) Pac Symp Biocomput , pp. 89-100
    • E, S.1    A, B.2    D, K.3
  • 31
    • 33747881178 scopus 로고    scopus 로고
    • Dense subgraph computation via stochastic search: application to detect transcriptional modules
    • 10.1093/bioinformatics/btl260, 16873461
    • Everett L, Wang LS, Hannenhalli S. Dense subgraph computation via stochastic search: application to detect transcriptional modules. Bioinformatics 2006, 22(14):e117-123. 10.1093/bioinformatics/btl260, 16873461.
    • (2006) Bioinformatics , vol.22 , Issue.14
    • Everett, L.1    Wang, L.S.2    Hannenhalli, S.3
  • 34
    • 0038074373 scopus 로고    scopus 로고
    • Topological structure analysis of the protein-protein interaction network in budding yeast
    • 10.1093/nar/gkg340, 154226, 12711690
    • Bu D, Zhao Y, Cai L, Xue H, Zhu X, Lu H, Zhang J, Sun S, Ling L, Zhang N, Li G, Chen R. Topological structure analysis of the protein-protein interaction network in budding yeast. Nucl Acids Res 2003, 31(9):2443-2450. 10.1093/nar/gkg340, 154226, 12711690.
    • (2003) Nucl Acids Res , vol.31 , Issue.9 , pp. 2443-2450
    • Bu, D.1    Zhao, Y.2    Cai, L.3    Xue, H.4    Zhu, X.5    Lu, H.6    Zhang, J.7    Sun, S.8    Ling, L.9    Zhang, N.10    Li, G.11    Chen, R.12
  • 35
    • 0035342724 scopus 로고    scopus 로고
    • Extended clique initialisation in examination timetabling
    • Carter M, Johnson D. Extended clique initialisation in examination timetabling. J Oper Res Soc 2001, 52:558-544.
    • (2001) J Oper Res Soc , vol.52 , pp. 558-1544
    • Carter, M.1    Johnson, D.2
  • 36
    • 33751380750 scopus 로고    scopus 로고
    • Natural document clustering by clique percolation in random graphs
    • Gao W, Wong KF. Natural document clustering by clique percolation in random graphs. Information Retrieval Technology, Springer 2006, 119-131.
    • (2006) Information Retrieval Technology, Springer , pp. 119-131
    • Gao, W.1    Wong, K.F.2
  • 38
    • 34547455408 scopus 로고    scopus 로고
    • Out-of-core coherent closed quasi-clique mining from large dense graph databases
    • Zeng Z, Wang J, Zhou L, Karypis G. Out-of-core coherent closed quasi-clique mining from large dense graph databases. ACM Trans Database Syst 2007, 32(2):13.
    • (2007) ACM Trans Database Syst , vol.32 , Issue.2 , pp. 13
    • Zeng, Z.1    Wang, J.2    Zhou, L.3    Karypis, G.4
  • 39
    • 65449131622 scopus 로고    scopus 로고
    • Core and periphery structures in protein interaction networks
    • 2788359, 19958518
    • Luo F, Li B, Wan XF, Scheuermann R. Core and periphery structures in protein interaction networks. BMC Bioinformatics 2009, 10(Suppl 4):S8. 2788359, 19958518.
    • (2009) BMC Bioinformatics , vol.10 , Issue.SUPPL. 4
    • Luo, F.1    Li, B.2    Wan, X.F.3    Scheuermann, R.4
  • 40
    • 84904316209 scopus 로고
    • A graph-theoretic generalization of the clique concept
    • Seidman S, Foster B. A graph-theoretic generalization of the clique concept. J Math Sociol 1978, 6:139-154.
    • (1978) J Math Sociol , vol.6 , pp. 139-154
    • Seidman, S.1    Foster, B.2
  • 41
    • 0011632190 scopus 로고
    • The evolution of sparse graphs
    • London-New York, UK: Academic Press
    • Bollobas B. The evolution of sparse graphs. Graph theory and combinatorics 1984, 35-57. London-New York, UK: Academic Press.
    • (1984) Graph theory and combinatorics , pp. 35-57
    • Bollobas, B.1
  • 42
    • 0003124595 scopus 로고
    • A method of matrix analysis of group structure
    • Luce R, Perry A. A method of matrix analysis of group structure. Psychometrika 1949, 14:94-116.
    • (1949) Psychometrika , vol.14 , pp. 94-116
    • Luce, R.1    Perry, A.2
  • 43
    • 19144367138 scopus 로고    scopus 로고
    • Prediction of functional modules based on comparative genome analysis and Gene Ontology application
    • 10.1093/nar/gki573, 1130488, 15901854
    • Wu H, Su Z, Mao F, Olman V, Xu Y. Prediction of functional modules based on comparative genome analysis and Gene Ontology application. Nucl Acids Res 2005, 33(9):2822-2837. 10.1093/nar/gki573, 1130488, 15901854.
    • (2005) Nucl Acids Res , vol.33 , Issue.9 , pp. 2822-2837
    • Wu, H.1    Su, Z.2    Mao, F.3    Olman, V.4    Xu, Y.5
  • 44
    • 57749210454 scopus 로고    scopus 로고
    • An in silico method for detecting overlapping functional modules from composite biological networks
    • 10.1186/1752-0509-2-93, 2600641, 18976494
    • Maraziotis I, Dimitrakopoulou K, Bezerianos A. An in silico method for detecting overlapping functional modules from composite biological networks. BMC Syst Biol 2008, 2:93. 10.1186/1752-0509-2-93, 2600641, 18976494.
    • (2008) BMC Syst Biol , vol.2 , pp. 93
    • Maraziotis, I.1    Dimitrakopoulou, K.2    Bezerianos, A.3
  • 45
    • 33748701649 scopus 로고    scopus 로고
    • Detecting functional modules in the yeast protein protein interaction network
    • 10.1093/bioinformatics/btl370, 16837529
    • Chen J, Yuan B. Detecting functional modules in the yeast protein protein interaction network. Bioinformatics 2006, 22(18):2283-2290. 10.1093/bioinformatics/btl370, 16837529.
    • (2006) Bioinformatics , vol.22 , Issue.18 , pp. 2283-2290
    • Chen, J.1    Yuan, B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.