메뉴 건너뛰기




Volumn 10, Issue 7, 2015, Pages

Comparison of gene coexpression profiles and construction of conserved gene networks to find functional modules

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL CYCLE; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; GENE REGULATORY NETWORK; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC DATABASE; HUMAN; IMMUNE SYSTEM; MOUSE; NONHUMAN; SEQUENCE HOMOLOGY; SPECIES COMPARISON; ANIMAL; COMPARATIVE STUDY; GENE EXPRESSION REGULATION;

EID: 84940063593     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0132039     Document Type: Article
Times cited : (10)

References (41)
  • 1
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • 11237011
    • International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921. PMID: 11237011
    • (2001) Nature , vol.409 , pp. 860-921
    • International Human Genome Sequencing Consortium1
  • 3
    • 7244245762 scopus 로고    scopus 로고
    • Finishing the euchromatic sequence of the human genome
    • 15496913
    • International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931-945. PMID: 15496913
    • (2004) Nature , vol.431 , pp. 931-945
    • International Human Genome Sequencing Consortium1
  • 4
    • 0018629550 scopus 로고
    • Use of a cDNA library for studies on evolution and developmental expression of the chorion multigene families
    • 519770
    • Sim G, Kafatos F, Jones C, Koehler M, Efstratiadis A, Maniatis T. (1979) Use of a cDNA library for studies on evolution and developmental expression of the chorion multigene families. Cell 18:1303-1316. PMID: 519770
    • (1979) Cell , vol.18 , pp. 1303-1316
    • Sim, G.1    Kafatos, F.2    Jones, C.3    Koehler, M.4    Efstratiadis, A.5    Maniatis, T.6
  • 5
    • 79959916374 scopus 로고    scopus 로고
    • Unamplified cap analysis of gene expression on a single-molecule sequencer
    • 21596820
    • Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, et al. (2011) Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res 21:1150-9. doi: 10.1101/gr.115469.110 PMID: 21596820
    • (2011) Genome Res , vol.21 , pp. 1150-1159
    • Kanamori-Katayama, M.1    Itoh, M.2    Kawaji, H.3    Lassmann, T.4    Katayama, S.5    Kojima, M.6
  • 7
    • 24344500211 scopus 로고    scopus 로고
    • Initial sequence of the chimpanzee genome and comparison with the human genome
    • 16136131
    • Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437:69-87. PMID: 16136131
    • (2005) Nature , vol.437 , pp. 69-87
    • Chimpanzee Sequencing and Analysis Consortium1
  • 8
    • 80054973803 scopus 로고    scopus 로고
    • A high-resolution map of human evolutionary constraint using 29 mammals
    • 21993624
    • Lindblad-Toh K, Garber M, Zuk O, Lin M, Parker B, Washietl S, et al. (2011) A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478:476-482. doi: 10.1038/nature10530 PMID: 21993624
    • (2011) Nature , vol.478 , pp. 476-482
    • Lindblad-Toh, K.1    Garber, M.2    Zuk, O.3    Lin, M.4    Parker, B.5    Washietl, S.6
  • 9
    • 84865760395 scopus 로고    scopus 로고
    • GENCODE: The reference human genome annotation for the ENCODE project
    • 22955987
    • Harrow J, Frankish A, Gonzalez J, Tapanari E, Diekhans M, Kokocinski F, et al. (2012) GENCODE: the reference human genome annotation for the ENCODE project. Genome Res 22:1760-1774. doi: 10. 1101/gr.135350.111 PMID: 22955987
    • (2012) Genome Res , vol.22 , pp. 1760-1774
    • Harrow, J.1    Frankish, A.2    Gonzalez, J.3    Tapanari, E.4    Diekhans, M.5    Kokocinski, F.6
  • 11
    • 0033518234 scopus 로고    scopus 로고
    • From molecular to modular cell biology
    • 10591225
    • Hartwell L, Hopfield J, Leibler S, Murray A (1999) From molecular to modular cell biology. Nature 402:C47-C52. PMID: 10591225
    • (1999) Nature , vol.402 , pp. C47-C52
    • Hartwell, L.1    Hopfield, J.2    Leibler, S.3    Murray, A.4
  • 12
    • 0024406857 scopus 로고
    • A novel genetic system to detect protein-protein interactions
    • 2547163
    • Fields S, Song O (1989) A novel genetic system to detect protein-protein interactions. Nature 340:245-246. PMID: 2547163
    • (1989) Nature , vol.340 , pp. 245-246
    • Fields, S.1    Song, O.2
  • 13
    • 0034628508 scopus 로고    scopus 로고
    • A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
    • 10688190
    • Uetz P, Giot L, Cagney G, Mansfield T, Judson R, Knight J, et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623-627. PMID: 10688190
    • (2000) Nature , vol.403 , pp. 623-627
    • Uetz, P.1    Giot, L.2    Cagney, G.3    Mansfield, T.4    Judson, R.5    Knight, J.6
  • 14
    • 0035836765 scopus 로고    scopus 로고
    • A comprehensive two-hybrid analysis to explore the yeast protein interactome
    • 11283351
    • Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98:4569-4574. PMID: 11283351
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 4569-4574
    • Ito, T.1    Chiba, T.2    Ozawa, R.3    Yoshida, M.4    Hattori, M.5    Sakaki, Y.6
  • 16
    • 0031742022 scopus 로고    scopus 로고
    • Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
    • 9843569
    • Spellman P, Sherlock G, Zhang M, Iyer V, Anders K, Eisen M, et al. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9:3273-3297. PMID: 9843569
    • (1998) Mol Biol Cell , vol.9 , pp. 3273-3297
    • Spellman, P.1    Sherlock, G.2    Zhang, M.3    Iyer, V.4    Anders, K.5    Eisen, M.6
  • 17
    • 0036649020 scopus 로고    scopus 로고
    • Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters
    • 12089522
    • Wu L, Hughes T, Davierwala A, Robinson M, Stoughton R, Altschuler S. (2002) Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat Genet 31:255-265. PMID: 12089522
    • (2002) Nat Genet , vol.31 , pp. 255-265
    • Wu, L.1    Hughes, T.2    Davierwala, A.3    Robinson, M.4    Stoughton, R.5    Altschuler, S.6
  • 18
    • 79751531038 scopus 로고    scopus 로고
    • The level of claudin-7 is reduced as an early event in colorectal carcinogenesis
    • 21310043
    • Bornholdt J, Friis S, Godiksen S, Poulsen S, Eric S, Bisgaard H, et al. (2011) The level of claudin-7 is reduced as an early event in colorectal carcinogenesis. BMC Cancer 11:65. doi: 10.1186/1471-2407-11-65 PMID: 21310043
    • (2011) BMC Cancer , vol.11 , pp. 65
    • Bornholdt, J.1    Friis, S.2    Godiksen, S.3    Poulsen, S.4    Eric, S.5    Bisgaard, H.6
  • 19
    • 2942572926 scopus 로고    scopus 로고
    • Quantifying the relationship between co-expression, coregulation and gene function
    • 15053845
    • Allocco D, Kohane I, Butte A (2004) Quantifying the relationship between co-expression, coregulation and gene function. BMC Bioinformatics 5:18. PMID: 15053845
    • (2004) BMC Bioinformatics , vol.5 , pp. 18
    • Allocco, D.1    Kohane, I.2    Butte, A.3
  • 20
    • 70449115789 scopus 로고    scopus 로고
    • Co-expression tools for plant biology: Opportunities for hypothesis generation and caveats
    • Usadel B, Obayashi T, Mutwil M, Giorgi F, Bassel G, Tanimoto M, et al. (2009) Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant, Cell Environ 32:1633-1651.
    • (2009) Plant, Cell Environ , vol.32 , pp. 1633-1651
    • Usadel, B.1    Obayashi, T.2    Mutwil, M.3    Giorgi, F.4    Bassel, G.5    Tanimoto, M.6
  • 21
    • 77952687416 scopus 로고    scopus 로고
    • Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression
    • 20507583
    • Shi Z, Derow C, Zhang B (2010) Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression. BMC Systems Biology 4:74. doi: 10.1186/1752-0509-4-74 PMID: 20507583
    • (2010) BMC Systems Biology , vol.4 , pp. 74
    • Shi, Z.1    Derow, C.2    Zhang, B.3
  • 22
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • Stuart J, Segal E, Koller D, Kim S (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science (New York, NY) 302:249-255.
    • (2003) Science (New York, NY) , vol.302 , pp. 249-255
    • Stuart, J.1    Segal, E.2    Koller, D.3    Kim, S.4
  • 23
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • Schena M, Shalon D, Davis R, Brown P (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science (New York, NY) 270:467-470.
    • (1995) Science (New York, NY) , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.3    Brown, P.4
  • 24
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • 18516045
    • Mortazavi A, Williams B, Kenneth M, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5:621-628. doi: 10.1038/nmeth.1226 PMID: 18516045
    • (2008) Nature Methods , vol.5 , pp. 621-628
    • Mortazavi, A.1    Williams, B.2    Kenneth, M.3    Schaeffer, L.4    Wold, B.5
  • 25
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • 22955616
    • The ENCODE Project Consortium (2012), An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74. doi: 10.1038/nature11247 PMID: 22955616
    • (2012) Nature , vol.489 , pp. 57-74
    • The ENCODE Project Consortium1
  • 26
    • 36048982458 scopus 로고    scopus 로고
    • Initial sequence and comparative analysis of the cat genome
    • 17975172 Team AS
    • Pontius J, Mullikin J, Smith D, Team AS, Lindblad-Toh K, Gnerre S, et al. (2007) Initial sequence and comparative analysis of the cat genome. Genome Res 17:1675-1689. PMID: 17975172
    • (2007) Genome Res , vol.17 , pp. 1675-1689
    • Pontius, J.1    Mullikin, J.2    Smith, D.3    Lindblad-Toh, K.4    Gnerre, S.5
  • 28
    • 80054976678 scopus 로고    scopus 로고
    • The evolution of gene expression levels in mammalian organs
    • 22012392
    • Brawand D, Soumillon M, Necsulea A, Julien P, Csrdi G, Harrigan P, et al. (2011) The evolution of gene expression levels in mammalian organs. Nature 478:343-348. doi: 10.1038/nature10532 PMID: 22012392
    • (2011) Nature , vol.478 , pp. 343-348
    • Brawand, D.1    Soumillon, M.2    Necsulea, A.3    Julien, P.4    Csrdi, G.5    Harrigan, P.6
  • 29
    • 77957235277 scopus 로고    scopus 로고
    • Cross-species queries of large gene expression databases
    • Le H, Oltvai Z, Ziv B (2010) Cross-species queries of large gene expression databases. Bioinformatics (Oxford, England) 26:2416-2423.
    • (2010) Bioinformatics (Oxford, England) , vol.26 , pp. 2416-2423
    • Le, H.1    Oltvai, Z.2    Ziv, B.3
  • 30
    • 84863529531 scopus 로고    scopus 로고
    • Matching experiments across species using expression values and textual information
    • Wise A, Oltvai Z, Ziv B (2012) Matching experiments across species using expression values and textual information. Bioinformatics (Oxford, England) 28:i258-i264.
    • (2012) Bioinformatics (Oxford, England) , vol.28 , pp. i258-i264
    • Wise, A.1    Oltvai, Z.2    Ziv, B.3
  • 32
    • 20444504323 scopus 로고    scopus 로고
    • Uncovering the overlapping community structure of complex networks in nature and society
    • 15944704
    • Palla G, Derényi I, Farkas I, Vicsek T (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature 435:814-818. PMID: 15944704
    • (2005) Nature , vol.435 , pp. 814-818
    • Palla, G.1    Derényi, I.2    Farkas, I.3    Vicsek, T.4
  • 33
    • 84941028211 scopus 로고    scopus 로고
    • COXPRESdb in 2015: Coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems
    • 25392420
    • Okamura Y, Aoki Y, Obayashi T, Tadaka S, Ito S, Narise T, et al. (2015) COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems. Nucleic Acids Res 43:D82-6. doi: 10.1093/nar/gku1163 PMID: 25392420
    • (2015) Nucleic Acids Res , vol.43 , pp. D82-D86
    • Okamura, Y.1    Aoki, Y.2    Obayashi, T.3    Tadaka, S.4    Ito, S.5    Narise, T.6
  • 35
    • 84876532610 scopus 로고    scopus 로고
    • Database resources of the national center for biotechnology information
    • 23193264
    • NCBI Resource Coordinators (2013) Database resources of the national center for biotechnology information. Nucleic Acids Res 41:D8-DD20. doi: 10.1093/nar/gks1189 PMID: 23193264
    • (2013) Nucleic Acids Res , vol.41 , pp. D8-DD20
    • NCBI Resource Coordinators1
  • 36
    • 84874253819 scopus 로고    scopus 로고
    • Gene ontology annotations and resources
    • 23161678
    • Gene Ontology Consortium (2013) Gene ontology annotations and resources. Nucleic Acids Res 41:D530-D535. doi: 10.1093/nar/gks1050 PMID: 23161678
    • (2013) Nucleic Acids Res , vol.41 , pp. D530-D535
    • Gene Ontology Consortium1
  • 37
    • 0037417817 scopus 로고    scopus 로고
    • Modular organization of cellular networks
    • 12538875
    • Rives A, Galitski T (2003) Modular organization of cellular networks. Proc Natl Acad Sci USA 100:1128-1133. PMID: 12538875
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 1128-1133
    • Rives, A.1    Galitski, T.2
  • 38
    • 0142059836 scopus 로고    scopus 로고
    • Protein complexes and functional modules in molecular networks
    • 14517352
    • Spirin V, Mirny L (2003) Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA 100:12123-12128. PMID: 14517352
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 12123-12128
    • Spirin, V.1    Mirny, L.2
  • 39
    • 33748701649 scopus 로고    scopus 로고
    • Detecting functional modules in the yeast protein-protein interaction network
    • Chen J, Yuan B (2006) Detecting functional modules in the yeast protein-protein interaction network. Bioinformatics (Oxford, England) 22:2283-2290.
    • (2006) Bioinformatics (Oxford, England) , vol.22 , pp. 2283-2290
    • Chen, J.1    Yuan, B.2
  • 40
    • 67249148362 scopus 로고    scopus 로고
    • Exploring network structure, dynamics, and function using networkx
    • Varoquaux G, Vaught T, Millman J, editors, Pasadena, CA USA
    • Hagberg A, Schult DA, Swart PJ (2008) Exploring network structure, dynamics, and function using networkx. In: Varoquaux G, Vaught T, Millman J, editors, Proceedings of the 7th Python in Science Conference. Pasadena, CA USA, pp. 11-15.
    • (2008) Proceedings of the 7th Python in Science Conference , pp. 11-15
    • Hagberg, A.1    Schult, D.A.2    Swart, P.J.3
  • 41
    • 79952392088 scopus 로고    scopus 로고
    • TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery
    • 21408081
    • Chen Y, Tripathi L, Mizuguchi K (2011) TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery. PloS One 6:e17844. doi: 10.1371/journal.pone.0017844 PMID: 21408081
    • (2011) PloS One , vol.6 , pp. e17844
    • Chen, Y.1    Tripathi, L.2    Mizuguchi, K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.