메뉴 건너뛰기




Volumn 2, Issue , 2012, Pages 76-82

GeneSetDB: A comprehensive meta-database, statistical and visualisation framework for gene set analysis

Author keywords

Database; Enrichment analysis; Functional genomics; Gene set

Indexed keywords

ARTICLE; DATA BASE; FUNCTIONAL GENOMICS; GENE SET ANALYSIS; GENETIC ANALYSIS; GENETIC IDENTIFICATION; HUMAN; PRIORITY JOURNAL;

EID: 84861212058     PISSN: 22115463     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fob.2012.04.003     Document Type: Article
Times cited : (60)

References (47)
  • 2
    • 3042514191 scopus 로고    scopus 로고
    • Coexpression analysis of human genes across many microarray data sets
    • Lee H.K., Hsu A.K., Sajdak J., Qin J., Pavlidis P. Coexpression analysis of human genes across many microarray data sets. Genome Res. 2004, 14:1085-1094.
    • (2004) Genome Res. , vol.14 , pp. 1085-1094
    • Lee, H.K.1    Hsu, A.K.2    Sajdak, J.3    Qin, J.4    Pavlidis, P.5
  • 3
    • 73249114746 scopus 로고    scopus 로고
    • Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression
    • Obayashi T., Kinoshita K. Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression. DNA Res. 2009, 16:249-260.
    • (2009) DNA Res. , vol.16 , pp. 249-260
    • Obayashi, T.1    Kinoshita, K.2
  • 4
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • Stuart J.M., Segal E., Koller D., Kim S.K. A gene-coexpression network for global discovery of conserved genetic modules. Science 2003, 302:249-255.
    • (2003) Science , vol.302 , pp. 249-255
    • Stuart, J.M.1    Segal, E.2    Koller, D.3    Kim, S.K.4
  • 5
    • 78651280402 scopus 로고    scopus 로고
    • COXPRESdb: a database to compare gene coexpression in seven model animals
    • Obayashi T., Kinoshita K. COXPRESdb: a database to compare gene coexpression in seven model animals. Nucleic Acids Res. 2011, 39:D1016-D1022.
    • (2011) Nucleic Acids Res. , vol.39
    • Obayashi, T.1    Kinoshita, K.2
  • 6
    • 58049141153 scopus 로고    scopus 로고
    • Microarray-based gene set analysis: a comparison of current methods
    • Song S., Black M.A. Microarray-based gene set analysis: a comparison of current methods. BMC Bioinformatics 2008, 9:502.
    • (2008) BMC Bioinformatics , vol.9 , pp. 502
    • Song, S.1    Black, M.A.2
  • 7
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
    • Huang D.W., Sherman B.T., Lempicki R.A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009, 37:1-13.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 1-13
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 10
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources
    • Huang da W., Sherman B.T., Lempicki R.A. Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nat. Protoc. 2009, 4:44-57.
    • (2009) Nat. Protoc. , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 11
    • 33751384465 scopus 로고    scopus 로고
    • GATHER: a systems approach to interpreting genomic signatures
    • Chang J.T., Nevins J.R. GATHER: a systems approach to interpreting genomic signatures. Bioinformatics 2006, 22:2926-2933.
    • (2006) Bioinformatics , vol.22 , pp. 2926-2933
    • Chang, J.T.1    Nevins, J.R.2
  • 14
    • 67849099281 scopus 로고    scopus 로고
    • WhichGenes: a web-based tool for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis
    • Glez-Peña D., Gómez-López G., Pisano D.G., Fdez-Riverola F. WhichGenes: a web-based tool for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis. Nucleic Acids Res. 2007, 37:W329-W334.
    • (2007) Nucleic Acids Res. , vol.37
    • Glez-Peña, D.1    Gómez-López, G.2    Pisano, D.G.3    Fdez-Riverola, F.4
  • 17
    • 33947159380 scopus 로고    scopus 로고
    • Event ontology: a pathway-centric ontology for biological processes
    • Kushida T., Takagi T., Fukuda K.I. Event ontology: a pathway-centric ontology for biological processes. Pac. Symp. Biocomput. 2006, 11:152-163.
    • (2006) Pac. Symp. Biocomput. , vol.11 , pp. 152-163
    • Kushida, T.1    Takagi, T.2    Fukuda, K.I.3
  • 24
    • 84954358609 scopus 로고    scopus 로고
    • The human phenotype ontology: a tool for annotating and analyzing human hereditary disease
    • Robinson P.N., Köhler S., Bauer S., Seelow D., Horn D., Mundlos S. The human phenotype ontology: a tool for annotating and analyzing human hereditary disease. Am. J. Hum. Genet. 2008, 83:610-615.
    • (2008) Am. J. Hum. Genet. , vol.83 , pp. 610-615
    • Robinson, P.N.1    Köhler, S.2    Bauer, S.3    Seelow, D.4    Horn, D.5    Mundlos, S.6
  • 25
    • 75549090213 scopus 로고    scopus 로고
    • KEGG for representation and analysis of molecular networks involving diseases and drugs
    • Kanehisa M., Goto S., Furumichi M., Tanabe M., Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 2010, 38:D355-D360.
    • (2010) Nucleic Acids Res. , vol.38
    • Kanehisa, M.1    Goto, S.2    Furumichi, M.3    Tanabe, M.4    Hirakawa, M.5
  • 28
    • 78249235739 scopus 로고    scopus 로고
    • The mammalian phenotype ontology: enabling robust annotation and comparative analysis
    • Smith C.L., Eppig J.T. The mammalian phenotype ontology: enabling robust annotation and comparative analysis. Wiley Interdiscip. Rev. Syst. Biol. Med. 2009, 1:390-399.
    • (2009) Wiley Interdiscip. Rev. Syst. Biol. Med. , vol.1 , pp. 390-399
    • Smith, C.L.1    Eppig, J.T.2
  • 35
    • 78651293534 scopus 로고    scopus 로고
    • MiRBase: integrating microRNA annotation and deep-sequencing data
    • Kozomara A., Griffiths-Jones S. MiRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2011, 39:D152-D157.
    • (2011) Nucleic Acids Res. , vol.39
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 37
    • 77954364953 scopus 로고    scopus 로고
    • Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data
    • Essaghir A., Toffalini F., Knoops L., Kallin A., van Helden J., Demoulin J.B. Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data. Nucleic Acids Res. 2010, 38:e120.
    • (2010) Nucleic Acids Res. , vol.38
    • Essaghir, A.1    Toffalini, F.2    Knoops, L.3    Kallin, A.4    van Helden, J.5    Demoulin, J.B.6
  • 38
    • 24044522270 scopus 로고    scopus 로고
    • BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
    • Durinck S., Moreau Y., Kasprzyk A., Davis S., De Moor B., Brazma A., Huber W. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 2005, 21:3439-3440.
    • (2005) Bioinformatics , vol.21 , pp. 3439-3440
    • Durinck, S.1    Moreau, Y.2    Kasprzyk, A.3    Davis, S.4    De Moor, B.5    Brazma, A.6    Huber, W.7
  • 39
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y., Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Stat. Soc. Ser. B 1995, 57:289-300.
    • (1995) J. Roy. Stat. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 40
    • 30044451191 scopus 로고    scopus 로고
    • The Gene Set Builder: collation, curation, and distribution of sets of genes
    • Yusuf D., Lim J.S., Wasserman W.W. The Gene Set Builder: collation, curation, and distribution of sets of genes. BMC Bioinformatics 2005, 6:305.
    • (2005) BMC Bioinformatics , vol.6 , pp. 305
    • Yusuf, D.1    Lim, J.S.2    Wasserman, W.W.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.