메뉴 건너뛰기




Volumn 6, Issue 1, 2015, Pages

Linking gene expression to phenotypes via pathway information

Author keywords

Gene expression; Ontologies; Pathways; Phenotypes

Indexed keywords


EID: 84938806173     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/s13326-015-0013-5     Document Type: Review
Times cited : (23)

References (46)
  • 1
    • 84862499271 scopus 로고    scopus 로고
    • Pathway analysis of genomic data: concepts, methods, and prospects for future development
    • Ramanan VK, Shen L, Moore JH, Saykin AJ. Pathway analysis of genomic data: concepts, methods, and prospects for future development. Trends Genet. 2012; 28(7):323-32. doi:10.1016/j.tig.2012.03.004.
    • (2012) Trends Genet , vol.28 , Issue.7 , pp. 323-332
    • Ramanan, V.K.1    Shen, L.2    Moore, J.H.3    Saykin, A.J.4
  • 3
  • 4
    • 84865595151 scopus 로고    scopus 로고
    • Identification of new susceptibility loci for osteoarthritis (arcogen): A genome-wide association study
    • Zeggini E, Panoutsopoulou K, Southam L, Rayner N, Day-Williams A, Lopes M, et al.Identification of new susceptibility loci for osteoarthritis (arcogen): A genome-wide association study. The Lancet. 2012; 380:815-23. doi:10.1016/S0140-6736(12)60681-3.
    • (2012) The Lancet , vol.380 , pp. 815-823
    • Zeggini, E.1    Panoutsopoulou, K.2    Southam, L.3    Rayner, N.4    Day-Williams, A.5    Lopes, M.6
  • 5
    • 84894273748 scopus 로고    scopus 로고
    • Global changes in gene expression associated with phenotypic switching of wild yeast
    • Stovicek V, Vachova L, Begany M, Wilkinson D, Palkova Z. Global changes in gene expression associated with phenotypic switching of wild yeast. BMC Genomics. 2014; 15(1):136. doi:10.1186/1471-2164-15-136.
    • (2014) BMC Genomics , vol.15 , Issue.1 , pp. 136
    • Stovicek, V.1    Vachova, L.2    Begany, M.3    Wilkinson, D.4    Palkova, Z.5
  • 6
    • 84878302099 scopus 로고    scopus 로고
    • Gene Expression Classification of Colon Cancer into Molecular Subtypes: Characterization, Validation, and Prognostic Value
    • Marisa L, de Reyniès A, Duval A, Selves J, Gaub MP, Vescovo L, et al.Gene Expression Classification of Colon Cancer into Molecular Subtypes: Characterization, Validation, and Prognostic Value. PLoS Med. 2013; 10(5):1001453. doi:10.1371/journal.pmed.1001453.
    • (2013) PLoS Med , vol.10 , Issue.5 , pp. 1001453
    • Marisa, L.1    de Reyniès, A.2    Duval, A.3    Selves, J.4    Gaub, M.P.5    Vescovo, L.6
  • 7
    • 84906564575 scopus 로고    scopus 로고
    • Linking tissues to phenotypes using gene expression profiles
    • Oellrich A, Project SMG, Smedley D. Linking tissues to phenotypes using gene expression profiles. Database 2014. 2014. doi:10.1093/database/bau017, http://database.oxfordjournals.org/content/2014/bau017.full.pdf+html .
    • (2014) Database 2014
    • Oellrich, A.1    Project, S.M.G.2    Smedley, D.3
  • 8
    • 84896132202 scopus 로고    scopus 로고
    • Comprehensive detection of genes causing a phenotype using phenotype sequencing and pathway analysis
    • Harper M, Gronenberg L, Liao J, Lee C. Comprehensive detection of genes causing a phenotype using phenotype sequencing and pathway analysis. PLoS ONE. 2014; 9(2):88072. doi:10.1371/journal.pone.0088072.
    • (2014) PLoS ONE , vol.9 , Issue.2 , pp. 88072
    • Harper, M.1    Gronenberg, L.2    Liao, J.3    Lee, C.4
  • 9
    • 79954986866 scopus 로고    scopus 로고
    • A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®)
    • Amberger J, Bocchini C, Hamosh A. A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®). Hum Mutat. 2011; 32(5):564-7.
    • (2011) Hum Mutat , vol.32 , Issue.5 , pp. 564-567
    • Amberger, J.1    Bocchini, C.2    Hamosh, A.3
  • 10
    • 78651275182 scopus 로고    scopus 로고
    • Reactome: a database of reactions, pathways and biological processes
    • Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, et al.Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. 2011; 39(suppl 1):691-697. doi:10.1093/nar/gkq1018.
    • (2011) Nucleic Acids Res , vol.39 , pp. 691-697
    • Croft, D.1    O'Kelly, G.2    Wu, G.3    Haw, R.4    Gillespie, M.5    Matthews, L.6
  • 12
    • 84867331444 scopus 로고    scopus 로고
    • The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data
    • Smith CL, Eppig JT. The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. Mamm Genome. 2012; 23(9-10):653-68.
    • (2012) Mamm Genome , vol.23 , Issue.9-10 , pp. 653-668
    • Smith, C.L.1    Eppig, J.T.2
  • 14
    • 78651302604 scopus 로고    scopus 로고
    • The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources
    • Gremse M, Chang A, Schomburg I, Grote A, Scheer M, Ebeling C, et al.The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. Nucleic Acids Res. 2011; 39(Database issue):507-13.
    • (2011) Nucleic Acids Res , vol.39 , Issue.DATABASE ISSUE , pp. 507-513
    • Gremse, M.1    Chang, A.2    Schomburg, I.3    Grote, A.4    Scheer, M.5    Ebeling, C.6
  • 15
    • 84891757565 scopus 로고    scopus 로고
    • The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data
    • Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, et al.The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. Nucleic Acids Res. 2013. doi:10.1093/nar/gkt977.
    • (2013) Nucleic Acids Res.
    • Koscielny, G.1    Yaikhom, G.2    Iyer, V.3    Meehan, T.F.4    Morgan, H.5    Atienza-Herrero, J.6
  • 16
    • 84949768868 scopus 로고    scopus 로고
    • A classification of existing phenotypical representations and methods for improvement
    • Mannheim, Germany.
    • Oellrich A, Rebholz-Schuhmann D. A classification of existing phenotypical representations and methods for improvement. In: Proceedings of the 2010 OMBL Workshop. Mannheim, Germany: 2010.
    • (2010) Proceedings of the 2010 OMBL Workshop
    • Oellrich, A.1    Rebholz-Schuhmann, D.2
  • 17
    • 0038670579 scopus 로고    scopus 로고
    • The Human Phenome Project
    • Freimer N, Sabatti C. The Human Phenome Project. Nat Genet. 2003; 34(1):15-21.
    • (2003) Nat Genet , vol.34 , Issue.1 , pp. 15-21
    • Freimer, N.1    Sabatti, C.2
  • 18
    • 84891749517 scopus 로고    scopus 로고
    • The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data
    • Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, et al.The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 2014; 42(Database issue):966-74.
    • (2014) Nucleic Acids Res , vol.42 , Issue.DATABASE ISSUE , pp. 966-974
    • Köhler, S.1    Doelken, S.C.2    Mungall, C.J.3    Bauer, S.4    Firth, H.V.5    Bailleul-Forestier, I.6
  • 24
    • 0038181144 scopus 로고    scopus 로고
    • Orphanet, an information site on rare diseases
    • Aymé S. Orphanet, an information site on rare diseases. Soins; la revue de référence infirmière. 2003; 672:46-7. http://www.ncbi.nlm.nih.gov/pubmed/12655825 .
    • (2003) Soins; la revue de référence infirmière , vol.672 , pp. 46-47
    • Aymé, S.1
  • 25
    • 84938792296 scopus 로고    scopus 로고
    • Annotations for human diseases based on the Human Phenotype Ontology
    • Annotations for human diseases based on the Human Phenotype Ontology. http://www.human-phenotype-ontology.org/contao/index.php/annotation-guide.html .
  • 26
    • 84861527388 scopus 로고    scopus 로고
    • The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
    • 7403. Nature Publishing Group (NPG).
    • Curtis C, Shah SP, Chin S-F, Turashvili G, Rueda OM, Dunning MJ, et al.The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. 7403; 486:436-52. Nature Publishing Group (NPG).
    • , vol.486 , pp. 436-452
    • Curtis, C.1    Shah, S.P.2    Chin, S.-F.3    Turashvili, G.4    Rueda, O.M.5    Dunning, M.J.6
  • 27
    • 84902476492 scopus 로고    scopus 로고
    • Methods for time series analysis of rna-seq data with application to human th17 cell differentiation
    • Äijö T, Butty V, Chen Z, Salo V, Tripathi S, Burge CB, et al.Methods for time series analysis of rna-seq data with application to human th17 cell differentiation. Bioinformatics. 2014; 30(12):113-20. doi:10.1093/bioinformatics/btu274, http://bioinformatics.oxfordjournals.org/content/30/12/i113.full.pdf+html .
    • (2014) Bioinformatics , vol.30 , Issue.12 , pp. 113-120
    • Butty, V.1    Chen, Z.2    Salo, V.3    Tripathi, S.4    Burge, C.B.5
  • 29
    • 84907546454 scopus 로고    scopus 로고
    • Next masigpro: updating masigpro bioconductor package for rna-seq time series
    • Nueda MJ, Tarazona S, Conesa A. Next masigpro: updating masigpro bioconductor package for rna-seq time series. Bioinformatics. 2014; 30(18):2598-602. doi:10.1093/bioinformatics/btu333, http://bioinformatics.oxfordjournals.org/content/30/18/2598.full.pdf+html .
    • (2014) Bioinformatics , vol.30 , Issue.18 , pp. 2598-2602
    • Nueda, M.J.1    Tarazona, S.2    Conesa, A.3
  • 30
    • 84876554734 scopus 로고    scopus 로고
    • Flyatlas: database of gene expression in the tissues of drosophila melanogaster
    • Robinson SW, Herzyk P, Dow JAT, Leader DP. Flyatlas: database of gene expression in the tissues of drosophila melanogaster. Nucleic Acids Res. 2013; 41(D1):744-50. doi:10.1093/nar/gks1141, http://nar.oxfordjournals.org/content/41/D1/D744.full.pdf+html .
    • (2013) Nucleic Acids Res , vol.41 , Issue.D1 , pp. 744-750
    • Robinson, S.W.1    Herzyk, P.2    Dow, J.A.T.3    Leader, D.P.4
  • 32
    • 11144358198 scopus 로고    scopus 로고
    • A gene atlas of the mouse and human protein-encoding transcriptomes
    • Su AI. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Nat Acad Sci. 2004; 101(16):6062-7.
    • (2004) Proc Nat Acad Sci , vol.101 , Issue.16 , pp. 6062-6067
    • Su, A.I.1
  • 33
    • 77950583715 scopus 로고    scopus 로고
    • The Sexually Antagonistic Genes of Drosophila melanogaster
    • Innocenti P, Morrow EH. The Sexually Antagonistic Genes of Drosophila melanogaster. PLoS Biol. 2010; 8(3):1000335. doi:10.1371/journal.pbio.1000335.
    • (2010) PLoS Biol , vol.8 , Issue.3 , pp. 1000335
    • Innocenti, P.1    Morrow, E.H.2
  • 34
    • 34249804498 scopus 로고    scopus 로고
    • Using FlyAtlas to identify better Drosophila melanogaster models of human disease
    • Chintapalli VR, Wang J, Dow JAT. Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nat Genet. 2007; 39(6):715-20. doi:10.1038/ng2049.
    • (2007) Nat Genet , vol.39 , Issue.6 , pp. 715-720
    • Chintapalli, V.R.1    Wang, J.2    Dow, J.A.T.3
  • 35
    • 84861123691 scopus 로고    scopus 로고
    • Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges
    • Khatri P, Sirota M, Butte AJ. Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges. PLoS Comput Biol. 2012; 8(2):1002375. doi:10.1371/journal.pcbi.1002375.
    • (2012) PLoS Comput Biol , vol.8 , Issue.2 , pp. 1002375
    • Khatri, P.1    Sirota, M.2    Butte, A.J.3
  • 37
    • 84879517894 scopus 로고    scopus 로고
    • Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress
    • Petelenz-Kurdziel E, Kuehn C, Nordlander B, Klein D, Hong K-K, Jacobson T, et al.Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress. PLoS Comput Biol. 2013; 9(6):1003084. doi:10.1371/journal.pcbi.1003084.
    • (2013) PLoS Comput Biol , vol.9 , Issue.6 , pp. 1003084
    • Petelenz-Kurdziel, E.1    Kuehn, C.2    Nordlander, B.3    Klein, D.4    Hong, K.-K.5    Jacobson, T.6
  • 38
    • 78651245722 scopus 로고    scopus 로고
    • Modeling mechanisms of in vivo variability in methotrexate accumulation and folate pathway inhibition in acute lymphoblastic leukemia cells
    • Panetta JC, Sparreboom A, Pui C-H, Relling MV, Evans WE. Modeling mechanisms of in vivo variability in methotrexate accumulation and folate pathway inhibition in acute lymphoblastic leukemia cells. PLoS Comput Biol. 2010; 6(12):1001019. doi:10.1371/journal.pcbi.1001019.
    • (2010) PLoS Comput Biol , vol.6 , Issue.12 , pp. 1001019
    • Panetta, J.C.1    Sparreboom, A.2    Pui, C.-H.3    Relling, M.V.4    Evans, W.E.5
  • 39
    • 84870955752 scopus 로고    scopus 로고
    • Using Answer Set Programming to Integrate RNA Expression with Signalling Pathway Information to Infer How Mutations Affect Ageing
    • Papatheodorou I, Ziehm M, Wieser D, Alic N, Partridge L, Thornton JM. Using Answer Set Programming to Integrate RNA Expression with Signalling Pathway Information to Infer How Mutations Affect Ageing. PLoS ONE. 2012; 7(12):50881. doi:10.1371/journal.pone.0050881.
    • (2012) PLoS ONE , vol.7 , Issue.12 , pp. 50881
    • Papatheodorou, I.1    Ziehm, M.2    Wieser, D.3    Alic, N.4    Partridge, L.5    Thornton, J.M.6
  • 40
    • 77950825394 scopus 로고    scopus 로고
    • Mathematical modelling of cell-fate decision in response to death receptor engagement
    • Calzone L, Tournier L, Fourquet S, Thieffry D, Zhivotovsky B, Barillot E, et al.Mathematical modelling of cell-fate decision in response to death receptor engagement. PLoS Comput Biol. 2010; 6(3):1000702. doi:10.1371/journal.pcbi.1000702.
    • (2010) PLoS Comput Biol , vol.6 , Issue.3 , pp. 1000702
    • Calzone, L.1    Tournier, L.2    Fourquet, S.3    Thieffry, D.4    Zhivotovsky, B.5    Barillot, E.6
  • 41
    • 84891760956 scopus 로고    scopus 로고
    • Data, information, knowledge and principle: back to metabolism in kegg
    • Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. Data, information, knowledge and principle: back to metabolism in kegg. Nucleic Acids Res. 2014; 42(D1):199-205. doi:10.1093/nar/gkt1076, http://nar.oxfordjournals.org/content/42/D1/D199.full.pdf+html .
    • (2014) Nucleic Acids Res , vol.42 , Issue.D1 , pp. 199-205
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3    Kawashima, M.4    Furumichi, M.5    Tanabe, M.6
  • 42
    • 84946069451 scopus 로고    scopus 로고
    • UniProt: a hub for protein information
    • UniProt Consortium. UniProt: a hub for protein information. Nucleic Acids Res. 2015; 43(Database issue):204-12.
    • (2015) Nucleic Acids Res , vol.43 , Issue.DATABASE ISSUE , pp. 204-212


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.