메뉴 건너뛰기




Volumn 10, Issue SUPPL. 3, 2009, Pages

Improving gene expression similarity measurement using pathway-based analytic dimension

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CELL TYPE; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENETIC DATABASE; INTERMETHOD COMPARISON; LIVER; MICROARRAY ANALYSIS; THALAMUS; METHODOLOGY;

EID: 71549129296     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-S3-S15     Document Type: Article
Times cited : (3)

References (26)
  • 1
    • 33846064113 scopus 로고    scopus 로고
    • NCBI GEO: mining tens of millions of expression profiles--database and tools update
    • 10.1093/nar/gkl887, 1669752, 17099226
    • Barrett T, Troup DB, Wilhite SE. NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucl Acids Res 2007, 35:D760-765. 10.1093/nar/gkl887, 1669752, 17099226.
    • (2007) Nucl Acids Res , vol.35
    • Barrett, T.1    Troup, D.B.2    Wilhite, S.E.3
  • 2
    • 58149204055 scopus 로고    scopus 로고
    • ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression
    • 10.1093/nar/gkn889, 2686529, 19015125
    • Parkinson H, Kapushesky M, Kolesnikov N. ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res 2009, 37:D868-872. 10.1093/nar/gkn889, 2686529, 19015125.
    • (2009) Nucleic Acids Res , vol.37
    • Parkinson, H.1    Kapushesky, M.2    Kolesnikov, N.3
  • 3
    • 30544439504 scopus 로고    scopus 로고
    • Creation and implications of a phenome-genome network
    • 10.1038/nbt1150, 16404398, 2716377
    • Butte AJ, Kohane IS. Creation and implications of a phenome-genome network. Nat Biotechnol 2006, 24:55-62. 10.1038/nbt1150, 16404398, 2716377.
    • (2006) Nat Biotechnol , vol.24 , pp. 55-62
    • Butte, A.J.1    Kohane, I.S.2
  • 4
    • 34547846862 scopus 로고    scopus 로고
    • Finding Disease-Related Genomic Experiments Within an International Repository: First Steps in Translational Bioinformatics
    • Butte AJ, Chen R. Finding Disease-Related Genomic Experiments Within an International Repository: First Steps in Translational Bioinformatics. AMIA Annu Symp Proc 2006, 2006:106-110.
    • (2006) AMIA Annu Symp Proc , vol.2006 , pp. 106-110
    • Butte, A.J.1    Chen, R.2
  • 5
    • 63049123830 scopus 로고    scopus 로고
    • Ontology-driven indexing of public datasets for translational bioinformatics
    • 10.1186/1471-2105-10-S2-S1, 2646250, 19208184
    • Shah NH, Jonquet C, Chiang AP. Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics 2009, 10(Suppl 2):S1. 10.1186/1471-2105-10-S2-S1, 2646250, 19208184.
    • (2009) BMC Bioinformatics , vol.10 , Issue.SUPPL. 2
    • Shah, N.H.1    Jonquet, C.2    Chiang, A.P.3
  • 6
    • 62349088493 scopus 로고    scopus 로고
    • GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed
    • 10.1186/1471-2105-9-548, 2629779, 19094235
    • Chen R, Mallelwar R, Thosar A, Venkatasubrahmanyam S, Butte A. GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed. BMC Bioinformatics 2008, 9:548. 10.1186/1471-2105-9-548, 2629779, 19094235.
    • (2008) BMC Bioinformatics , vol.9 , pp. 548
    • Chen, R.1    Mallelwar, R.2    Thosar, A.3    Venkatasubrahmanyam, S.4    Butte, A.5
  • 7
    • 56649093037 scopus 로고    scopus 로고
    • GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus
    • 10.1093/bioinformatics/btn520, 2639278, 18842599
    • Zhu Y, Davis S, Stephens R, Meltzer PS, Chen Y. GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. Bioinformatics 2008, 24:2798-2800. 10.1093/bioinformatics/btn520, 2639278, 18842599.
    • (2008) Bioinformatics , vol.24 , pp. 2798-2800
    • Zhu, Y.1    Davis, S.2    Stephens, R.3    Meltzer, P.S.4    Chen, Y.5
  • 8
    • 84984934346 scopus 로고    scopus 로고
    • Gene expression informatics--it's all in your mine
    • 10.1038/4478, 9915502
    • Bassett DE, Eisen MB, Boguski MS. Gene expression informatics--it's all in your mine. Nat Genet 1999, 21:51-55. 10.1038/4478, 9915502.
    • (1999) Nat Genet , vol.21 , pp. 51-55
    • Bassett, D.E.1    Eisen, M.B.2    Boguski, M.S.3
  • 9
    • 0000412069 scopus 로고    scopus 로고
    • GEST: a gene expression search tool based on a novel Bayesian similarity metric
    • 10.1093/bioinformatics/17.2.115, 11473000
    • Hunter L, Taylor RC, Leach SM, Simon R. GEST: a gene expression search tool based on a novel Bayesian similarity metric. Bioinformatics 2001, 17:S115-122. 10.1093/bioinformatics/17.2.115, 11473000.
    • (2001) Bioinformatics , vol.17
    • Hunter, L.1    Taylor, R.C.2    Leach, S.M.3    Simon, R.4
  • 10
    • 34250179130 scopus 로고    scopus 로고
    • RaPiDS: an algorithm for rapid expression profile database search
    • Horton PB, Kiseleva L, Fujibuchi W. RaPiDS: an algorithm for rapid expression profile database search. Genome Inform 2006, 17:67-76.
    • (2006) Genome Inform , vol.17 , pp. 67-76
    • Horton, P.B.1    Kiseleva, L.2    Fujibuchi, W.3
  • 11
    • 36448955001 scopus 로고    scopus 로고
    • CellMontage: similar expression profile search server
    • 10.1093/bioinformatics/btm462, 17895274
    • Fujibuchi W, Kiseleva L, Taniguchi T, Harada H, Horton P. CellMontage: similar expression profile search server. Bioinformatics 2007, 23:3103-3104. 10.1093/bioinformatics/btm462, 17895274.
    • (2007) Bioinformatics , vol.23 , pp. 3103-3104
    • Fujibuchi, W.1    Kiseleva, L.2    Taniguchi, T.3    Harada, H.4    Horton, P.5
  • 12
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    • 10.1073/pnas.0506580102, 1239896,1239896, 16199517
    • Subramanian A, Tamayo P, Mootha VK. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:15545-15550. 10.1073/pnas.0506580102, 1239896,1239896, 16199517.
    • (2005) Proceedings of the National Academy of Sciences of the United States of America , vol.102 , pp. 15545-15550
    • Subramanian, A.1    Tamayo, P.2    Mootha, V.K.3
  • 13
    • 0037252705 scopus 로고    scopus 로고
    • Database resources of the National Center for Biotechnology
    • 10.1093/nar/gkg033, 165480, 12519941
    • Wheeler DL, Church DM, Federhen S. Database resources of the National Center for Biotechnology. Nucl Acids Res 2003, 31:28-33. 10.1093/nar/gkg033, 165480, 12519941.
    • (2003) Nucl Acids Res , vol.31 , pp. 28-33
    • Wheeler, D.L.1    Church, D.M.2    Federhen, S.3
  • 14
    • 2642561079 scopus 로고    scopus 로고
    • Are data from different gene expression microarray platforms comparable?
    • 10.1016/j.ygeno.2004.01.004, 15177569
    • Järvinen A, Hautaniemi S, Edgren H. Are data from different gene expression microarray platforms comparable?. Genomics 2004, 83:1164-1168. 10.1016/j.ygeno.2004.01.004, 15177569.
    • (2004) Genomics , vol.83 , pp. 1164-1168
    • Järvinen, A.1    Hautaniemi, S.2    Edgren, H.3
  • 15
    • 0141905890 scopus 로고    scopus 로고
    • Evaluation of gene expression measurements from commercial microarray platforms
    • 10.1093/nar/gkg763, 14500831, 206463
    • Tan PK, Downey TJ, Spitznagel EL. Evaluation of gene expression measurements from commercial microarray platforms. Nucl Acids Res 2003, 31:5676-5684. 10.1093/nar/gkg763, 14500831, 206463.
    • (2003) Nucl Acids Res , vol.31 , pp. 5676-5684
    • Tan, P.K.1    Downey, T.J.2    Spitznagel, E.L.3
  • 16
    • 27644528185 scopus 로고    scopus 로고
    • Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential
    • 10.1186/1471-2105-6-S2-S12, 1637032, 16026597
    • Shi L, Tong W, Fang H. Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential. BMC Bioinformatics 2005, 6(Suppl 2):S12. 10.1186/1471-2105-6-S2-S12, 1637032, 16026597.
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 2
    • Shi, L.1    Tong, W.2    Fang, H.3
  • 17
    • 33746420065 scopus 로고    scopus 로고
    • A case study in pathway knowledgebase verification
    • 10.1186/1471-2105-7-196, 1522024, 16603083
    • Racunas S, Shah N, Fedoroff N. A case study in pathway knowledgebase verification. BMC Bioinformatics 2006, 7:196. 10.1186/1471-2105-7-196, 1522024, 16603083.
    • (2006) BMC Bioinformatics , vol.7 , pp. 196
    • Racunas, S.1    Shah, N.2    Fedoroff, N.3
  • 18
    • 34347250516 scopus 로고    scopus 로고
    • Application of genomic biomarkers to predict increased lung tumor incidence in 2-year rodent cancer bioassays
    • 10.1093/toxsci/kfm023, 17311802
    • Thomas RS, Pluta L, Yang L, Halsey TA. Application of genomic biomarkers to predict increased lung tumor incidence in 2-year rodent cancer bioassays. Toxicol Sci 2007, 97:55-64. 10.1093/toxsci/kfm023, 17311802.
    • (2007) Toxicol Sci , vol.97 , pp. 55-64
    • Thomas, R.S.1    Pluta, L.2    Yang, L.3    Halsey, T.A.4
  • 19
    • 33847329758 scopus 로고    scopus 로고
    • A comparison of transcriptomic and metabonomic technologies for identifying biomarkers predictive of two-year rodent cancer bioassays
    • 10.1093/toxsci/kfl171, 17114358
    • Thomas RS, O'Connell TM, Pluta L. A comparison of transcriptomic and metabonomic technologies for identifying biomarkers predictive of two-year rodent cancer bioassays. Toxicol Sci 2007, 96:40-46. 10.1093/toxsci/kfl171, 17114358.
    • (2007) Toxicol Sci , vol.96 , pp. 40-46
    • Thomas, R.S.1    O'Connell, T.M.2    Pluta, L.3
  • 20
    • 0000801240 scopus 로고    scopus 로고
    • Discovering regulatory and signalling circuits in molecular interaction networks
    • Ideker T, Ozier O, Schwikowski B, Siegel AF. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 2002, 18(Suppl 1):S233-240.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Ideker, T.1    Ozier, O.2    Schwikowski, B.3    Siegel, A.F.4
  • 21
    • 26444608611 scopus 로고    scopus 로고
    • Discovering statistically significant pathways in expression profiling studies
    • 10.1073/pnas.0506577102, 1200092,1200092, 16174746
    • Tian L, Greenberg SA, Kong SW. Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci USA 2005, 102:13544-13549. 10.1073/pnas.0506577102, 1200092,1200092, 16174746.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 13544-13549
    • Tian, L.1    Greenberg, S.A.2    Kong, S.W.3
  • 22
    • 57149092133 scopus 로고    scopus 로고
    • Inferring pathway activity toward precise disease classification
    • 10.1371/journal.pcbi.1000217, 2563693, 18989396
    • Lee E, Chuang H, Kim J, Ideker T, Lee D. Inferring pathway activity toward precise disease classification. PLoS Comput Biol 2008, 4:e1000217. 10.1371/journal.pcbi.1000217, 2563693, 18989396.
    • (2008) PLoS Comput Biol , vol.4
    • Lee, E.1    Chuang, H.2    Kim, J.3    Ideker, T.4    Lee, D.5
  • 23
    • 0036578644 scopus 로고    scopus 로고
    • GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways
    • 10.1038/ng0502-19, 11984561
    • Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, Conklin BR. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet 2002, 31:19-20. 10.1038/ng0502-19, 11984561.
    • (2002) Nat Genet , vol.31 , pp. 19-20
    • Dahlquist, K.D.1    Salomonis, N.2    Vranizan, K.3    Lawlor, S.C.4    Conklin, B.R.5
  • 24
    • 0141905890 scopus 로고    scopus 로고
    • Evaluation of gene expression measurements from commercial microarray platforms
    • 10.1093/nar/gkg763, 206463, 14500831
    • Tan PK, Downey TJ, Spitznagel EL. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 2003, 31:5676-5684. 10.1093/nar/gkg763, 206463, 14500831.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5676-5684
    • Tan, P.K.1    Downey, T.J.2    Spitznagel, E.L.3
  • 25
    • 18944394950 scopus 로고    scopus 로고
    • An array of problems
    • 10.1038/nrd1746, 15902768
    • Frantz S. An array of problems. Nat Rev Drug Discov 2005, 4:362-363. 10.1038/nrd1746, 15902768.
    • (2005) Nat Rev Drug Discov , vol.4 , pp. 362-363
    • Frantz, S.1
  • 26
    • 22744458472 scopus 로고    scopus 로고
    • Pathways to the analysis of microarray data
    • 10.1016/j.tibtech.2005.05.011, 15950303
    • Curtis RK, Oresic M, Vidal-Puig A. Pathways to the analysis of microarray data. Trends Biotechnol 2005, 23:429-435. 10.1016/j.tibtech.2005.05.011, 15950303.
    • (2005) Trends Biotechnol , vol.23 , pp. 429-435
    • Curtis, R.K.1    Oresic, M.2    Vidal-Puig, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.