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Volumn 12, Issue 10, 2011, Pages

SpeCond: A method to detect condition-specific gene expression

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ANALYTIC METHOD; ARTICLE; COMPUTER PROGRAM; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; HUMAN; INTERNET; RECEIVER OPERATING CHARACTERISTIC; STATISTICAL ANALYSIS; TRANSCRIPTOMICS; ALGORITHM; BIOLOGY; DNA MICROARRAY; GENE; GENETIC DATABASE; GENOMICS; HUMAN GENOME; METHODOLOGY; SENSITIVITY AND SPECIFICITY;

EID: 80054113139     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2011-12-10-r101     Document Type: Article
Times cited : (15)

References (31)
  • 1
    • 33344460411 scopus 로고    scopus 로고
    • Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins.
    • 10.1186/gb-2005-6-7-r56, 1175987, 15998445
    • Freilich S, Massingham T, Bhattacharyya S, Ponsting H, Lyons PA, Freeman TC, Thornton JM. Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins. Genome Biology 2005, 6:R56. 10.1186/gb-2005-6-7-r56, 1175987, 15998445.
    • (2005) Genome Biology , vol.6
    • Freilich, S.1    Massingham, T.2    Bhattacharyya, S.3    Ponsting, H.4    Lyons, P.A.5    Freeman, T.C.6    Thornton, J.M.7
  • 2
    • 62549128139 scopus 로고    scopus 로고
    • A census of human transcription factors: function, expression and evolution.
    • 10.1038/nrg2538, 19274049
    • Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM. A census of human transcription factors: function, expression and evolution. Nature reviews. Genetics 2009, 10:252-63. 10.1038/nrg2538, 19274049.
    • (2009) Nature reviews. Genetics , vol.10 , pp. 252-263
    • Vaquerizas, J.M.1    Kummerfeld, S.K.2    Teichmann, S.A.3    Luscombe, N.M.4
  • 3
    • 0034720002 scopus 로고    scopus 로고
    • Comparison of human adult and fetal expression and identification of 535 housekeeping/maintenance genes.
    • Warrington JA, Nair A, Mahadevappa M, Tsyganskaya M. Comparison of human adult and fetal expression and identification of 535 housekeeping/maintenance genes. Physiological genomics 2000, 2:143-7.
    • (2000) Physiological genomics , vol.2 , pp. 143-147
    • Warrington, J.A.1    Nair, A.2    Mahadevappa, M.3    Tsyganskaya, M.4
  • 4
    • 0035931097 scopus 로고    scopus 로고
    • Further defining housekeeping, or "maintenance," genes Focus on "A compendium of gene expression in normal human tissues".
    • Butte AJ, Dzau VJ, Glueck SB. Further defining housekeeping, or "maintenance," genes Focus on "A compendium of gene expression in normal human tissues". Physiological genomics 2001, 7:95-6.
    • (2001) Physiological genomics , vol.7 , pp. 95-96
    • Butte, A.J.1    Dzau, V.J.2    Glueck, S.B.3
  • 5
    • 33644872577 scopus 로고    scopus 로고
    • Limma: linear models for microarray data.
    • New York: Springer, Gentleman R, Carey V, Dudoit S, R Irizarry WH
    • Smyth GK. Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions using R and Bioconductor 2005, 397-420. New York: Springer, Gentleman R, Carey V, Dudoit S, R Irizarry WH.
    • (2005) Bioinformatics and Computational Biology Solutions using R and Bioconductor , pp. 397-420
    • Smyth, G.K.1
  • 7
    • 34547684291 scopus 로고    scopus 로고
    • A comprehensive evaluation of SAM, the SAM R-package and a simple modification to improve its performance.
    • 10.1186/1471-2105-8-230, 1955751, 17603887
    • Zhang S. A comprehensive evaluation of SAM, the SAM R-package and a simple modification to improve its performance. BMC bioinformatics 2007, 8:230. 10.1186/1471-2105-8-230, 1955751, 17603887.
    • (2007) BMC bioinformatics , vol.8 , pp. 230
    • Zhang, S.1
  • 8
    • 78149454849 scopus 로고    scopus 로고
    • Systematical Detection of Significant Genes in Microarray Data by Incorporating Gene Interaction Relationship in Biological Systems.
    • 10.1371/journal.pone.0013721, 2966410, 21060778
    • Wang J, Jia M, Zhu L, Yuan Z, Li P, Chang C, Luo J, Liu M, Shi T. Systematical Detection of Significant Genes in Microarray Data by Incorporating Gene Interaction Relationship in Biological Systems. PLoS ONE 2010, 5(10):e13721. 10.1371/journal.pone.0013721, 2966410, 21060778.
    • (2010) PLoS ONE , vol.5 , Issue.10
    • Wang, J.1    Jia, M.2    Zhu, L.3    Yuan, Z.4    Li, P.5    Chang, C.6    Luo, J.7    Liu, M.8    Shi, T.9
  • 9
    • 0036203115 scopus 로고    scopus 로고
    • A mixture model-based approach to the clustering of microarray expression data.
    • 10.1093/bioinformatics/18.3.413, 11934740
    • McLachlan GJ, Bean RW, Peel D. A mixture model-based approach to the clustering of microarray expression data. Bioinformatics 2002, 18:413-422. 10.1093/bioinformatics/18.3.413, 11934740.
    • (2002) Bioinformatics , vol.18 , pp. 413-422
    • McLachlan, G.J.1    Bean, R.W.2    Peel, D.3
  • 10
    • 33745606461 scopus 로고    scopus 로고
    • A simple implementation of a normal mixture approach to differential gene expression in multiclass microarrays.
    • 10.1093/bioinformatics/btl148, 16632494
    • McLachlan GJ, Bean RW, Ben-Tovim Jones L. A simple implementation of a normal mixture approach to differential gene expression in multiclass microarrays. Bioinformatics 2006, 22:1608-1615. 10.1093/bioinformatics/btl148, 16632494.
    • (2006) Bioinformatics , vol.22 , pp. 1608-1615
    • McLachlan, G.J.1    Bean, R.W.2    Ben-Tovim Jones, L.3
  • 11
    • 33745951206 scopus 로고    scopus 로고
    • ROKU: a novel method for identification of tissue-specific genes.
    • 10.1186/1471-2105-7-294, 1501047, 16764735
    • Kadota K, Ye J, Nakai Y, Terada T, Shimizu K. ROKU: a novel method for identification of tissue-specific genes. BMC bioinformatics 2006, 7:294. 10.1186/1471-2105-7-294, 1501047, 16764735.
    • (2006) BMC bioinformatics , vol.7 , pp. 294
    • Kadota, K.1    Ye, J.2    Nakai, Y.3    Terada, T.4    Shimizu, K.5
  • 18
    • 84855280477 scopus 로고    scopus 로고
    • SpeCond Bioconductor package.
    • SpeCond Bioconductor package. , http://bioconductor.org/packages/release/bioc/html/SpeCond.html
  • 19
    • 22844453564 scopus 로고    scopus 로고
    • MCLUST: Software for model-based cluster analysis.
    • Fraley C, Raftery AE. MCLUST: Software for model-based cluster analysis. Journal of Classification 1999, 16:297-306.
    • (1999) Journal of Classification , vol.16 , pp. 297-306
    • Fraley, C.1    Raftery, A.E.2
  • 20
    • 0742306126 scopus 로고    scopus 로고
    • Enhanced software for model-based clustering, density estimation, and discriminant analysis: MCLUST.
    • Fraley C, Raftery AE. Enhanced software for model-based clustering, density estimation, and discriminant analysis: MCLUST. Journal of Classification 2003, 20:263-286.
    • (2003) Journal of Classification , vol.20 , pp. 263-286
    • Fraley, C.1    Raftery, A.E.2
  • 22
    • 0035733108 scopus 로고    scopus 로고
    • The control of the false discovery rate in multiple testing under dependency.
    • Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Annals of Statistics 2001, 29:1165-1188.
    • (2001) Annals of Statistics , vol.29 , pp. 1165-1188
    • Benjamini, Y.1    Yekutieli, D.2
  • 23
    • 34547571030 scopus 로고    scopus 로고
    • G:Profiler-a web-based toolset for functional profiling of gene lists from large-scale experiments.
    • 10.1093/nar/gkm226, 1933153, 17478515
    • Reimand J, Kull M, Peterson H, Hansen J, Vilo J. g:Profiler-a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic acids research 2007, 35:W193-200. 10.1093/nar/gkm226, 1933153, 17478515.
    • (2007) Nucleic acids research , vol.35
    • Reimand, J.1    Kull, M.2    Peterson, H.3    Hansen, J.4    Vilo, J.5
  • 24
    • 0037223832 scopus 로고    scopus 로고
    • The role of the nuclear receptor CAR as a coordinate regulator of hepatic gene expression in defense against chemical toxicity.
    • 10.1016/S0003-9861(02)00456-3, 12464260
    • Yamamoto Y, Kawamoto T, Negishi M. The role of the nuclear receptor CAR as a coordinate regulator of hepatic gene expression in defense against chemical toxicity. Archives of biochemistry and biophysics 2003, 409:207-11. 10.1016/S0003-9861(02)00456-3, 12464260.
    • (2003) Archives of biochemistry and biophysics , vol.409 , pp. 207-211
    • Yamamoto, Y.1    Kawamoto, T.2    Negishi, M.3
  • 25
    • 0031213639 scopus 로고    scopus 로고
    • Cloning, human chromosomal assignment, and adipose and hepatic expression of the CL-6/INSIG1 gene.
    • 10.1006/geno.1997.4821, 9268630
    • Peng Y, Schwarz EJ, Lazar MA, Genin A, Spinner NB, Taub R. Cloning, human chromosomal assignment, and adipose and hepatic expression of the CL-6/INSIG1 gene. Genomics 1997, 43:278-84. 10.1006/geno.1997.4821, 9268630.
    • (1997) Genomics , vol.43 , pp. 278-284
    • Peng, Y.1    Schwarz, E.J.2    Lazar, M.A.3    Genin, A.4    Spinner, N.B.5    Taub, R.6
  • 26
    • 44149094808 scopus 로고    scopus 로고
    • ATF5 Is a Highly Abundant Liver-Enriched Transcription Factor that Cooperates with Constitutive Androstane Receptor in the Transactivation of CYP2B6: Implications in Hepatic Stress Responses.
    • Pascual M, Jose M, Castell V, Jover R. ATF5 Is a Highly Abundant Liver-Enriched Transcription Factor that Cooperates with Constitutive Androstane Receptor in the Transactivation of CYP2B6: Implications in Hepatic Stress Responses. Pharmacology 2008, 36:1063-1072.
    • (2008) Pharmacology , vol.36 , pp. 1063-1072
    • Pascual, M.1    Jose, M.2    Castell, V.3    Jover, R.4
  • 27
    • 0027965106 scopus 로고
    • The Mouse and Human Excitatory Amino Acid Transporter Gene (EAAT1) Maps to Mouse Chromosome 15 and a Region of Syntenic Homology on Human Chromosome 5.
    • 10.1006/geno.1994.1437, 8001975
    • Kirschner MA, Arriza JL, Copeland NG, Gilbert DJ, Jenkins NA, Magenis E, Amara SG. The Mouse and Human Excitatory Amino Acid Transporter Gene (EAAT1) Maps to Mouse Chromosome 15 and a Region of Syntenic Homology on Human Chromosome 5. Genomics 1994, 22:631-633. 10.1006/geno.1994.1437, 8001975.
    • (1994) Genomics , vol.22 , pp. 631-633
    • Kirschner, M.A.1    Arriza, J.L.2    Copeland, N.G.3    Gilbert, D.J.4    Jenkins, N.A.5    Magenis, E.6    Amara, S.G.7
  • 29
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data.
    • 10.1186/gb-2010-11-10-r106, 3218662, 20979621
    • Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biology 2010, 11:R106. 10.1186/gb-2010-11-10-r106, 3218662, 20979621.
    • (2010) Genome Biology , vol.11
    • Anders, S.1    Huber, W.2
  • 30
    • 35748952199 scopus 로고    scopus 로고
    • A gene expression bar code for microarray data.
    • 10.1038/nmeth1102, 3154617, 17906632
    • Zilliox MJ, Irizarry RA. A gene expression bar code for microarray data. Nature Methods 2007, 4:911-3. 10.1038/nmeth1102, 3154617, 17906632.
    • (2007) Nature Methods , vol.4 , pp. 911-913
    • Zilliox, M.J.1    Irizarry, R.A.2
  • 31
    • 78651271261 scopus 로고    scopus 로고
    • The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes.
    • 10.1093/nar/gkq1259, 3013751, 21177656
    • McCall MN, Uppal K, Jaffee HA, Zilliox MJ, Irizarry RA. The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. Nucleic Acids Research 2011, 39:D1011-5. 10.1093/nar/gkq1259, 3013751, 21177656.
    • (2011) Nucleic Acids Research , vol.39
    • McCall, M.N.1    Uppal, K.2    Jaffee, H.A.3    Zilliox, M.J.4    Irizarry, R.A.5


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