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Volumn 6, Issue 4, 2011, Pages

Functional cohesion of gene sets determined by Latent Semantic Indexing of pubmed abstracts

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CALCULATION; COMPUTER PROGRAM; DOCUMENTATION; GENE FUNCTION; GENE INTERACTION; GENETIC ANALYSIS; HUMAN; INTERNET; LATENT SEMANTIC INDEXING; METHODOLOGY; MOUSE; NONHUMAN; PUBLICATION; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS; ANIMAL; GENE; MEDLINE;

EID: 79955004406     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0018851     Document Type: Article
Times cited : (22)

References (34)
  • 1
    • 0036051492 scopus 로고    scopus 로고
    • How many replicates of arrays are required to detect gene expression changes in microarray experiments? A mixture model approach
    • research0022
    • Pan W, Lin J, Le CT, (2002) How many replicates of arrays are required to detect gene expression changes in microarray experiments? A mixture model approach. Genome Biol 3: research0022.
    • (2002) Genome Biol , vol.3
    • Pan, W.1    Lin, J.2    Le, C.T.3
  • 2
    • 0037368548 scopus 로고    scopus 로고
    • Selecting differentially expressed genes from microarray experiments
    • Pepe MS, Longton G, Anderson GL, Schummer M, (2003) Selecting differentially expressed genes from microarray experiments. Biometrics 59: 133-142.
    • (2003) Biometrics , vol.59 , pp. 133-142
    • Pepe, M.S.1    Longton, G.2    Anderson, G.L.3    Schummer, M.4
  • 3
    • 33747344944 scopus 로고    scopus 로고
    • Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data
    • Jeffery IB, Higgins DG, Culhane AC, (2006) Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. BMC Bioinformatics 7: 359.
    • (2006) BMC Bioinformatics , vol.7 , pp. 359
    • Jeffery, I.B.1    Higgins, D.G.2    Culhane, A.C.3
  • 5
    • 1342330530 scopus 로고    scopus 로고
    • A graph-theoretic modeling on GO space for biological interpretation of gene clusters
    • Lee SG, Hur JU, Kim YS, (2004) A graph-theoretic modeling on GO space for biological interpretation of gene clusters. Bioinformatics 20: 381-388.
    • (2004) Bioinformatics , vol.20 , pp. 381-388
    • Lee, S.G.1    Hur, J.U.2    Kim, Y.S.3
  • 6
    • 20444365683 scopus 로고    scopus 로고
    • GOToolBox: functional analysis of gene datasets based on Gene Ontology
    • Martin D, Brun C, Remy E, Mouren P, Thieffry D, et al. (2004) GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol 5: R101.
    • (2004) Genome Biol , vol.5
    • Martin, D.1    Brun, C.2    Remy, E.3    Mouren, P.4    Thieffry, D.5
  • 7
    • 23144464901 scopus 로고    scopus 로고
    • WebGestalt: an integrated system for exploring gene sets in various biological contexts
    • Zhang B, Kirov S, Snoddy J, (2005) WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res 33: W741-748.
    • (2005) Nucleic Acids Res , vol.33 , pp. 741-748
    • Zhang, B.1    Kirov, S.2    Snoddy, J.3
  • 8
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5
  • 9
    • 39749095475 scopus 로고    scopus 로고
    • Novel metrics for evaluating the functional coherence of protein groups via protein semantic network
    • Zheng B, Lu X, (2007) Novel metrics for evaluating the functional coherence of protein groups via protein semantic network. Genome Biol 8: R153.
    • (2007) Genome Biol , vol.8
    • Zheng, B.1    Lu, X.2
  • 10
    • 0036796319 scopus 로고    scopus 로고
    • Using text analysis to identify functionally coherent gene groups
    • Raychaudhuri S, Schutze H, Altman RB, (2002) Using text analysis to identify functionally coherent gene groups. Genome Res 12: 1582-1590.
    • (2002) Genome Res , vol.12 , pp. 1582-1590
    • Raychaudhuri, S.1    Schutze, H.2    Altman, R.B.3
  • 12
    • 56149108807 scopus 로고    scopus 로고
    • Using protein-semantic network metrics to evaluate functional coherence of protein groups
    • Zheng B, Lu X, (2007) Using protein-semantic network metrics to evaluate functional coherence of protein groups. AMIA Annu Symp Proc 1174.
    • (2007) AMIA Annu Symp Proc , vol.1174
    • Zheng, B.1    Lu, X.2
  • 13
  • 14
    • 12744279636 scopus 로고    scopus 로고
    • Gene clustering by latent semantic indexing of MEDLINE abstracts
    • Homayouni R, Heinrich K, Wei L, Berry MW, (2005) Gene clustering by latent semantic indexing of MEDLINE abstracts. Bioinformatics 21: 104-115.
    • (2005) Bioinformatics , vol.21 , pp. 104-115
    • Homayouni, R.1    Heinrich, K.2    Wei, L.3    Berry, M.W.4
  • 15
    • 0003490106 scopus 로고    scopus 로고
    • Understanding Search Engines: Mathematical Modeling and Text Retrieval
    • SIAM, Philadelphia
    • Berry MW, Browne M, (1999) Understanding Search Engines: Mathematical Modeling and Text Retrieval. SIAM, Philadelphia.
    • (1999)
    • Berry, M.W.1    Browne, M.2
  • 16
    • 1842738366 scopus 로고    scopus 로고
    • From paragraph to graph: latent semantic analysis for information visualization
    • Landauer TK, Laham D, Derr M, (2004) From paragraph to graph: latent semantic analysis for information visualization. Proc Natl Acad Sci U S A 101 (Suppl 1): 5214-5219.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , Issue.SUPPL. 1 , pp. 5214-5219
    • Landauer, T.K.1    Laham, D.2    Derr, M.3
  • 17
    • 0037433059 scopus 로고    scopus 로고
    • A literature-based method for assessing the functional coherence of a gene group
    • Raychaudhuri S, Altman RB, (2003) A literature-based method for assessing the functional coherence of a gene group. Bioinformatics 19: 396-401.
    • (2003) Bioinformatics , vol.19 , pp. 396-401
    • Raychaudhuri, S.1    Altman, R.B.2
  • 18
    • 51349164382 scopus 로고    scopus 로고
    • Bioinformatic analysis reveals cRel as a regulator of a subset of interferon-stimulated genes
    • Wei L, Fan M, Xu L, Heinrich K, Berry MW, et al. (2008) Bioinformatic analysis reveals cRel as a regulator of a subset of interferon-stimulated genes. J Interferon Cytokine Res 28: 541-551.
    • (2008) J Interferon Cytokine Res , vol.28 , pp. 541-551
    • Wei, L.1    Fan, M.2    Xu, L.3    Heinrich, K.4    Berry, M.W.5
  • 20
    • 1642317557 scopus 로고    scopus 로고
    • Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival
    • Chiaretti S, Li X, Gentleman R, Vitale A, Vignetti M, et al. (2004) Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival. Blood 103: 2771-2778.
    • (2004) Blood , vol.103 , pp. 2771-2778
    • Chiaretti, S.1    Li, X.2    Gentleman, R.3    Vitale, A.4    Vignetti, M.5
  • 22
    • 33947726437 scopus 로고    scopus 로고
    • Assignment of protein function and discovery of novel nucleolar proteins based on automatic analysis of MEDLINE
    • Schuemie M, Chichester C, Lisacek F, Coute Y, Roes PJ, et al. (2007) Assignment of protein function and discovery of novel nucleolar proteins based on automatic analysis of MEDLINE. Proteomics 7: 921-931.
    • (2007) Proteomics , vol.7 , pp. 921-931
    • Schuemie, M.1    Chichester, C.2    Lisacek, F.3    Coute, Y.4    Roes, P.J.5
  • 23
    • 1342330525 scopus 로고    scopus 로고
    • Knowledge discovery by automated identification and ranking of implicit relationships
    • Wren JD, Bekeredjian R, Stewart JA, Shohet RV, Garner HR, (2004) Knowledge discovery by automated identification and ranking of implicit relationships. Bioinformatics 20: 389-398.
    • (2004) Bioinformatics , vol.20 , pp. 389-398
    • Wren, J.D.1    Bekeredjian, R.2    Stewart, J.A.3    Shohet, R.V.4    Garner, H.R.5
  • 24
    • 33847004014 scopus 로고    scopus 로고
    • Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation
    • Jelier R, Jenster G, Dorssers LC, Wouters BJ, Hendriksen PJ, et al. (2007) Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation. BMC Bioinformatics 8: 14.
    • (2007) BMC Bioinformatics , vol.8 , pp. 14
    • Jelier, R.1    Jenster, G.2    Dorssers, L.C.3    Wouters, B.J.4    Hendriksen, P.J.5
  • 25
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102: 15545-15550.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 15545-15550
    • Subramanian, A.1    Tamayo, P.2    Mootha, V.K.3    Mukherjee, S.4    Ebert, B.L.5
  • 26
    • 1542399989 scopus 로고    scopus 로고
    • FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes
    • Al-Shahrour F, Diaz-Uriarte R, Dopazo J, (2004) FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 20: 578-580.
    • (2004) Bioinformatics , vol.20 , pp. 578-580
    • Al-Shahrour, F.1    Diaz-Uriarte, R.2    Dopazo, J.3
  • 27
    • 67149094751 scopus 로고    scopus 로고
    • Comparing algorithms for clustering of expression data: how to assess gene clusters
    • Yona G, Dirks W, Rahman S, (2009) Comparing algorithms for clustering of expression data: how to assess gene clusters. Methods Mol Biol 541: 479-509.
    • (2009) Methods Mol Biol , vol.541 , pp. 479-509
    • Yona, G.1    Dirks, W.2    Rahman, S.3
  • 28
    • 67849101190 scopus 로고    scopus 로고
    • SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks
    • Minguez P, Gotz S, Montaner D, Al-Shahrour F, Dopazo J, (2009) SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. Nucleic Acids Res 37: W109-114.
    • (2009) Nucleic Acids Res , vol.37 , pp. 109-114
    • Minguez, P.1    Gotz, S.2    Montaner, D.3    Al-Shahrour, F.4    Dopazo, J.5
  • 29
    • 33847324900 scopus 로고    scopus 로고
    • Extensions to gene set enrichment
    • Jiang Z, Gentleman R, (2007) Extensions to gene set enrichment. Bioinformatics 23: 306-313.
    • (2007) Bioinformatics , vol.23 , pp. 306-313
    • Jiang, Z.1    Gentleman, R.2
  • 30
    • 0038054341 scopus 로고    scopus 로고
    • PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
    • Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, et al. (2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34: 267-273.
    • (2003) Nat Genet , vol.34 , pp. 267-273
    • Mootha, V.K.1    Lindgren, C.M.2    Eriksson, K.F.3    Subramanian, A.4    Sihag, S.5
  • 31
    • 43149116763 scopus 로고    scopus 로고
    • Gene-set approach for expression pattern analysis
    • Nam D, Kim SY, (2008) Gene-set approach for expression pattern analysis. Brief Bioinform 9: 189-197.
    • (2008) Brief Bioinform , vol.9 , pp. 189-197
    • Nam, D.1    Kim, S.Y.2
  • 32
    • 55749111082 scopus 로고    scopus 로고
    • Gene set enrichment analysis using linear models and diagnostics
    • Oron AP, Jiang Z, Gentleman R, (2008) Gene set enrichment analysis using linear models and diagnostics. Bioinformatics 24: 2586-2591.
    • (2008) Bioinformatics , vol.24 , pp. 2586-2591
    • Oron, A.P.1    Jiang, Z.2    Gentleman, R.3
  • 33
    • 38749102349 scopus 로고    scopus 로고
    • Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis
    • Kim TM, Chung YJ, Rhyu MG, Jung MH, (2007) Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis. BMC Bioinformatics 8: 453.
    • (2007) BMC Bioinformatics , vol.8 , pp. 453
    • Kim, T.M.1    Chung, Y.J.2    Rhyu, M.G.3    Jung, M.H.4
  • 34
    • 21444454257 scopus 로고    scopus 로고
    • False discovery rate, sensitivity and sample size for microarray studies
    • Pawitan Y, Michiels S, Koscielny S, Gusnanto A, Ploner A, (2005) False discovery rate, sensitivity and sample size for microarray studies. Bioinformatics 21: 3017-3024.
    • (2005) Bioinformatics , vol.21 , pp. 3017-3024
    • Pawitan, Y.1    Michiels, S.2    Koscielny, S.3    Gusnanto, A.4    Ploner, A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.