메뉴 건너뛰기




Volumn , Issue , 2007, Pages 212-218

Semantic analysis of genome annotations using weighting schemes

Author keywords

[No Author keywords available]

Indexed keywords

ARTIFICIAL INTELLIGENCE; BIOINFORMATICS; DATABASE SYSTEMS; GENES; MOLECULAR BIOLOGY;

EID: 84886067407     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/cibcb.2007.4221226     Document Type: Conference Paper
Times cited : (12)

References (42)
  • 2
    • 1542399989 scopus 로고    scopus 로고
    • FatiGO: A web tool for finding significant associations of Gene Ontology terms with groups of genes
    • DOI 10.1093/bioinformatics/btg455
    • Fatima Al-Shahrour, Ramon Diaz-Uriarte, and Joaquin Dopazo. FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics, 20(4): 578-580, 2004. (Pubitemid 38344339)
    • (2004) Bioinformatics , vol.20 , Issue.4 , pp. 578-580
    • Al-Shahrour, F.1    Diaz-Uriarte, R.2    Dopazo, J.3
  • 3
    • 0034730140 scopus 로고    scopus 로고
    • Singular value decomposition for genome-wide expression data processing and modeling
    • O. Alter, P.O. Brown, and D. Botstein. Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl. Acad. Sci. USA, 97(18): 10101-10106, 2000.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , Issue.18 , pp. 10101-10106
    • Alter, O.1    Brown, P.O.2    Botstein, D.3
  • 5
    • 3142665525 scopus 로고    scopus 로고
    • GOstat: Find statistically overrepresented Gene Ontologies with a group of genes
    • DOI 10.1093/bioinformatics/bth088
    • T Beissbarth and TP. Speed. GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics., 20:1464-1465, June 2004. (Pubitemid 38931420)
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1464-1465
    • Beissbarth, T.1    Speed, T.P.2
  • 6
    • 0032624581 scopus 로고    scopus 로고
    • Matrices, vector spaces, and information retrieval
    • M. W. Berry, Z. Drmac, and E. R. Jessup. Matrices, vector spaces, and information retrieval. SIAM Review, 41(2): 335-362, 1999.
    • (1999) SIAM Review , vol.41 , Issue.2 , pp. 335-362
    • Berry, M.W.1    Drmac, Z.2    Jessup, E.R.3
  • 7
    • 0029546874 scopus 로고
    • Using linear algebra for intelligent information retrieval
    • Michael W. Berry, Susan T. Dumais, and G. W. O'Brien. Using linear algebra for intelligent information retrieval. SIAM: Review, 37(4):573-595, 1995.
    • (1995) SIAM: Review , vol.37 , Issue.4 , pp. 573-595
    • Berry, M.W.1    Dumais, S.T.2    O'Brien, G.W.3
  • 8
    • 15944407681 scopus 로고    scopus 로고
    • Evaluation of the vector space representation in text-based gene clustering
    • O. Bodenreider, M. Aubry, and A. Burgun. Evaluation of the vector space representation in text-based gene clustering. In Pacific Symposium on Biocomputing, pages 91-102, 2005.
    • (2005) Pacific Symposium on Biocomputing , pp. 91-102
    • Bodenreider, O.1    Aubry, M.2    Burgun, A.3
  • 11
    • 0034308142 scopus 로고    scopus 로고
    • Practical limits of function prediction
    • DOI 10.1002/1097-0134(20001001)41:1<98::AID-PROT120>3.0.CO;2-S
    • Damien Devos and Alfonso Valencia. Practical limits of function prediction. PROTEINS: Structure, Function, and Genetics, 41: 98-107, 2000. (Pubitemid 30666916)
    • (2000) Proteins: Structure, Function and Genetics , vol.41 , Issue.1 , pp. 98-107
    • Devos, D.1    Valencia, A.2
  • 12
    • 0042121055 scopus 로고    scopus 로고
    • Onto-tools the toolkit of the modern biologist: Onto-express, onto-compare, onto-design and onto- translate
    • July
    • Sorin Drǎghici, Purvesh Khatri, Pratik Bhavsar, Abhik Shah, Stephen A. Krawetz, and Michael A. Tainsky. Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto- Translate. Nucleic Acids Research, 31(13): 3775-81, July 2003.
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3775-3781
    • Drǎghici, S.1    Khatri, P.2    Bhavsar, P.3    Shah, A.4    Krawetz, S.A.5    Tainsky, M.A.6
  • 13
    • 0037293075 scopus 로고    scopus 로고
    • Global functional profiling of gene expression
    • DOI 10.1016/S0888-7543(02)00021-6
    • Sorin Drǎghici, Purvesh Khatri, Rui P. Martins, G. Charles Ostermeier, and Stephen A. Krawetz. Global functional profiling of gene expression. Genomics, 81(2): 98-104, February 2003. (Pubitemid 36298600)
    • (2003) Genomics , vol.81 , Issue.2 , pp. 98-104
    • Draghici, S.1    Khatri, P.2    Martins, R.P.3    Ostermeier, G.C.4    Krawetz, S.A.5
  • 15
    • 0035059281 scopus 로고    scopus 로고
    • Genomic-scale comparison of sequence- and structure-based methods of function prediction: Does structure provide additional insight?
    • DOI 10.1110/ps.49201
    • Jacquelyn S. Fetrow, Naomi Siew, Jeannine A Di Gennaro, Maria Martinez-Yamout, H. Jane Dyson, and Jeffrey Skolnick. Genomicscale comparison of sequence- and structure-baed methods of function prediction: Does structure provide additional insight? Protein Science, 10: 1005-1014, 2001. (Pubitemid 32367492)
    • (2001) Protein Science , vol.10 , Issue.5 , pp. 1005-1014
    • Fetrow, J.S.1    Siew, N.2    Di Gennaro, J.A.3    Martinez-Yamout, M.4    Dyson, H.J.5    Skolnick, J.6
  • 16
    • 0043089918 scopus 로고    scopus 로고
    • Transformation and normalization of oligonucleotide microarray data
    • DOI 10.1093/bioinformatics/btg245
    • Sue C. Geller, Jeff P. Gregg, Paul Hagerman, and David M. Rocke. Transformation and normalization of oligonucleotide microarray data. Bioinformatics, 19: 1817-1823, 2003. (Pubitemid 37220474)
    • (2003) Bioinformatics , vol.19 , Issue.14 , pp. 1817-1823
    • Geller, S.C.1    Gregg, J.P.2    Hagerman, P.3    Rocke, D.M.4
  • 21
    • 12744279636 scopus 로고    scopus 로고
    • Gene clustering by latent semantic indexing of medline abstracts
    • R. Homayouni, K. Heinrich, L. Wei, and M. W. Berry. Gene clustering by latent semantic indexing of medline abstracts. Bioinformatics, 21(1):104-115, 2005.
    • (2005) Bioinformatics , vol.21 , Issue.1 , pp. 104-115
    • Homayouni, R.1    Heinrich, K.2    Wei, L.3    Berry, M.W.4
  • 24
    • 0031797096 scopus 로고    scopus 로고
    • What we do not know about sequence analysis and sequence databases
    • Peter D. Karp. What we do not know about sequence analysis and sequence databases. Bioinformatics, 14(9): 753-754, 1998. (Pubitemid 28552107)
    • (1998) Bioinformatics , vol.14 , Issue.9 , pp. 753-754
    • Karp, P.D.1
  • 25
    • 3242887152 scopus 로고    scopus 로고
    • Onto-Tools: An ensemble of web-accessible ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments
    • DOI 10.1093/nar/gkh409
    • Purvesh Khatri, Pratik Bhavsar, Gagandeep Bawa, and Sorin Drǎghici. Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments. Nucleic Acids Research, 32:W449-56, Jul 2004. (Pubitemid 38997375)
    • (2004) Nucleic Acids Research , vol.32 , Issue.WEB SERVER ISS.
    • Khatri, P.1    Bhavsar, P.2    Bawa, G.3    Draghici, S.4
  • 26
    • 24044446835 scopus 로고    scopus 로고
    • A semantic analysis of the annotations of the human genome
    • DOI 10.1093/bioinformatics/bti538
    • Purvesh Khatri, Bogdan Done, Archana Rao, Arina Done, and Sorin Draghici. A semantic analysis of the annotations of the human genome. Bioinformatics, 21(16): 3416-3421, 2005. (Pubitemid 41222447)
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3416-3421
    • Khatri, P.1    Done, B.2    Rao, A.3    Done, A.4    Draghici, S.5
  • 27
    • 0035704901 scopus 로고    scopus 로고
    • Profiling gene expression using onto-express
    • February
    • Purvesh Khatri, Sorin Drǎghici, G. Charles Ostermeier, and Stephen A. Krawetz. Profiling gene expression using Onto-Express. Genomics, 79(2): 266-270, February 2002.
    • (2002) Genomics , vol.79 , Issue.2 , pp. 266-270
    • Khatri, P.1    Drǎghici, S.2    Charles Ostermeier, G.3    Krawetz, S.A.4
  • 28
    • 0037767293 scopus 로고    scopus 로고
    • Predicting gene function from patterns of annotation
    • DOI 10.1101/gr.440803
    • Oliver D. King, Rebecca E. Foulger, Selian S. Dwight, James V. White, and Frederick P. Roth. Predicting gene function from patterns of annotation. Genome Research, 13: 896-904, 2003. (Pubitemid 36621749)
    • (2003) Genome Research , vol.13 , Issue.5 , pp. 896-904
    • King, O.D.1    Foulger, R.E.2    Dwight, S.S.3    White, J.V.4    Roth, F.P.5
  • 29
    • 0036259463 scopus 로고    scopus 로고
    • Aquaporin water channels: Atomic structure and molecular dynamics meet clinical medicine
    • DOI 10.1172/JCI200215851
    • David Kozono, Masato Yasui, Landon S. King, and Peter Agre. Aquaporin water channels: atomic structure molecular dynamics meet clinical medicine. J. Clin. Invest., 109(11): 1395-1399, 2002. (Pubitemid 34596163)
    • (2002) Journal of Clinical Investigation , vol.109 , Issue.11 , pp. 1395-1399
    • Kozono, D.1    Yasui, M.2    King, L.S.3    Agre, P.4
  • 30
    • 0036372266 scopus 로고    scopus 로고
    • Model-based cluster analysis of microarray gene expression data
    • W. Pan, J. Lin, and C. Le. Model-based cluster analysis of microarray gene expression data. Genome Biology, 3(2):research0009.1-0009.8, 2002.
    • (2002) Genome Biology , vol.3 , Issue.2
    • Pan, W.1    Lin, J.2    Le, C.3
  • 31
    • 0141958996 scopus 로고    scopus 로고
    • Microarrays-guilt by association
    • John Quackenbush. Microarrays-Guilt by Association. Science, 302(5643): 240-241, 2003.
    • (2003) Science , vol.302 , Issue.5643 , pp. 240-241
    • Quackenbush, J.1
  • 32
    • 0036144742 scopus 로고    scopus 로고
    • Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature
    • DOI 10.1101/gr.199701
    • Soumya Raychaudhuri, Jeffrey T. Chang, Patrick D. Sutphin, and Russ B. Altman. Associating genes with Gene Ontology codes using a maximum entropy analysis of biomedical literature. Genome Research, 12: 203-214, 2002. (Pubitemid 34065603)
    • (2002) Genome Research , vol.12 , Issue.1 , pp. 203-214
    • Raychaudhuri, S.1    Chang, J.T.2    Sutphin, P.D.3    Altman, R.B.4
  • 35
    • 0036228634 scopus 로고    scopus 로고
    • Predicting gene ontology functions from ProDom and CDD protein domains
    • DOI 10.1101/gr.222902
    • Jonathan Schug, Sharon Diskin, Joan Mazzarelli, Brian P. Brunk, and Christian J. Stoeckert Jr. Predicting Gene Ontology functions from PromDom and CDD protein domains. Genome Research, 12: 648-655, 2002. (Pubitemid 34308644)
    • (2002) Genome Research , vol.12 , Issue.4 , pp. 648-655
    • Schug, J.1    Diskin, S.2    Mazzarelli, J.3    Brunk, B.P.4    Stoeckert Jr., C.J.5
  • 36
    • 0033964710 scopus 로고    scopus 로고
    • From genes to protein structure and function: Novel applications of computational approaches in the genomic era
    • Jeffrey Skolnick and Jacquelyn S. Fetrow. From genes to protein structure and function: Novel applications of computational approaches in the genomic era. Trends in Biotechnology, 18: 283-287, 2000.
    • (2000) Trends in Biotechnology , vol.18 , pp. 283-287
    • Skolnick, J.1    Fetrow, J.S.2
  • 37
    • 0033452362 scopus 로고    scopus 로고
    • Prediction of gene function by genome-scale expression analysis: Prostate cancer-associated genes
    • DOI 10.1101/gr.9.12.1198
    • Michael G. Walker, Wayne Volkmuth, Einat Sprinzak, David Hodgson, and Tod Klingler. Prediction of Gene Function by Genome-Scale Expression Analysis: Prostate Cancer-Associated Genes. Genome Research, 9(12): 1198-1203, 1999. (Pubitemid 30042503)
    • (1999) Genome Research , vol.9 , Issue.12 , pp. 1198-1203
    • Walker, M.G.1    Volkmuth, W.2    Sprinzak, E.3    Hodgson, D.4    Klingler, T.5
  • 39
    • 0036649020 scopus 로고    scopus 로고
    • Large-scale prediction of saccharomyces cerevisiae gene function using overlapping transcriptional clusters
    • July
    • LF Wu, TR Hughes, AP Davierwala, MD Robinson, R Stoughton, and SJ. Altschuler. Large-scale prediction of saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nature Genetics, 31(3): 255-265, July 2002.
    • (2002) Nature Genetics , vol.31 , Issue.3 , pp. 255-265
    • Wu, L.F.1    Hughes, T.R.2    Davierwala, A.P.3    Robinson, M.D.4    Stoughton, R.5    Altschuler, S.J.6
  • 41
    • 2942550697 scopus 로고    scopus 로고
    • GOTree machine (gotm): A web-based platform for interpreting sets of interesting genes using gene ontology hierarchies
    • February
    • B Zhang, D Schmoyer, S Kirvo, and J. Snoddy. GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics., 5(16), February 2004.
    • (2004) BMC Bioinformatics , vol.5 , Issue.16
    • Zhang, B.1    Schmoyer, D.2    Kirvo, S.3    Snoddy, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.