메뉴 건너뛰기




Volumn 7, Issue , 2006, Pages

Combining evidence, biomedical literature and statistical dependence: New insights for functional annotation of gene sets

Author keywords

[No Author keywords available]

Indexed keywords

BIOMEDICAL LITERATURE; CELLULAR COMPONENTS; FUNCTIONAL ANNOTATION; GENE ONTOLOGY ANNOTATIONS; MOLECULAR FUNCTION; SCIENTIFIC LITERATURE; SEMI-AUTOMATIC ANNOTATION; STATISTICAL DEPENDENCE;

EID: 33745634665     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-241     Document Type: Article
Times cited : (11)

References (58)
  • 1
    • 0037880376 scopus 로고    scopus 로고
    • Ontologies: Formalising biological knowledge for bioinformatics
    • Bard J: Ontologies: Formalising biological knowledge for bioinformatics. Bioessays 2003, 25(5):501-506.
    • (2003) Bioessays , vol.25 , Issue.5 , pp. 501-506
    • Bard, J.1
  • 2
    • 84886760793 scopus 로고    scopus 로고
    • Toward principles for the design of ontologies used for knowledge sharing
    • Toward principles for the design of ontologies used for knowledge sharing [http://ksl-web.stanford.edu/KSL Abstracts/KSL-93-04.html]
  • 3
    • 84874665426 scopus 로고    scopus 로고
    • The Gene Ontology Consortium
    • The Gene Ontology Consortium [http://www.geneontology.org]
  • 4
    • 1542290452 scopus 로고    scopus 로고
    • Ontologies in biology: Design, applications and future challenges
    • Bard JB, Rhee SY: Ontologies in biology: design, applications and future challenges. Nat Rev Genet 2004, 5(3):213-222.
    • (2004) Nat Rev Genet , vol.5 , Issue.3 , pp. 213-222
    • Bard, J.B.1    Rhee, S.Y.2
  • 5
    • 84874648682 scopus 로고    scopus 로고
    • AmiGO browser
    • AmiGO browser [http://www.godatabase.org/cgi-bin/amigo/go.cgi]
  • 6
    • 84874666076 scopus 로고    scopus 로고
    • GenNav browser
    • GenNav browser [http://mor.nlm.nih.gov/perl/gennav.pl]
  • 7
    • 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: FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes Bioinformatics 2004, 20(4):578-580.
    • (2004) Bioinformatics , vol.20 , Issue.4 , pp. 578-580
    • Al-Shahrour, F.1    Diaz-Uriarte, R.2    Dopazo, J.3
  • 9
    • 0037263812 scopus 로고    scopus 로고
    • MAPPFinder: Using Gene Ontology and Gen-MAPP to create a global gene-expression profile from microarray data
    • Doniger SW, Salomonis N, Dahlquist KD, Vranizan K, Lawlor SC, Conklin BR: MAPPFinder: using Gene Ontology and Gen-MAPP to create a global gene-expression profile from microarray data. Genome Biol 2003, 4(1):R7.
    • (2003) Genome Biol , vol.4 , Issue.1
    • Doniger, S.W.1    Salomonis, N.2    Dahlquist, K.D.3    Vranizan, K.4    Lawlor, S.C.5    Conklin, B.R.6
  • 10
    • 2942550697 scopus 로고    scopus 로고
    • GOTree Machine (GOTM): A web-based platform for interpreting sets of interesting genes using Gene On-tology hierarchies
    • Zhang B, Schmoyer D, Kirov S, Snoddy J: GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene On-tology hierarchies. BMC Bioinformatics 2004, 5(1):16.
    • (2004) BMC Bioinformatics , vol.5 , Issue.1 , pp. 16
    • Zhang, B.1    Schmoyer, D.2    Kirov, S.3    Snoddy, J.4
  • 12
    • 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, Jacq B: GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol 2004, 5(12):R101.
    • (2004) Genome Biol , vol.5 , Issue.12
    • Martin, D.1    Brun, C.2    Remy, E.3    Mouren, P.4    Thieffry, D.5    Jacq, B.6
  • 13
    • 24644470505 scopus 로고    scopus 로고
    • Ontological analysis of gene expression data: Current tools, limitations, and open problems
    • Khatri P, Draghici S: Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 2005, 21(18):3587-3595.
    • (2005) Bioinformatics , vol.21 , Issue.18 , pp. 3587-3595
    • Khatri, P.1    Draghici, S.2
  • 14
    • 0036144742 scopus 로고    scopus 로고
    • Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature
    • Raychaudhuri S, Chang JT, Sutphin PD, Altman RB: Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res 2002, 12(1):203-214.
    • (2002) Genome Res , vol.12 , Issue.1 , pp. 203-214
    • Raychaudhuri, S.1    Chang, J.T.2    Sutphin, P.D.3    Altman, R.B.4
  • 15
    • 0038017587 scopus 로고    scopus 로고
    • Mining microarray expression data by literature profiling
    • Research0055
    • Chaussabel D, Sher A: Mining microarray expression data by literature profiling. Genome Biol 2002, 3(10):. RESEARCH0055
    • (2002) Genome Biol , vol.3 , Issue.10
    • Chaussabel, D.1    Sher, A.2
  • 17
    • 22244459539 scopus 로고    scopus 로고
    • Text-mining and information-retrieval services for molecular biology
    • Krallinger M, Valencia A: Text-mining and information-retrieval services for molecular biology. Genome Biol 2005, 6(7):224.
    • (2005) Genome Biol , vol.6 , Issue.7 , pp. 224
    • Krallinger, M.1    Valencia, A.2
  • 19
    • 0032795144 scopus 로고    scopus 로고
    • Med-Miner: An Internet text-mining tool for biomedical information, with application to gene expression profiling
    • 1210-1214
    • Tanabe L, Scherf U, Smith LH, Lee JK, Hunter L, Weinstein JN: Med-Miner: an Internet text-mining tool for biomedical information, with application to gene expression profiling. Biotechniques 1999, 27(6):1210-1214. 1216-1217
    • (1999) Biotechniques , vol.27 , Issue.6 , pp. 1216-1217
    • Tanabe, L.1    Scherf, U.2    Smith, L.H.3    Lee, J.K.4    Hunter, L.5    Weinstein, J.N.6
  • 20
    • 0035042776 scopus 로고    scopus 로고
    • A literature network of human genes for high-throughput analysis of gene expression
    • Jenssen TK, Laegreid A, Komorowski J, Hovig E: A literature network of human genes for high-throughput analysis of gene expression. Nat Ge-net 2001, 28(1):21-28.
    • (2001) Nat Ge-net , vol.28 , Issue.1 , pp. 21-28
    • Jenssen, T.K.1    Laegreid, A.2    Komorowski, J.3    Hovig, E.4
  • 21
    • 4544263564 scopus 로고    scopus 로고
    • Gene annotation from scientific literature using mappings between keyword systems
    • Perez AJ, Perez-Iratxeta C, Bork P, Thode G, Andrade MA: Gene annotation from scientific literature using mappings between keyword systems. Bioinformatics 2004, 20(13):2084-2091.
    • (2004) Bioinformatics , vol.20 , Issue.13 , pp. 2084-2091
    • Perez, A.J.1    Perez-Iratxeta, C.2    Bork, P.3    Thode, G.4    Andrade, M.A.5
  • 22
    • 84874662467 scopus 로고    scopus 로고
    • Gene Ontology Annotation database
    • Gene Ontology Annotation database [http://www.ebi.ac.uk/GOA/]
  • 23
    • 84874665080 scopus 로고    scopus 로고
    • PubGene database and tools
    • PubGene database and tools [http://www.pubgene.org/]
  • 24
    • 15944407681 scopus 로고    scopus 로고
    • Non-lexical approaches to identifying associative relations in the Gene Ontology
    • Bodenreider O, Aubry M, Burgun A: Non-lexical approaches to identifying associative relations in the Gene Ontology. Pac Symp Biocomput 2005:91-102.
    • (2005) Pac Symp Biocomput , pp. 91-102
    • Bodenreider, O.1    Aubry, M.2    Burgun, A.3
  • 26
    • 84874663696 scopus 로고    scopus 로고
    • GO Evidence Codes
    • GO Evidence Codes [http://geneontology.org/GO.evidence.html]
  • 27
    • 2442506744 scopus 로고    scopus 로고
    • Iron deficiency in the pregnant rat has differential effects on maternal and fetal copper levels
    • Gambling L, Dunford S, McArdle HJ: Iron deficiency in the pregnant rat has differential effects on maternal and fetal copper levels. J Nutr Biochem 2004, 15(6):366-372.
    • (2004) J Nutr Biochem , vol.15 , Issue.6 , pp. 366-372
    • Gambling, L.1    Dunford, S.2    McArdle, H.J.3
  • 28
    • 0031941654 scopus 로고    scopus 로고
    • Sum I, a highly conserved WD-repeat protein, suppresses S-M checkpoint mutants and inhibits the osmotic stress cell cycle response in fission yeast
    • Humphrey T, Enoch T: Sum I, a highly conserved WD-repeat protein, suppresses S-M checkpoint mutants and inhibits the osmotic stress cell cycle response in fission yeast. Genetics 1998, 148(4):1731-1742.
    • (1998) Genetics , vol.148 , Issue.4 , pp. 1731-1742
    • Humphrey, T.1    Enoch, T.2
  • 29
    • 0029956388 scopus 로고    scopus 로고
    • Sequences within the 5′ untranslated region regulate the levels of a kinetoplast DNA topoisome-rase mRNA during the cell cycle
    • Pasion SG, Hines JC, Ou X, Mahmood R, Ray DS: Sequences within the 5′untranslated region regulate the levels of a kinetoplast DNA topoisome-rase mRNA during the cell cycle. Mol Cell Biol 1996, 16(12):6724-6735.
    • (1996) Mol Cell Biol , vol.16 , Issue.12 , pp. 6724-6735
    • Pasion, S.G.1    Hines, J.C.2    Ou, X.3    Mahmood, R.4    Ray, D.S.5
  • 30
    • 84874661105 scopus 로고    scopus 로고
    • Mappings of External Classification Systems to GO
    • Mappings of External Classification Systems to GO [http://www.geneontology.org/GO.indices.shtml]
  • 33
    • 0036796319 scopus 로고    scopus 로고
    • Using text analysis to identify functionally coherent gene groups
    • Raychaudhuri S, Schutze H, Altman RB: Using text analysis to identify functionally coherent gene groups. Genome Res 2002, 12(10):1582-1590.
    • (2002) Genome Res , vol.12 , Issue.10 , pp. 1582-1590
    • Raychaudhuri, S.1    Schutze, H.2    Altman, R.B.3
  • 35
    • 0034725698 scopus 로고    scopus 로고
    • Association of the cyclin-dependent kinases and 14-3-3 sigma negatively regulates cell cycle progression
    • Laronga C, Yang HY, Neal C, Lee MH: Association of the cyclin-dependent kinases and 14-3-3 sigma negatively regulates cell cycle progression. J Biol Chem 2000, 275(30):23106-23112.
    • (2000) J Biol Chem , vol.275 , Issue.30 , pp. 23106-23112
    • Laronga, C.1    Yang, H.Y.2    Neal, C.3    Lee, M.H.4
  • 36
    • 0029018303 scopus 로고
    • Disruption of the architectural factor HMGI-C: DNA-binding AT hook motifs fused in lipomas to distinct transcriptional regulatory domains
    • Ashar HR, Fejzo MS, Tkachenko A, Zhou X, Fletcher JA, Weremowicz S, Morton CC, Chada K: Disruption of the architectural factor HMGI-C: DNA-binding AT hook motifs fused in lipomas to distinct transcriptional regulatory domains. Cell 1995, 82(1):57-65.
    • (1995) Cell , vol.82 , Issue.1 , pp. 57-65
    • Ashar, H.R.1    Fejzo, M.S.2    Tkachenko, A.3    Zhou, X.4    Fletcher, J.A.5    Weremowicz, S.6    Morton, C.C.7    Chada, K.8
  • 38
    • 0024330628 scopus 로고
    • Polyamine metabolism and cell-cycle-dependent gene expression in IMR-90 human diploid fibro-blasts during senescence in culture
    • Chen KY, Chang ZF, Pang JH, He GS, Liu AY: Polyamine metabolism and cell-cycle-dependent gene expression in IMR-90 human diploid fibro-blasts during senescence in culture. Exp Gerontol 1989, 24(5-6):523-537.
    • (1989) Exp Gerontol , vol.24 , Issue.5-6 , pp. 523-537
    • Chen, K.Y.1    Chang, Z.F.2    Pang, J.H.3    He, G.S.4    Liu, A.Y.5
  • 39
    • 3142533071 scopus 로고    scopus 로고
    • Changes in gene expression associated with acclimation to constant temperatures and fluctuating daily temperatures in an annual killifish Austrofundulus limnaeus
    • Podrabsky JE, Somero GN: Changes in gene expression associated with acclimation to constant temperatures and fluctuating daily temperatures in an annual killifish Austrofundulus limnaeus. J Exp Biol 2004, 207(Pt 13):2237-2254.
    • (2004) J Exp Biol , vol.207 , Issue.PART 13 , pp. 2237-2254
    • Podrabsky, J.E.1    Somero, G.N.2
  • 40
    • 0344896553 scopus 로고    scopus 로고
    • Linking the growth inhibition response from the National Cancer Institute's anti-cancer screen to gene expression levels and other molecular target data
    • Wallqvist A, Rabow AA, Shoemaker RH, Sausville EA, Covell DG: Linking the growth inhibition response from the National Cancer Institute's anti-cancer screen to gene expression levels and other molecular target data. Bioinformatics 2003, 19(17):2212-2224.
    • (2003) Bioinformatics , vol.19 , Issue.17 , pp. 2212-2224
    • Wallqvist, A.1    Rabow, A.A.2    Shoemaker, R.H.3    Sausville, E.A.4    Covell, D.G.5
  • 41
    • 0032005459 scopus 로고    scopus 로고
    • Carbenoxolone does not cause a syndrome of mineralocorticoid excess in sheep
    • Dodic M, May CN, Coghlan JP: Carbenoxolone does not cause a syndrome of mineralocorticoid excess in sheep. Steroids 1998, 63(2):99-104.
    • (1998) Steroids , vol.63 , Issue.2 , pp. 99-104
    • Dodic, M.1    May, C.N.2    Coghlan, J.P.3
  • 43
    • 0034697126 scopus 로고    scopus 로고
    • Cyclooxygena-se-2 expression inhibits trophic withdrawal apoptosis in nerve growth factor-differentiated PC12 cells
    • McGinty & Chang YW, Sorokin A, Bokemeyer D, Dunn MJ: Cyclooxygena-se-2 expression inhibits trophic withdrawal apoptosis in nerve growth factor-differentiated PC12 cells. J Biol Chem 2000, 275(16):12095-12101.
    • (2000) J Biol Chem , vol.275 , Issue.16 , pp. 12095-12101
    • McGinty, A.1    Chang, Y.W.2    Sorokin, A.3    Bokemeyer, D.4    Dunn, M.J.5
  • 44
    • 84874651614 scopus 로고    scopus 로고
    • HUGO Gene Nomenclature Committee
    • HUGO Gene Nomenclature Committee [http://www.gene.ucl.ac.uk/ nomenclature/]
  • 45
    • 84874664166 scopus 로고    scopus 로고
    • GO Slims
    • GO Slims [http://www.geneontology.org/GO.slims.shtml]
  • 47
    • 0020841653 scopus 로고
    • Activity of the maturation-promoting factor and the extent of protein phosphorylation oscillate simulta-neously during meiotic maturation of starfish oocytes
    • Doree M, Peaucellier G, Picard A: Activity of the maturation-promoting factor and the extent of protein phosphorylation oscillate simulta-neously during meiotic maturation of starfish oocytes. Dev Biol 1983, 99(2):489-501.
    • (1983) Dev Biol , vol.99 , Issue.2 , pp. 489-501
    • Doree, M.1    Peaucellier, G.2    Picard, A.3
  • 48
    • 1542506097 scopus 로고    scopus 로고
    • Estimating equations for association structures
    • discussion 875-857, 879-880
    • Yan J, Fine J: Estimating equations for association structures. Stat Med 2004, 23(6):859-874. discussion 875-857,879-880
    • (2004) Stat Med , vol.23 , Issue.6 , pp. 859-874
    • Yan, J.1    Fine, J.2
  • 49
    • 23144448699 scopus 로고    scopus 로고
    • GoPubMed: Exploring PubMed with the Gene On-tology
    • Doms A, Schroeder M: GoPubMed: exploring PubMed with the Gene On-tology. Nucliec Acids Res 2005:W783-786.
    • (2005) Nucleic Acids Res
    • Doms, A.1    Schroeder, M.2
  • 51
    • 0032212447 scopus 로고    scopus 로고
    • Clinical significance of Philadelphia chromosome positive pediatric acute lymphoblastic leukemia in the context of contemporary intensive therapies: A report from the Children's Cancer Group
    • Uckun FM, Nachman JB, Sather HN, Sensel MG, Kraft P, Steinherz PG, Lange B, Hutchinson R, Reaman GH, Gaynon PS, Heerema NA: Clinical significance of Philadelphia chromosome positive pediatric acute lymphoblastic leukemia in the context of contemporary intensive therapies: a report from the Children's Cancer Group. Cancer 1998, 83(9):2030-2039.
    • (1998) Cancer , vol.83 , Issue.9 , pp. 2030-2039
    • Uckun, F.M.1    Nachman, J.B.2    Sather, H.N.3    Sensel, M.G.4    Kraft, P.5    Steinherz, P.G.6    Lange, B.7    Hutchinson, R.8    Reaman, G.H.9    Gaynon, P.S.10    Heerema, N.A.11
  • 52
    • 0032556921 scopus 로고    scopus 로고
    • BCR-ABL activates pathways mediating cytokine independence and protection against apoptosis in murine hematopoietic cells in a dose-dependent manner
    • Cambier N, Chopra R, Strasser A, Metcalf D, Elefanty AG: BCR-ABL activates pathways mediating cytokine independence and protection against apoptosis in murine hematopoietic cells in a dose-dependent manner. Oncogene 1998, 16(3):335-348.
    • (1998) Oncogene , vol.16 , Issue.3 , pp. 335-348
    • Cambier, N.1    Chopra, R.2    Strasser, A.3    Metcalf, D.4    Elefanty, A.G.5
  • 53
    • 0037111665 scopus 로고    scopus 로고
    • BCR/ABL induces expression of vascular endothelial growth factor and its transcriptional activator, hypoxia inducible factor-1-alpha, through a pathway involving phosphoinositide 3-kinase and the mammalian target of rapamycin
    • Mayerhofer M, Valent P, Sperr WP, Griffin JD, Sillaber C: BCR/ABL induces expression of vascular endothelial growth factor and its transcriptional activator, hypoxia inducible factor-1-alpha, through a pathway involving phosphoinositide 3-kinase and the mammalian target of rapamycin. Blood 2002, 100(10):3767-3775.
    • (2002) Blood , vol.100 , Issue.10 , pp. 3767-3775
    • Mayerhofer, M.1    Valent, P.2    Sperr, W.P.3    Griffin, J.D.4    Sillaber, C.5
  • 56
    • 30044432338 scopus 로고    scopus 로고
    • Gene expression profile of cultured adult compared to immortalized human RPE
    • Cai H, Del Priore LV: Gene expression profile of cultured adult compared to immortalized human RPE. Mol Vis 2006, 12:1-14.
    • (2006) Mol Vis , vol.12 , pp. 1-14
    • Cai, H.1    Del Priore, L.V.2
  • 57
    • 1242341923 scopus 로고    scopus 로고
    • Incipient Alzheimer's disease: Microarray correlation analyses reveal major transcriptional and tumor suppressor responses
    • Blalock EM, Geddes JW, Chen KC, Porter NM, Markesbery WR, Landfield PW: Incipient Alzheimer's disease: microarray correlation analyses reveal major transcriptional and tumor suppressor responses. Proc Natl Acad Sci U S A 2004, 101(7):2173-2178.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , Issue.7 , pp. 2173-2178
    • Blalock, E.M.1    Geddes, J.W.2    Chen, K.C.3    Porter, N.M.4    Markesbery, W.R.5    Landfield, P.W.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.