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Volumn 9, Issue , 2008, Pages

Extending pathways based on gene lists using InterPro domain signatures

Author keywords

[No Author keywords available]

Indexed keywords

CANDIDATE GENES; FUNCTIONAL GENES; GENE EXPRESSION ANALYSIS; HIGH-THROUGHPUT SCREENING; HIGH-THROUGHPUT TECHNOLOGIES; SENSITIVE METHOD; SIMULATION STUDIES; WELL-ESTABLISHED TECHNIQUES;

EID: 39449130447     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-3     Document Type: Article
Times cited : (12)

References (24)
  • 1
    • 33747890811 scopus 로고    scopus 로고
    • Interpreting experimental results using gene ontologies
    • 10.1016/S0076-6879(06)11018-6 16939799
    • Beissbarth T Interpreting experimental results using gene ontologies Methods Enzymol 2006, 411:340-352. 10.1016/S0076-6879(06)11018-6 16939799
    • (2006) Methods Enzymol , vol.411 , pp. 340-352
    • Beissbarth, T.1
  • 2
    • 3142665525 scopus 로고    scopus 로고
    • GOstat: Find statistically overrepresented Gene Ontologies within a group of genes
    • 10.1093/bioinformatics/bth088 14962934
    • Beissbarth T Speed TP GOstat: Find statistically overrepresented Gene Ontologies within a group of genes Bioinformatics 2004, 20(9):1464-1465. 10.1093/bioinformatics/bth088 14962934
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1464-1465
    • Beissbarth, T.1    Speed, T.P.2
  • 3
    • 33745626459 scopus 로고    scopus 로고
    • Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
    • 10.1093/bioinformatics/btl140 16606683
    • Alexa A Rahnenfuehrer J Lengauer T Improved scoring of functional groups from gene expression data by decorrelating GO graph structure Bioinformatics 2006, 22(13):1600-1607. 10.1093/bioinformatics/btl140 16606683
    • (2006) Bioinformatics , vol.22 , Issue.13 , pp. 1600-1607
    • Alexa, A.1    Rahnenfuehrer, J.2    Lengauer, T.3
  • 4
    • 33749999763 scopus 로고    scopus 로고
    • Group testing for pathway analysis improves comparability of different microarray datasets
    • 10.1093/bioinformatics/btl424 16895928
    • Manoli T Gretz N Groene HJ Kenzelmann M Eils R Brors B Group testing for pathway analysis improves comparability of different microarray datasets Bioinformatics 2006, 22(20):2500-2506. 10.1093/bioinformatics/btl424 16895928
    • (2006) Bioinformatics , vol.22 , Issue.20 , pp. 2500-2506
    • Manoli, T.1    Gretz, N.2    Groene, H.J.3    Kenzelmann, M.4    Eils, R.5    Brors, B.6
  • 5
    • 34547561588 scopus 로고    scopus 로고
    • FatiGO +: A functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments
    • Web Server issue 1933151 17478504 10.1093/nar/gkm260
    • Al-Shahrour F Minguez P Tárraga J Medina I Alloza E Montaner D Dopazo J FatiGO +: A functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments Nucleic Acids Res 2007, 35 Web Server issue:W91-W96. 1933151 17478504 10.1093/nar/gkm260
    • (2007) Nucleic Acids Res , vol.35
    • Al-Shahrour, F.1    Minguez, P.2    Tárraga, J.3    Medina, I.4    Alloza, E.5    Montaner, D.6    Dopazo, J.7
  • 6
    • 34250764323 scopus 로고    scopus 로고
    • GOSim - An R-package for computation of information theoretic GO similarities between terms and gene products
    • 1892785 17519018 10.1186/1471-2105-8-166
    • Froehlich H Speer N Poustka A Beissbarth T GOSim - An R-package for computation of information theoretic GO similarities between terms and gene products BMC Bioinformatics 2007, 8:166. 1892785 17519018 10.1186/ 1471-2105-8-166
    • (2007) BMC Bioinformatics , vol.8 , pp. 166
    • Froehlich, H.1    Speer, N.2    Poustka, A.3    Beissbarth, T.4
  • 7
    • 38849147181 scopus 로고    scopus 로고
    • Large scale statistical inference of signaling pathways from RNAi and microarray data
    • 10.1186/1471-2105-8-386 17937790
    • Froehlich H Fellmann M Sueltmann H Poustka A Beissbarth T Large scale statistical inference of signaling pathways from RNAi and microarray data BMC Bioinformatics 2007, 8:386. 10.1186/1471-2105-8-386 17937790
    • (2007) BMC Bioinformatics , vol.8 , pp. 386
    • Froehlich, H.1    Fellmann, M.2    Sueltmann, H.3    Poustka, A.4    Beissbarth, T.5
  • 8
    • 36048997864 scopus 로고    scopus 로고
    • Discrimination of direct and indirect interactions in a network of regulatory effects
    • 10.1089/cmb.2007.0085 17990974
    • Tresch A Beissbarth T Sueltmann H Kuner R Poustka A Buness A Discrimination of direct and indirect interactions in a network of regulatory effects J Comput Biol 2007, 14(9):1217-1228. 10.1089/ cmb.2007.0085 17990974
    • (2007) J Comput Biol , vol.14 , Issue.9 , pp. 1217-1228
    • Tresch, A.1    Beissbarth, T.2    Sueltmann, H.3    Kuner, R.4    Poustka, A.5    Buness, A.6
  • 9
    • 0345863935 scopus 로고    scopus 로고
    • The KEGG resource for deciphering the genome
    • Database 308797 14681412 10.1093/nar/gkh063
    • Kanehisa M Goto S Kawashima S Okuno Y Hattori M The KEGG resource for deciphering the genome Nucleic Acids Res 2004, 32 Database:D277-D280. 308797 14681412 10.1093/nar/gkh063
    • (2004) Nucleic Acids Res
    • Kanehisa, M.1    Goto, S.2    Kawashima, S.3    Okuno, Y.4    Hattori, M.5
  • 10
    • 3042818018 scopus 로고    scopus 로고
    • The International Protein Index: An integrated database for proteomics experiments
    • 10.1002/pmic.200300721 15221759
    • Kersey PJ Duarte J Williams A Karavidopoulou Y Birney E Apweiler R The International Protein Index: An integrated database for proteomics experiments Proteomics 2004, 4(7):1985-1988. 10.1002/pmic.200300721 15221759
    • (2004) Proteomics , vol.4 , Issue.7 , pp. 1985-1988
    • Kersey, P.J.1    Duarte, J.2    Williams, A.3    Karavidopoulou, Y.4    Birney, E.5    Apweiler, R.6
  • 11
    • 33846056843 scopus 로고    scopus 로고
    • Entrez Gene: Gene-centered information at NCBI
    • Database 1761442 17148475 10.1093/nar/gkl993
    • Maglott D Ostell J Pruitt KD Tatusova T Entrez Gene: Gene-centered information at NCBI Nucleic Acids Res 2007, 35 Database:D26-D31. 1761442 17148475 10.1093/nar/gkl993
    • (2007) Nucleic Acids Res
    • Maglott, D.1    Ostell, J.2    Pruitt, K.D.3    Tatusova, T.4
  • 12
    • 33846796225 scopus 로고    scopus 로고
    • Ontology annotation: Mapping genomic regions to biological function
    • 10.1016/j.cbpa.2006.11.039 17208035
    • Thomas PD Mi H Lewis S Ontology annotation: Mapping genomic regions to biological function Curr Opin Chem Biol 2007, 11:4-11. 10.1016/ j.cbpa.2006.11.039 17208035
    • (2007) Curr Opin Chem Biol , vol.11 , pp. 4-11
    • Thomas, P.D.1    Mi, H.2    Lewis, S.3
  • 14
    • 2942602905 scopus 로고    scopus 로고
    • Pathway databases
    • 10.1196/annals.1310.009 15208185
    • Schaefer CF Pathway databases Ann N Y Acad Sci 2004, 1020:77-91. 10.1196/ annals.1310.009 15208185
    • (2004) Ann N Y Acad Sci , vol.1020 , pp. 77-91
    • Schaefer, C.F.1
  • 15
    • 15744403559 scopus 로고    scopus 로고
    • Structural insights into biological roles of protein-glycosaminoglycan interactions
    • 10.1016/j.chembiol.2004.11.020 15797210
    • Raman R Sasisekharan V Sasisekharan R Structural insights into biological roles of protein-glycosaminoglycan interactions Chem Biol 2005, 12(3):267-277. 10.1016/j.chembiol.2004.11.020 15797210
    • (2005) Chem Biol , vol.12 , Issue.3 , pp. 267-277
    • Raman, R.1    Sasisekharan, V.2    Sasisekharan, R.3
  • 16
    • 1342343091 scopus 로고    scopus 로고
    • Involvement of stromal proteoglycans in tumour progression
    • 10.1016/j.critrevonc.2003.10.005 15036265
    • Wegrowski Y Maquart FX Involvement of stromal proteoglycans in tumour progression Crit Rev Oncol Hematol 2004, 49(3):259-268. 10.1016/ j.critrevonc.2003.10.005 15036265
    • (2004) Crit Rev Oncol Hematol , vol.49 , Issue.3 , pp. 259-268
    • Wegrowski, Y.1    Maquart, F.X.2
  • 17
    • 0037113167 scopus 로고    scopus 로고
    • Cytoplasmic interactions of syndecan-4 orchestrate adhesion receptor and growth factor receptor signalling
    • 1222989 12241528 10.1042/BJ20021228
    • Bass MD Humphries MJ Cytoplasmic interactions of syndecan-4 orchestrate adhesion receptor and growth factor receptor signalling Biochem J 2002, 368(Pt 1):1-15. 1222989 12241528 10.1042/BJ20021228
    • (2002) Biochem J , vol.368 , Issue.PART 1 , pp. 1-15
    • Bass, M.D.1    Humphries, M.J.2
  • 18
    • 0035988837 scopus 로고    scopus 로고
    • Proteoglycans and tumor progression: Janus-faced molecules with contradictory functions in cancer
    • 10.1016/S1044-579X(02)00021-4 12083848
    • Timar J Lapis K Dudis J Sebestyen A Kopper L Kovalszky I Proteoglycans and tumor progression: Janus-faced molecules with contradictory functions in cancer Semin Cancer Biol 2002, 12(3):173-186. 10.1016/ S1044-579X(02)00021-4 12083848
    • (2002) Semin Cancer Biol , vol.12 , Issue.3 , pp. 173-186
    • Timar, J.1    Lapis, K.2    Dudis, J.3    Sebestyen, A.4    Kopper, L.5    Kovalszky, I.6
  • 19
    • 84870816675 scopus 로고    scopus 로고
    • Bioconductor http://www.bioconductor.org
    • Bioconductor
  • 22
    • 84871717384 scopus 로고    scopus 로고
    • Entrez Gene http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
    • Entrez Gene
  • 23
    • 24044522270 scopus 로고    scopus 로고
    • BioMart and Bioconductor: A powerful link between biological databases and microarray data analysis
    • 10.1093/bioinformatics/bti525 16082012
    • Durinck S Moreau Y Kasprzyk A Davis S Moor BD Brazma A Huber W BioMart and Bioconductor: A powerful link between biological databases and microarray data analysis Bioinformatics 2005, 21(16):3439-3440. 10.1093/ bioinformatics/bti525 16082012
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3439-3440
    • Durinck, S.1    Moreau, Y.2    Kasprzyk, A.3    Davis, S.4    Moor, B.D.5    Brazma, A.6    Huber, W.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.