메뉴 건너뛰기




Volumn 7, Issue , 2006, Pages

GO-Diff: Mining functional differentiation between EST-based transcriptomes

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PHENOMENA; DIFFERENTIAL GENE EXPRESSIONS; DIFFERENTIALLY EXPRESSED GENE; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION ANALYSIS; LEVELS OF CONSISTENCY; MICROARRAY ANALYSIS; STATISTICAL SIGNIFICANCE;

EID: 33644779837     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-72     Document Type: Article
Times cited : (16)

References (58)
  • 2
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270:467-470.
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 4
    • 13244284551 scopus 로고    scopus 로고
    • Dynamic complex formation during the yeast cell cycle
    • de Lichtenberg U, Jensen LJ, Brunak S, Bork P: Dynamic complex formation during the yeast cell cycle. Science 2005, 307:724-727.
    • (2005) Science , vol.307 , pp. 724-727
    • de Lichtenberg, U.1    Jensen, L.J.2    Brunak, S.3    Bork, P.4
  • 5
    • 0344872506 scopus 로고    scopus 로고
    • Molecular classification of cancer types from microarray data using the combination of genetic algorithms and support vector machines
    • Peng S, Xu Q, Ling XB, Peng X, Du W, Chen L: Molecular classification of cancer types from microarray data using the combination of genetic algorithms and support vector machines. FEBS Lett 2003, 555:358-362.
    • (2003) FEBS Lett , vol.555 , pp. 358-362
    • Peng, S.1    Xu, Q.2    Ling, X.B.3    Peng, X.4    Du, W.5    Chen, L.6
  • 6
  • 7
    • 84874651168 scopus 로고    scopus 로고
    • Gene Ontology Home Page
    • Gene Ontology Home Page [http://www.geneontology.org]
  • 10
    • 0034756358 scopus 로고    scopus 로고
    • DIAN: A novel algorithm for genome ontological classification
    • Pouliot Y, Gao J, Su QJ, Liu GG, Ling XB. DIAN: a novel algorithm for genome ontological classification. Genome Res 2001, 11:1766-1779.
    • (2001) Genome Res , vol.11 , pp. 1766-1779
    • Pouliot, Y.1    Gao, J.2    Su, Q.J.3    Liu, G.G.4    Ling, X.B.5
  • 11
    • 13244268370 scopus 로고    scopus 로고
    • Gotcha: A new method for prediction of protein function assessed by the annotation of seven genomes
    • Martin DM, Berriman M, Barton GJ: Gotcha. a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics 2004, 5:178.
    • (2004) BMC Bioinformatics , vol.5 , pp. 178
    • Martin, D.M.1    Berriman, M.2    Barton, G.J.3
  • 12
    • 25444458848 scopus 로고    scopus 로고
    • AutoFACT: An automatic functional annotation and classification tool
    • Koski LB, Gray MW, Lang BF, Burger G: AutoFACT: an automatic functional annotation and classification tool. BMC Bioinformatics 2005, 6:151.
    • (2005) BMC Bioinformatics , vol.6 , pp. 151
    • Koski, L.B.1    Gray, M.W.2    Lang, B.F.3    Burger, G.4
  • 15
    • 0042121250 scopus 로고    scopus 로고
    • ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis
    • Zhong S, Li C, Wong WH: ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis. Nucleic Acids Res 2003, 31:3483-3486.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3483-3486
    • Zhong, S.1    Li, C.2    Wong, W.H.3
  • 19
    • 1542399989 scopus 로고    scopus 로고
    • FatiGO: A web tool for finding significant associations of Gene Ontology terms with groups of genes
    • A I-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, 20:578-580.
    • (2004) Bioinformatics , vol.20 , pp. 578-580
    • Al-Shahrour, F.1    Diaz-Uriarte, R.2    Dopazo, J.3
  • 20
    • 3142665525 scopus 로고    scopus 로고
    • GOstat: Find statistically overrepresented Gene Ontologies within a group of genes
    • Beissbarth T, Speed TP: GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 2004, 20:1464-1465.
    • (2004) Bioinformatics , vol.20 , pp. 1464-1465
    • Beissbarth, T.1    Speed, T.P.2
  • 22
    • 8844265260 scopus 로고    scopus 로고
    • GO-Mapper: Functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms
    • Smid M, Dorssers LC: GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms. Bioinformatics 2004, 20:2618-2625.
    • (2004) Bioinformatics , vol.20 , pp. 2618-2625
    • Smid, M.1    Dorssers, L.C.2
  • 24
    • 16344373908 scopus 로고    scopus 로고
    • Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expression
    • Ben-Shaul Y, Bergman H, Soreq H: Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expression. Bioinformatics 2005, 21:1129-1137.
    • (2005) Bioinformatics , vol.21 , pp. 1129-1137
    • Ben-Shaul, Y.1    Bergman, H.2    Soreq, H.3
  • 25
    • 0027249595 scopus 로고
    • dbEST - Database for "expressed sequence tags"
    • Boguski MS, Lowe TM, Tolstoshev CM: dbEST - database for "expressed sequence tags". Nat Genet 1993, 4:332-333.
    • (1993) Nat Genet , vol.4 , pp. 332-333
    • Boguski, M.S.1    Lowe, T.M.2    Tolstoshev, C.M.3
  • 26
    • 84874652438 scopus 로고    scopus 로고
    • Digital Differential Display
    • Digital Differential Display [http://www.ncbi.nlm.nih.guy/Uni Gene/ info_ddd.html]
  • 28
    • 84874665292 scopus 로고    scopus 로고
    • cDNA xProfiler
    • cDNA x Profiler [http://cgap.nci.nih.gov/Tissues/xProfiler]
  • 29
    • 84874663468 scopus 로고    scopus 로고
    • cDNA Digital Gene Expression Displayer
    • cDNA Digital Gene Expression Displayer [http://cgap.nci.nih.gov/Tissues/ GXS]
  • 30
    • 0037460993 scopus 로고    scopus 로고
    • DigiNorthern, digital expression analysis of query genes based on ESTs
    • Wang J, Liang P: DigiNorthern, digital expression analysis of query genes based on ESTs. Bioinformatics 2003, 19:653-654.
    • (2003) Bioinformatics , vol.19 , pp. 653-654
    • Wang, J.1    Liang, P.2
  • 32
    • 0034352940 scopus 로고    scopus 로고
    • POWER_SAGE: Comparing statistical tests for SAGE experiments
    • Man MZ, Wang X, Wang Y: POWER_SAGE: comparing statistical tests for SAGE experiments. Bioinformatics 2000, 16:953-959.
    • (2000) Bioinformatics , vol.16 , pp. 953-959
    • Man, M.Z.1    Wang, X.2    Wang, Y.3
  • 33
    • 84874655908 scopus 로고    scopus 로고
    • Gene Ontology OBO file
    • Gene Ontology OBO file [http://www.geneontology.org./ontology/ gene_ontology.obo]
  • 34
    • 84874655064 scopus 로고    scopus 로고
    • Gene-GO mapping and Gene-Unigene mappings [ftp://ftp.ncbi.nih.gov/gene/ DATA]
    • Gene-GO mapping and Gene-Unigene mappings [ftp://ftp.ncbi.nih.gov/gene/ DATA]
  • 35
    • 84874657872 scopus 로고    scopus 로고
    • GOA Uniprot-GO, Uniprot-Gene mappings [ftp://ftp.ebi.ac.uk/pub/databases /GO/goa]
    • GOA Uniprot-GO, Uniprot-Gene mappings [ftp:// ftp.ebi.ac.uk/pub/ databases/GO/goa]
  • 36
    • 84874665697 scopus 로고    scopus 로고
    • Unigene FTP site [ftp://ftp.ncbi.nih.gov/repository/UniGene/]
    • Unigene FTP site [ftp://ftp.ncbi.nih.gov/repository/UniGene/]
  • 37
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: A DNA sequence assembly program
    • Huang X, Madan A: CAP3: A DNA sequence assembly program. Genome 1999, 9:868-877.
    • (1999) Genome , vol.9 , pp. 868-877
    • Huang, X.1    Madan, A.2
  • 38
    • 84874665805 scopus 로고    scopus 로고
    • Phrap
    • Phrap [http://www.phrap.org/]
  • 39
    • 84874653593 scopus 로고    scopus 로고
    • TIGR Assembler
    • TIGR Assembler [http://www.tigr.org/software/assembler/]
  • 40
    • 84874667609 scopus 로고    scopus 로고
    • GoPipe
    • GoPipe [http://vvww.fishgenome.org./bioinfo/gopipe/index.php]
  • 41
    • 18644368893 scopus 로고    scopus 로고
    • GoPipe: Streamlined Gene Ontology Annotation for Batch Anonymous Sequences with Statistics
    • Chen Z, Xue C, Zhu SX, Zhou F, Ling XB, Liu G, Chen L: GoPipe: Streamlined Gene Ontology Annotation for Batch Anonymous Sequences with Statistics. Prog Biochem Blophys 2005, 32:187-191.
    • (2005) Prog Biochem Biophys , vol.32 , pp. 187-191
    • Chen, Z.1    Xue, C.2    Zhu, S.X.3    Zhou, F.4    Ling, X.B.5    Liu, G.6    Chen, L.7
  • 42
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc B 1995, 57:289-300.
    • (1995) J Roy Stat Soc B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 43
    • 0018344861 scopus 로고
    • Program of early development in the mammal: Changes in patterns and absolute rates of tubulin and total protein synthesis during oogenesis and early embryogenesis in the mouse
    • Schultz RM, Letourneau GE, Wassarman PM: Program of early development in the mammal: changes in patterns and absolute rates of tubulin and total protein synthesis during oogenesis and early embryogenesis in the mouse. Dev Biol 1979, 68:341-359.
    • (1979) Dev Biol , vol.68 , pp. 341-359
    • Schultz, R.M.1    Letourneau, G.E.2    Wassarman, P.M.3
  • 44
    • 0018631422 scopus 로고
    • Program of early development in the mammal: Changes in absolute rates of synthesis of ribosamal proteins during oogenesis and early embryogenesis in the mouse
    • LaMarca MJ, Wassarman PM: Program of early development in the mammal: changes in absolute rates of synthesis of ribosamal proteins during oogenesis and early embryogenesis in the mouse. Dev Biol 1979, 73:103-119.
    • (1979) Dev Biol , vol.73 , pp. 103-119
    • LaMarca, M.J.1    Wassarman, P.M.2
  • 45
    • 3342929529 scopus 로고    scopus 로고
    • Transcript profiling during preimplantation mouse development
    • Zeng F, Baldwin DA, Schultz RM: Transcript profiling during preimplantation mouse development. Dev Biol 2004, 272:483-496.
    • (2004) Dev Biol , vol.272 , pp. 483-496
    • Zeng, F.1    Baldwin, D.A.2    Schultz, R.M.3
  • 46
    • 0034965289 scopus 로고    scopus 로고
    • Meta-analysis of gene expression in mouse preimplantation embryo development
    • Stanton JL, Green DP: Meta-analysis of gene expression in mouse preimplantation embryo development. Mol Hum Reprod 2001, 7:545-552.
    • (2001) Mol Hum Reprod , vol.7 , pp. 545-552
    • Stanton, J.L.1    Green, D.P.2
  • 47
    • 0347763875 scopus 로고    scopus 로고
    • Dynamics of global gene expression changes during mouse preimplantation development
    • Hamatani T, Carter MG, Sharov AA, Ko MS: Dynamics of global gene expression changes during mouse preimplantation development. Dev Cell 2004, 6:117-131.
    • (2004) Dev Cell , vol.6 , pp. 117-131
    • Hamatani, T.1    Carter, M.G.2    Sharov, A.A.3    Ko, M.S.4
  • 48
    • 0019519923 scopus 로고
    • Protein degradation during preimplantation development of the mouse
    • Merz EA, Brinster RL, Brunner S, Chen HY: Protein degradation during preimplantation development of the mouse. J Reprod Fertil 1981, 61:415-418.
    • (1981) J Reprod Fertil , vol.61 , pp. 415-418
    • Merz, E.A.1    Brinster, R.L.2    Brunner, S.3    Chen, H.Y.4
  • 50
    • 0036789519 scopus 로고    scopus 로고
    • Variation in gene expression within and among natural populations
    • Oleksiak MF, Churchill GA, Crawford DL: Variation in gene expression within and among natural populations. Nat Genet 2002, 32:261-266.
    • (2002) Nat Genet , vol.32 , pp. 261-266
    • Oleksiak, M.F.1    Churchill, G.A.2    Crawford, D.L.3
  • 51
    • 11244260808 scopus 로고    scopus 로고
    • Natural variation in cardiac metabolism and gene expression in Fundulus heteroclitus
    • Oleksiak MF, Roach JL, Crawford DL: Natural variation in cardiac metabolism and gene expression in Fundulus heteroclitus. Nat Genet 2005, 37:67-72.
    • (2005) Nat Genet , vol.37 , pp. 67-72
    • Oleksiak, M.F.1    Roach, J.L.2    Crawford, D.L.3
  • 52
    • 16344391539 scopus 로고    scopus 로고
    • Variation in tissue-specific gene expression among natural populations
    • Whitehead A, Crawford DL: Variation in tissue-specific gene expression among natural populations. Genome Biol 2005, 6:R13.
    • (2005) Genome Biol , vol.6
    • Whitehead, A.1    Crawford, D.L.2
  • 53
    • 84874647053 scopus 로고    scopus 로고
    • AmiGO
    • AmiGO [http://www.godatabase.org/cgi-bin/amigo/go.cgi]
  • 54
    • 4344598209 scopus 로고    scopus 로고
    • Cross-species comparison of genome-wide expression patterns
    • Zhou XJ, Gibson G: Cross-species comparison of genome-wide expression patterns. Genome Biol 2004, 5:232.
    • (2004) Genome Biol , vol.5 , pp. 232
    • Zhou, X.J.1    Gibson, G.2
  • 55
    • 19344374050 scopus 로고    scopus 로고
    • Similarities and differences in genome-wide expression data of six organisms
    • Bergmann S, Ihmels J, Barkai N: Similarities and differences in genome-wide expression data of six organisms. PLoS Biol 2004, 2:E9.
    • (2004) PLoS Biol , vol.2
    • Bergmann, S.1    Ihmels, J.2    Barkai, N.3
  • 56
    • 0037313182 scopus 로고    scopus 로고
    • Evolution of gene expression in the Drosophila melanogaster subgroup
    • Rifkin SA, Kim J, White KP: Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet 2003, 33:138-144.
    • (2003) Nat Genet , vol.33 , pp. 138-144
    • Rifkin, S.A.1    Kim, J.2    White, K.P.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.