메뉴 건너뛰기




Volumn 7, Issue , 2006, Pages

GONOME: Measuring correlations between GO terms and genomic positions

Author keywords

[No Author keywords available]

Indexed keywords

CONTROL ELEMENTS; GENE ONTOLOGY; GENOMIC POSITIONS; INTERGENIC REGIONS; MOTIF DISCOVERY; PROMOTER SEQUENCES; SYSTEMATIC BIAS; TRANSLATIONAL ELONGATION;

EID: 33645224575     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-94     Document Type: Article
Times cited : (13)

References (35)
  • 2
    • 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
  • 3
    • 12344269924 scopus 로고    scopus 로고
    • GO::TermFinder - Open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    • Boyle El, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G: GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 2004.
    • (2004) Bioinformatics
    • Boyle, E.I.1    Weng, S.2    Gollub, J.3    Jin, H.4    Botstein, D.5    Cherry, J.M.6    Sherlock, G.7
  • 6
    • 84886755664 scopus 로고    scopus 로고
    • GONOME - Finding associations between genomic positions and Gene Ontology (GO) terms
    • GONOME - Finding associations between genomic positions and Gene Ontology (GO) terms [http://gonome.imb.uq.edu.au/]
  • 7
    • 4544267694 scopus 로고    scopus 로고
    • Gene-Ontology analysis reveals association of tissue-specific 5′ CpG-island genes with development and embryogenesis
    • Robinson PN, Bohme U, Lopez R, Mundlos S, Nurnberg P. Gene-Ontology analysis reveals association of tissue-specific 5′ CpG-island genes with development and embryogenesis. Hum Mol Genet 2004, 13:1969-1978.
    • (2004) Hum Mol Genet , vol.13 , pp. 1969-1978
    • Robinson, P.N.1    Bohme, U.2    Lopez, R.3    Mundlos, S.4    Nurnberg, P.5
  • 8
    • 0042329754 scopus 로고    scopus 로고
    • Structure, function and evolution of CpG island promoters
    • Antequera F: Structure, function and evolution of CpG island promoters. Cell Mol Life Sci 2003, 60:1647-1658.
    • (2003) Cell Mol Life Sci , vol.60 , pp. 1647-1658
    • Antequera, F.1
  • 9
    • 0035183199 scopus 로고    scopus 로고
    • Determinants of CpG islands: Expression in early embryo and isochore structure
    • Ponger L, Duret L, Mouchiroud D: Determinants of CpG islands: expression in early embryo and isochore structure. Genome Res 2001, 11:1854-1860.
    • (2001) Genome Res , vol.11 , pp. 1854-1860
    • Ponger, L.1    Duret, L.2    Mouchiroud, D.3
  • 10
    • 0027141519 scopus 로고
    • Number of CpG islands and genes in human and mouse
    • Antequera F, Bird A. Number of CpG islands and genes in human and mouse. Proc Natl Acad Sci U S A 1993, 90:11995-11999.
    • (1993) Proc Natl Acad Sci U S A , vol.90 , pp. 11995-11999
    • Antequera, F.1    Bird, A.2
  • 11
    • 0026742792 scopus 로고
    • CpG islands as gene markers in the human genome
    • Larsen F, Gundersen G, Lopez R, Prydz H: CpG islands as gene markers in the human genome. Genomics 1992, 13:1095-1107.
    • (1992) Genomics , vol.13 , pp. 1095-1107
    • Larsen, F.1    Gundersen, G.2    Lopez, R.3    Prydz, H.4
  • 13
    • 84886764070 scopus 로고    scopus 로고
    • GONOME resources and examples
    • GONOME resources and examples http://gonome.imb,uq.edu.au/Resources.html]
  • 14
    • 0035346389 scopus 로고    scopus 로고
    • Isolation and identification of PACE-binding protein rpn4 - A new transcription activator, participating in regulation of 26S proteosome and other genes
    • Kapranov AB, Kuriatova MV, Preobrazheriskaia OV, Tiutiaeva VV. Shtuka R, Feldmann H, Karpov VL: [Isolation and identification of PACE-binding protein rpn4 - a new transcription activator, participating in regulation of 26S proteosome and other genes]. Mol Bioi (Mask) 2001, 35:420-431.
    • (2001) Mol Bioi (Mask) , vol.35 , pp. 420-431
    • Kapranov, A.B.1    Kuriatova, M.V.2    Preobrazheriskaia, O.V.3    Tiutiaeva, V.V.4    Shtuka, R.5    Feldmann, H.6    Karpov, V.L.7
  • 15
    • 2942580909 scopus 로고    scopus 로고
    • Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrepresented upstream motifs
    • Cora D, Di Cunto F, Provero P, Silengo L, Caselle M: Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrepresented upstream motifs. BMC Bioinformatics 2004, 5:57.
    • (2004) BMC Bioinformatics , vol.5 , pp. 57
    • Cora, D.1    Di Cunto, F.2    Provero, P.3    Silengo, L.4    Caselle, M.5
  • 16
    • 0033004441 scopus 로고    scopus 로고
    • Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast
    • Mannhaupt G, Schnall R, Karpov V, Vetter I, Feldmann H: Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast. FEBS Lett 1999, 450:27-34.
    • (1999) FEBS Lett , vol.450 , pp. 27-34
    • Mannhaupt, G.1    Schnall, R.2    Karpov, V.3    Vetter, I.4    Feldmann, H.5
  • 17
    • 11244343965 scopus 로고    scopus 로고
    • Rpn4 is a physiological substrate of the Ubr2 ubiquitin ligase
    • Wang L, Mao X, Ju D, Xie Y: Rpn4 is a physiological substrate of the Ubr2 ubiquitin ligase. J Biol Chem 2004, 279:55218-55223.
    • (2004) J Biol Chem , vol.279 , pp. 55218-55223
    • Wang, L.1    Mao, X.2    Ju, D.3    Xie, Y.4
  • 18
    • 0034100041 scopus 로고    scopus 로고
    • Glucose depletion rapidly inhibits translation initiation in yeast
    • Ashe MP, De Long SK, Sachs AB: Glucose depletion rapidly inhibits translation initiation in yeast. Mol Biol Cell 2000, 11:833-848.
    • (2000) Mol Biol Cell , vol.11 , pp. 833-848
    • Ashe, M.P.1    De Long, S.K.2    Sachs, A.B.3
  • 20
    • 0035829361 scopus 로고    scopus 로고
    • Controlling the false discovery rate in behavior genetics research
    • Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I: Controlling the false discovery rate in behavior genetics research. Behav Brain Res 2001, 125:279-284.
    • (2001) Behav Brain Res , vol.125 , pp. 279-284
    • Benjamini, Y.1    Drai, D.2    Elmer, G.3    Kafkafi, N.4    Golani, I.5
  • 21
    • 13444305456 scopus 로고    scopus 로고
    • A simple procedure for estimating the false discovery rate
    • Dalmasso C, Broet P, Moreau T: A simple procedure for estimating the false discovery rate. Bioinformatics 2004.
    • (2004) Bioinformatics
    • Dalmasso, C.1    Broet, P.2    Moreau, T.3
  • 22
    • 0036020892 scopus 로고    scopus 로고
    • A direct approach to false discovery rates
    • Storey JD: A direct approach to false discovery rates. J Royal Statistical Soc 8 2002, 64:479-498.
    • (2002) J Royal Statistical Soc B , Issue.64 , pp. 479-498
    • Storey, J.D.1
  • 23
    • 3042562270 scopus 로고    scopus 로고
    • Genomics, Prior Probability, and Statistical Tests of Multiple Hypotheses
    • Manly KF, Nettleton D, Hwang JTG: Genomics, Prior Probability, and Statistical Tests of Multiple Hypotheses. Genome Res 2004, 14:997-1001.
    • (2004) Genome Res , vol.14 , pp. 997-1001
    • Manly, K.F.1    Nettleton, D.2    Hwang, J.T.G.3
  • 24
    • 0003756375 scopus 로고
    • Discrete multivariate analysis: Theory and practice
    • Cambridge,Massachusetts and London, England, The MIT Press
    • Bishop YMM, Feinberg SE, Holland PW: Discrete multivariate analysis: theory and practice. Cambridge,Massachusetts and London, England, The MIT Press; 1975.
    • (1975)
    • Bishop, Y.M.M.1    Feinberg, S.E.2    Holland, P.W.3
  • 25
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey TL, Elkan C: Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994, 2:28-36.
    • (1994) Proc Int Conf Intell Syst Mol Biol , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 26
    • 13444306641 scopus 로고    scopus 로고
    • NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt KD, Tatusova T, Maglott DR: NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nud Acids Res 2005, 33:DS01-504.
    • (2005) Nud Acids Res , vol.33
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 27
    • 84874649656 scopus 로고    scopus 로고
    • Saccharomyces cerevisiae data
    • [ftp://genome-ftp.stanford.edu/pub/yeast/chromosomalfeature/ SGDfeatures.tab]
    • Saccharomyces cerevisiae data [ftp://genome-ftp.stanford.edu/pub/yeast/ chromosomalfeature/SGDfeatures.tab]
  • 28
    • 84874656895 scopus 로고    scopus 로고
    • Schizosaccharomyces pombe data
    • [ftp://ftp.sanger.ac.uk/pub/yeast/pombe/]
    • Schizosaccharomyces pombe data [ftp://ftp.sanger.ac.uk/pub/yeast/pombe/]
  • 29
    • 84874656374 scopus 로고    scopus 로고
    • Caenorhabditis elegans data
    • [ftp://ftp.wormbase.org/pub/worm base/genomes/elegans]
    • Caenorhabditis elegans data [ftp://ftp.wormbase.org/pub/worm base/ genomes/elegans]
  • 30
    • 84874654967 scopus 로고    scopus 로고
    • Drosophila melanogaster data
    • [ftp://flybase.bio.indiana.edu/genomes/Drosophila melanogaster/]
    • Drosophila melanogaster data [ftp://flybase.bio.indiana.edu/genomes/ Drosophila melanogaster/]
  • 33
    • 84874667626 scopus 로고    scopus 로고
    • Transcription factor consensus motifs
    • [ftp://genome-ftp.stanford.edu/pub/yeast/data download/ systematicresultregulatoryregions/harbisonpmid15343339/ Motifreferences-verified.txt]
    • Transcription factor consensus motifs [ftp://genome-ftp.stanford.edu/pub/ yeast/data download/systematicresultregulatoryregions/ harbisonpmid15343339/Motifreferences-verified.txt]


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.