메뉴 건너뛰기




Volumn 29, Issue 4, 2013, Pages 468-475

Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

EID: 84874294912     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts720     Document Type: Article
Times cited : (4)

References (43)
  • 1
    • 33646568805 scopus 로고    scopus 로고
    • Gene prioritization through genomic data fusion
    • Aerts, S. et al. (2006) Gene prioritization through genomic data fusion. Nat. Biotechnol., 24, 537-544.
    • (2006) Nat. Biotechnol , vol.24 , pp. 537-544
    • Aerts, S.1
  • 2
    • 58149189856 scopus 로고    scopus 로고
    • McKusick's online mendelian inheritance in man (OMIM)
    • Amberger, J. et al. (2009) McKusick's online mendelian inheritance in man (OMIM). Nucleic Acids Res., 37, D793-D796.
    • (2009) Nucleic Acids Res , vol.37
    • Amberger, J.1
  • 3
    • 0020679044 scopus 로고
    • A new alopecia/mental retardation syndrome
    • Baraitser, M. et al. (1983) A new alopecia/mental retardation syndrome. J. Med. Genet., 20, 64-65.
    • (1983) J. Med. Genet , vol.20 , pp. 64-65
    • Baraitser, M.1
  • 4
    • 0035114251 scopus 로고    scopus 로고
    • The molecular basis of human 3-methylcrotonyl-CoA carboxylase deficiency
    • Baumgartner, M.R. et al. (2001) The molecular basis of human 3-methylcrotonyl-CoA carboxylase deficiency. J. Clin. Invest., 107, 495-504.
    • (2001) J. Clin. Invest , vol.107 , pp. 495-504
    • Baumgartner, M.R.1
  • 5
    • 84870474023 scopus 로고    scopus 로고
    • An unbiased evaluation of gene prioritization tools
    • Börnigen, D. et al. (2012) An unbiased evaluation of gene prioritization tools. Bioinformatics, 28, 3081-3088.
    • (2012) Bioinformatics , vol.28 , pp. 3081-3088
    • Börnigen, D.1
  • 6
    • 38549096565 scopus 로고    scopus 로고
    • JASPAR, the open access database of transcription factorbinding profiles: New content and tools in the 2008 update
    • Bryne, J.C. et al. (2008) JASPAR, the open access database of transcription factorbinding profiles: new content and tools in the 2008 update. Nucleic Acids Res., 36, D102-D106.
    • (2008) Nucleic Acids Res , vol.36
    • Bryne, J.C.1
  • 7
    • 22744439568 scopus 로고    scopus 로고
    • Evolution at two levels: On genes and form
    • Carroll, S.B. (2005) Evolution at two levels: on genes and form. PLoS Biol., 3, e245.
    • (2005) PLoS Biol , vol.3
    • Carroll, S.B.1
  • 8
    • 23944483709 scopus 로고    scopus 로고
    • ERM is required for transcriptional control of the spermatogonial stem cell niche
    • Chen, C. et al. (2005) ERM is required for transcriptional control of the spermatogonial stem cell niche. Nature, 436, 1030-1034.
    • (2005) Nature , vol.436 , pp. 1030-1034
    • Chen, C.1
  • 9
    • 0003054847 scopus 로고
    • Parameter adjustment in Bayes networks. The generalized noisy OR-gate
    • Morgan Kaufmann, San Francisco, CA
    • Díez, F.J. (1993) Parameter adjustment in Bayes networks. The generalized noisy OR-gate. In: Proceedings of the 9th Conference on Uncertainty in Artificial Intelligence. Morgan Kaufmann, San Francisco, CA, pp. 99-105.
    • (1993) Proceedings of the 9th Conference on Uncertainty in Artificial Intelligence , pp. 99-105
    • Díez, F.J.1
  • 10
    • 33748191291 scopus 로고    scopus 로고
    • Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE
    • Foat, B.C. et al. (2006) Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics, 22, e141-e149.
    • (2006) Bioinformatics , vol.22
    • Foat, B.C.1
  • 11
    • 0035133319 scopus 로고    scopus 로고
    • The molecular basis of 3-methylcrotonylglycinuria a disorder of leucine catabolism
    • Gallardo, M.E. et al. (2001) The molecular basis of 3- methylcrotonylglycinuria, a disorder of leucine catabolism. Am. J. Hum. Genet., 68, 334-346.
    • (2001) Am. J. Hum. Genet , vol.68 , pp. 334-346
    • Gallardo, M.E.1
  • 12
    • 2942582468 scopus 로고    scopus 로고
    • Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
    • Gao, F. et al. (2004) Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics, 5, 31.
    • (2004) BMC Bioinformatics , vol.5 , pp. 31
    • Gao, F.1
  • 13
    • 44349109637 scopus 로고    scopus 로고
    • Eukaryotic transcription factor binding sites-modeling and integrative search methods
    • Hannenhalli, S. (2008) Eukaryotic transcription factor binding sites-modeling and integrative search methods. Bioinformatics, 24, 1325-1331.
    • (2008) Bioinformatics , vol.24 , pp. 1325-1331
    • Hannenhalli, S.1
  • 14
    • 33845198063 scopus 로고    scopus 로고
    • A patient with Werner syndrome and adiponectin gene mutation
    • Hashimoto, N. et al. (2007) A patient with Werner syndrome and adiponectin gene mutation. Diabetes Res. Clin. Pract., 75, 27-29.
    • (2007) Diabetes Res. Clin. Pract , vol.75 , pp. 27-29
    • Hashimoto, N.1
  • 15
    • 0344091562 scopus 로고    scopus 로고
    • Mutations in CLCN2 encoding a voltage-gated chloride channel are associated with idiopathic generalized epilepsies
    • Haug, K. et al. (2003) Mutations in CLCN2 encoding a voltage-gated chloride channel are associated with idiopathic generalized epilepsies. Nat. Genet., 33, 527-532.
    • (2003) Nat. Genet , vol.33 , pp. 527-532
    • Haug, K.1
  • 16
    • 17544382289 scopus 로고    scopus 로고
    • AdipoQ is a novel adipose-specific gene dysregulated in obesity
    • Hu, E. et al. (1996) AdipoQ is a novel adipose-specific gene dysregulated in obesity. J. Biol. Chem., 271, 10697-10703.
    • (1996) J. Biol. Chem , vol.271 , pp. 10697-10703
    • Hu, E.1
  • 17
    • 29244469662 scopus 로고    scopus 로고
    • Localization of a novel locus for alopecia with mental retardation syndrome to chromosome 3q26.33-q27.3
    • John, P. et al. (2006) Localization of a novel locus for alopecia with mental retardation syndrome to chromosome 3q26.33-q27.3. Hum. Genet., 118, 665-667.
    • (2006) Hum. Genet , vol.118 , pp. 665-667
    • John, P.1
  • 18
    • 77950351474 scopus 로고    scopus 로고
    • Advances in translational bioinformatics: Computational approaches for the hunting of disease genes
    • Kann, M.G. (2010) Advances in translational bioinformatics: computational approaches for the hunting of disease genes. Brief. Bioinform., 11, 96-110.
    • (2010) Brief. Bioinform , vol.11 , pp. 96-110
    • Kann, M.G.1
  • 19
    • 33846252240 scopus 로고    scopus 로고
    • Genome-wide atlas of gene expression in the adult mouse brain
    • Lein, E.S. et al. (2007) Genome-wide atlas of gene expression in the adult mouse brain. Nature, 445, 168-176.
    • (2007) Nature , vol.445 , pp. 168-176
    • Lein, E.S.1
  • 20
    • 0019364785 scopus 로고
    • Inherited disorders of 3-methylcrotonyl CoA carboxylation
    • Leonard, J.V. et al. (1981) Inherited disorders of 3-methylcrotonyl CoA carboxylation. Arch. Dis. Child., 56, 53-59.
    • (1981) Arch. Dis. Child , vol.56 , pp. 53-59
    • Leonard, J.V.1
  • 21
    • 84856328897 scopus 로고    scopus 로고
    • ETV5 transcription factor is overexpressed in ovarian cancer and regulates cell adhesion in ovarian cancer cells
    • Llauradó, M. et al. (2012) ETV5 transcription factor is overexpressed in ovarian cancer and regulates cell adhesion in ovarian cancer cells. Int. J. Cancer, 130, 1532-1543.
    • (2012) Int. J. Cancer , vol.130 , pp. 1532-1543
    • Llauradó, M.1
  • 22
    • 70649095116 scopus 로고    scopus 로고
    • Etv4 and Etv5 are required downstream of GDNF and Ret for kidney branching morphogenesis
    • Lu, B.C. et al. (2009) Etv4 and Etv5 are required downstream of GDNF and Ret for kidney branching morphogenesis. Nat. Genet., 41, 1295-1302.
    • (2009) Nat. Genet , vol.41 , pp. 1295-1302
    • Lu, B.C.1
  • 23
    • 49249095893 scopus 로고    scopus 로고
    • Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data
    • Miozzi, L. et al. (2008) Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data. PLoS ONE, 3, e2439.
    • (2008) PLoS ONE , vol.3
    • Miozzi, L.1
  • 24
    • 79961071787 scopus 로고    scopus 로고
    • Evolution of promoter affinity for transcription factors in the human lineage
    • Molineris, I. et al. (2011) Evolution of promoter affinity for transcription factors in the human lineage. Mol. Biol. Evol., 28, 2173-2183.
    • (2011) Mol. Biol. Evol , vol.28 , pp. 2173-2183
    • Molineris, I.1
  • 25
    • 0030920022 scopus 로고    scopus 로고
    • Isolated 3-methylcrotonyl-CoA carboxylase deficiency in a 15-year-old girl
    • Murayama, K. et al. (1997) Isolated 3-methylcrotonyl-CoA carboxylase deficiency in a 15-year-old girl. Brain Dev., 19, 303-305.
    • (1997) Brain Dev , vol.19 , pp. 303-305
    • Murayama, K.1
  • 26
    • 77956522546 scopus 로고    scopus 로고
    • Candidate gene prioritization based on spatially mapped gene expression: An application to XLMR
    • Piro, R.M. et al. (2010) Candidate gene prioritization based on spatially mapped gene expression: an application to XLMR. Bioinformatics, 26, i618-i624.
    • (2010) Bioinformatics , vol.26
    • Piro, R.M.1
  • 27
    • 80054818700 scopus 로고    scopus 로고
    • An atlas of tissue-specific conserved coexpression for functional annotation and disease gene prediction
    • Piro, R.M. et al. (2011) An atlas of tissue-specific conserved coexpression for functional annotation and disease gene prediction. Eur. J. Hum. Genet., 19, 1173-1180.
    • (2011) Eur. J. Hum. Genet , vol.19 , pp. 1173-1180
    • Piro, R.M.1
  • 28
    • 84857658973 scopus 로고    scopus 로고
    • Computational approaches to disease-gene prediction: Rationale, classification and successes
    • Piro, R.M. and Di Cunto, F. (2012) Computational approaches to disease-gene prediction: rationale, classification and successes. FEBS J., 279, 678-696.
    • (2012) FEBS J , vol.279 , pp. 678-696
    • Piro, R.M.1    Di Cunto, F.2
  • 29
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt, K.D. et al. (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61-D65.
    • (2007) Nucleic Acids Res , vol.35
    • Pruitt, K.D.1
  • 30
    • 79960680885 scopus 로고    scopus 로고
    • Discovery, structure-activity relationship studies, and crystal structure of nonpeptide inhibitors bound to the Shank3 PDZ domain
    • Saupe, J. et al. (2011) Discovery, structure-activity relationship studies, and crystal structure of nonpeptide inhibitors bound to the Shank3 PDZ domain. ChemMedChem, 6, 1411-1422.
    • (2011) Chem Med Chem , vol.6 , pp. 1411-1422
    • Saupe, J.1
  • 31
    • 84857745267 scopus 로고    scopus 로고
    • Database resources of the National Center for Biotechnology Information
    • Sayers, E.W. et al. (2012) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 40, D13-D25.
    • (2012) Nucleic Acids Res , vol.40
    • Sayers, E.W.1
  • 32
    • 57549100209 scopus 로고    scopus 로고
    • GeneDistiller-distilling candidate genes from linkage intervals
    • Seelow, D. et al. (2008) GeneDistiller-distilling candidate genes from linkage intervals. PLoS One, 3, e3874.
    • (2008) PLoS One , vol.3
    • Seelow, D.1
  • 33
    • 38749127589 scopus 로고    scopus 로고
    • Predicting expression patterns from regulatory sequence in Drosophila segmentation
    • Segal, E. et al. (2008) Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature, 451, 535-540.
    • (2008) Nature , vol.451 , pp. 535-540
    • Segal, E.1
  • 34
    • 0032799472 scopus 로고    scopus 로고
    • Metabolic stroke in isolated 3-methylcrotonyl-CoA carboxylase deficiency
    • Steen, C. et al. (1999) Metabolic stroke in isolated 3-methylcrotonyl-CoA carboxylase deficiency. Eur. J. Pediatr., 158, 730-733.
    • (1999) Eur. J. Pediatr , vol.158 , pp. 730-733
    • Steen, C.1
  • 35
    • 33746691336 scopus 로고    scopus 로고
    • Extensive low-affinity transcriptional interactions in the yeast genome
    • Tanay, A. (2006) Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res., 16, 962-972.
    • (2006) Genome Res , vol.16 , pp. 962-972
    • Tanay, A.1
  • 36
    • 66749148353 scopus 로고    scopus 로고
    • A systematic large-scale resequencing screen of X-chromosome coding exons in mental retardation
    • Tarpey, P.S. et al. (2009) A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation. Nat. Genet., 41, 535-543.
    • (2009) Nat. Genet , vol.41 , pp. 535-543
    • Tarpey, P.S.1
  • 37
    • 84857686155 scopus 로고    scopus 로고
    • Adiponectin-deficiency exaggerates sepsis-induced microvascular dysfunction in the mouse brain
    • Vachharajani, V. et al. (2012) Adiponectin-deficiency exaggerates sepsis-induced microvascular dysfunction in the mouse brain. Obesity (Silver Spring), 20, 498-504.
    • (2012) Obesity (Silver Spring , vol.20 , pp. 498-504
    • Vachharajani, V.1
  • 38
    • 0030016056 scopus 로고    scopus 로고
    • Cloning and characterization of DXS6673E a candidate gene for X-linked mental retardation in Xq13.1
    • van der Maarel, S.M. et al. (1996) Cloning and characterization of DXS6673E, a candidate gene for X-linked mental retardation in Xq13.1. Hum. Mol. Genet., 5, 887-897.
    • (1996) Hum. Mol. Genet , vol.5 , pp. 887-897
    • Van Der Maarel, S.M.1
  • 39
    • 33646058032 scopus 로고    scopus 로고
    • A text-mining analysis of the human phenome
    • van Driel, M.A. et al. (2006) A text-mining analysis of the human phenome. Eur. J. Hum. Genet., 14, 535-542.
    • (2006) Eur. J. Hum. Genet , vol.14 , pp. 535-542
    • Van Driel, M.A.1
  • 40
    • 66749095401 scopus 로고    scopus 로고
    • DCUN1D1 is a risk factor for frontotemporal lobar degeneration
    • Villa, C. et al. (2009) DCUN1D1 is a risk factor for frontotemporal lobar degeneration. Eur. J. Neurol., 16, 870-873.
    • (2009) Eur. J. Neurol , vol.16 , pp. 870-873
    • Villa, C.1
  • 41
    • 46249089455 scopus 로고    scopus 로고
    • Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences
    • Ward, L.D. and Bussemaker, H.J. (2008) Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Bioinformatics, 24, i165-i171.
    • (2008) Bioinformatics , vol.24
    • Ward, L.D.1    Bussemaker, H.J.2
  • 42
    • 0037212661 scopus 로고    scopus 로고
    • Promoters can contribute to the elucidation of protein function
    • Werner, T. (2003) Promoters can contribute to the elucidation of protein function. Trends Biotechnol., 21, 9-13.
    • (2003) Trends Biotechnol , vol.21 , pp. 9-13
    • Werner, T.1
  • 43
    • 84455192486 scopus 로고    scopus 로고
    • Adiponectin stimulates proliferation of adult hippocampal neural stem/progenitor cells through activation of p38 mitogen-activated protein kinase (p38MAPK)/glycogen synthase kinase 3 (GSK-3)/-catenin signaling cascade
    • Zhang, D. et al. (2011) Adiponectin stimulates proliferation of adult hippocampal neural stem/progenitor cells through activation of p38 mitogen-activated protein kinase (p38MAPK)/glycogen synthase kinase 3 (GSK-3)/-catenin signaling cascade. J. Biol. Chem., 286, 44913-44920.
    • (2011) J. Biol. Chem , vol.286 , pp. 44913-44920
    • Zhang, D.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.