메뉴 건너뛰기




Volumn 42, Issue 13, 2014, Pages

ChIP-Enrich: Gene set enrichment testing for ChIP-seq data

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; GLUCOCORTICOID RECEPTOR ALPHA; TRANSCRIPTION FACTOR CTCF; TRANSCRIPTION FACTOR JUND;

EID: 84905583004     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku463     Document Type: Article
Times cited : (103)

References (52)
  • 1
  • 3
    • 33847264343 scopus 로고    scopus 로고
    • Enrichment or depletion of a GO category within a class of genes: Which test?
    • Rivals, I., Personnaz, L., Taing, L. and Potier, M.C. (2007) Enrichment or depletion of a GO category within a class of genes: which test? Bioinformatics, 23, 401-407.
    • (2007) Bioinformatics , vol.23 , pp. 401-407
    • Rivals, I.1    Personnaz, L.2    Taing, L.3    Potier, M.C.4
  • 5
    • 84876045450 scopus 로고    scopus 로고
    • Gene set control analysis predicts hematopoietic control mechanisms from genome-wide transcription factor binding data
    • e314
    • Joshi, A., Hannah, R., Diamanti, E. and Gottgens, B. (2013) Gene set control analysis predicts hematopoietic control mechanisms from genome-wide transcription factor binding data. Exp. Hematol., 41, 354-366, e314.
    • (2013) Exp. Hematol. , vol.41 , pp. 354-366
    • Joshi, A.1    Hannah, R.2    Diamanti, E.3    Gottgens, B.4
  • 6
    • 77957243164 scopus 로고    scopus 로고
    • ChEA: Transcription factor regulation inferred from integrating genome-wide ChIP-X experiments
    • Lachmann, A., Xu, H., Krishnan, J., Berger, S.I., Mazloom, A.R. and Ma'ayan, A. (2010) ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics, 26, 2438-2444.
    • (2010) Bioinformatics , vol.26 , pp. 2438-2444
    • Lachmann, A.1    Xu, H.2    Krishnan, J.3    Berger, S.I.4    Mazloom, A.R.5    Ma'ayan, A.6
  • 7
    • 58349105009 scopus 로고    scopus 로고
    • LRpath: A logistic regression approach for identifying enriched biological groups in gene expression data
    • Sartor, M.A., Leikauf, G.D. and Medvedovic, M. (2009) LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data. Bioinformatics, 25, 211-217.
    • (2009) Bioinformatics , vol.25 , pp. 211-217
    • Sartor, M.A.1    Leikauf, G.D.2    Medvedovic, M.3
  • 8
    • 84866911829 scopus 로고    scopus 로고
    • Camera: A competitive gene set test accounting for inter-gene correlation
    • Wu, D. and Smyth, G.K. (2012) Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Res., 40, e133.
    • (2012) Nucleic Acids Res. , vol.40
    • Wu, D.1    Smyth, G.K.2
  • 11
    • 35348890683 scopus 로고    scopus 로고
    • On testing the significance of sets of genes
    • Efron, B. and Tibshirani, R. (2007) On testing the significance of sets of genes. Ann. Appl. Stat., 1, 107-129.
    • (2007) Ann. Appl. Stat. , vol.1 , pp. 107-129
    • Efron, B.1    Tibshirani, R.2
  • 17
    • 77957942910 scopus 로고    scopus 로고
    • Common inherited variation in mitochondrial genes is not enriched for associations with type 2 diabetes or related glycemic traits
    • Segre, A.V., Consortium, D. and investigators, M. investigators, M., Groop, L., Mootha, V.K., Daly, M.J. and Altshuler, D. (2010) Common inherited variation in mitochondrial genes is not enriched for associations with type 2 diabetes or related glycemic traits. PLoS Genet., 6.
    • (2010) PLoS Genet. , vol.6
    • Segre, A.V.1    Consortium, D.2    Groop, L.3    Mootha, V.K.4    Daly, M.J.5    Altshuler, D.6
  • 18
    • 61449212191 scopus 로고    scopus 로고
    • Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements
    • Taher, L. and Ovcharenko, I. (2009) Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements. Bioinformatics, 25, 578-584.
    • (2009) Bioinformatics , vol.25 , pp. 578-584
    • Taher, L.1    Ovcharenko, I.2
  • 19
    • 77953212372 scopus 로고    scopus 로고
    • Gene ontology analysis for RNA-seq: Accounting for selection bias
    • Young, M.D., Wakefield, M.J., Smyth, G.K. and Oshlack, A. (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol., 11, R14.
    • (2010) Genome Biol. , vol.11
    • Young, M.D.1    Wakefield, M.J.2    Smyth, G.K.3    Oshlack, A.4
  • 24
    • 57449100870 scopus 로고    scopus 로고
    • Design and analysis of ChIP-seq experiments for DNA-binding proteins
    • Kharchenko, P.V., Tolstorukov, M.Y. and Park, P.J. (2008) Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat. Biotechnol., 26, 1351-1359.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1351-1359
    • Kharchenko, P.V.1    Tolstorukov, M.Y.2    Park, P.J.3
  • 26
    • 0030474271 scopus 로고    scopus 로고
    • A simulation study of the number of events per variable in logistic regression analysis
    • Peduzzi, P., Concato, J., Kemper, E., Holford, T.R. and Feinstein, A.R. (1996) A simulation study of the number of events per variable in logistic regression analysis. J. Clin. Epidemiol., 49, 1373-1379.
    • (1996) J. Clin. Epidemiol. , vol.49 , pp. 1373-1379
    • Peduzzi, P.1    Concato, J.2    Kemper, E.3    Holford, T.R.4    Feinstein, A.R.5
  • 27
    • 0018686970 scopus 로고
    • Testing the goodness of fit of the binomial distribution
    • Tarone, R.E. (1979) Testing the goodness of fit of the binomial distribution. Biometrika, 66, 585-590.
    • (1979) Biometrika , vol.66 , pp. 585-590
    • Tarone, R.E.1
  • 29
    • 78650862532 scopus 로고    scopus 로고
    • Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models
    • Wood, S.N. (2011) Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models. J. R. Stat. Soc.: Ser. B (Stat. Methodol.), 73, 3-36.
    • (2011) J. R. Stat. Soc.: Ser. B (Stat. Methodol.) , vol.73 , pp. 3-36
    • Wood, S.N.1
  • 30
    • 80052736663 scopus 로고    scopus 로고
    • Mgcv: GAMs with GCV/AIC/REML smoothness estimation and GAMMs by PQL
    • Wood, S.N. (2010) mgcv: GAMs with GCV/AIC/REML smoothness estimation and GAMMs by PQL. R Package Version 1.6-2.
    • (2010) R Package Version , pp. 16-12
    • Wood, S.N.1
  • 31
    • 0001677717 scopus 로고
    • Controlling the false discovery rate - A practical and powerful approach to multiple testing
    • Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate - A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B-Methodol., 57, 289-300.
    • (1995) J. R. Stat. Soc. Ser. B-Methodol. , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 33
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang da, W., Sherman, B.T. and Lempicki, R.A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc., 4, 44-57.
    • (2009) Nat. Protoc. , vol.4 , pp. 44-57
    • Huang Da, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 34
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • Storey, J.D. and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. U.S.A., 100, 9440-9445.
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 36
    • 55549087940 scopus 로고    scopus 로고
    • EBV Immortalization of human B lymphocytes separated from small volumes of cryo-preserved whole blood
    • Amoli, M.M., Carthy, D., Platt, H. and Ollier, W.E. (2008) EBV Immortalization of human B lymphocytes separated from small volumes of cryo-preserved whole blood. Int. J. Epidemiol., 37(Suppl. 1), i41-45.
    • (2008) Int. J. Epidemiol. , vol.37 , Issue.SUPPL. 1
    • Amoli, M.M.1    Carthy, D.2    Platt, H.3    Ollier, W.E.4
  • 38
    • 49649113832 scopus 로고    scopus 로고
    • Multiple facets of junD gene expression are atypical among AP-1 family members
    • Hernandez, J.M., Floyd, D.H., Weilbaecher, K.N., Green, P.L. and Boris-Lawrie, K. (2008) Multiple facets of junD gene expression are atypical among AP-1 family members. Oncogene, 27, 4757-4767.
    • (2008) Oncogene , vol.27 , pp. 4757-4767
    • Hernandez, J.M.1    Floyd, D.H.2    Weilbaecher, K.N.3    Green, P.L.4    Boris-Lawrie, K.5
  • 40
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identified by analysis of chromatin interactions
    • Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J.S. and Ren, B. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485, 376-380.
    • (2012) Nature , vol.485 , pp. 376-380
    • Dixon, J.R.1    Selvaraj, S.2    Yue, F.3    Kim, A.4    Li, Y.5    Shen, Y.6    Hu, M.7    Liu, J.S.8    Ren, B.9
  • 41
    • 4344649442 scopus 로고    scopus 로고
    • The Werner syndrome protein at the crossroads of DNA repair and apoptosis
    • Comai, L. and Li, B. (2004) The Werner syndrome protein at the crossroads of DNA repair and apoptosis. Mech. Ageing Dev., 125, 521-528.
    • (2004) Mech. Ageing Dev. , vol.125 , pp. 521-528
    • Comai, L.1    Li, B.2
  • 42
  • 43
    • 84855469822 scopus 로고    scopus 로고
    • Chromodomain helicase DNA-binding protein 2 affects the repair of X-ray and UV-induced DNA damage
    • Rajagopalan, S., Nepa, J. and Venkatachalam, S. (2012) Chromodomain helicase DNA-binding protein 2 affects the repair of X-ray and UV-induced DNA damage. Environ. Mol. Mutagen., 53, 44-50.
    • (2012) Environ. Mol. Mutagen. , vol.53 , pp. 44-50
    • Rajagopalan, S.1    Nepa, J.2    Venkatachalam, S.3
  • 44
    • 34547766645 scopus 로고    scopus 로고
    • ZNF143 interacts with p73 and is involved in cisplatin resistance through the transcriptional regulation of DNA repair genes
    • Wakasugi, T., Izumi, H., Uchiumi, T., Suzuki, H., Arao, T., Nishio, K. and Kohno, K. (2007) ZNF143 interacts with p73 and is involved in cisplatin resistance through the transcriptional regulation of DNA repair genes. Oncogene, 26, 5194-5203.
    • (2007) Oncogene , vol.26 , pp. 5194-5203
    • Wakasugi, T.1    Izumi, H.2    Uchiumi, T.3    Suzuki, H.4    Arao, T.5    Nishio, K.6    Kohno, K.7
  • 45
    • 77951254240 scopus 로고    scopus 로고
    • From hematopoietic progenitors to B cells: Mechanisms of lineage restriction and commitment
    • Ramirez, J., Lukin, K. and Hagman, J. (2010) From hematopoietic progenitors to B cells: mechanisms of lineage restriction and commitment. Curr. Opin. Immunol., 22, 177-184.
    • (2010) Curr. Opin. Immunol. , vol.22 , pp. 177-184
    • Ramirez, J.1    Lukin, K.2    Hagman, J.3
  • 46
    • 70449731229 scopus 로고    scopus 로고
    • Differential regulation of telomere and centromere cohesion by the Scc3 homologues SA1 and SA2, respectively, in human cells
    • Canudas, S. and Smith, S. (2009) Differential regulation of telomere and centromere cohesion by the Scc3 homologues SA1 and SA2, respectively, in human cells. J. Cell Biol., 187, 165-173.
    • (2009) J. Cell Biol. , vol.187 , pp. 165-173
    • Canudas, S.1    Smith, S.2
  • 47
    • 73249130316 scopus 로고    scopus 로고
    • Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation
    • Reddy, T.E., Pauli, F., Sprouse, R.O., Neff, N.F., Newberry, K.M., Garabedian, M.J. and Myers, R.M. (2009) Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation. Genome Res., 19, 2163-2171.
    • (2009) Genome Res. , vol.19 , pp. 2163-2171
    • Reddy, T.E.1    Pauli, F.2    Sprouse, R.O.3    Neff, N.F.4    Newberry, K.M.5    Garabedian, M.J.6    Myers, R.M.7
  • 48
    • 78650882261 scopus 로고    scopus 로고
    • Genome-wide analysis of glucocorticoid receptor binding regions in adipocytes reveal gene network involved in triglyceride homeostasis
    • Yu, C.Y., Mayba, O., Lee, J.V., Tran, J., Harris, C., Speed, T.P. and Wang, J.C. (2010) Genome-wide analysis of glucocorticoid receptor binding regions in adipocytes reveal gene network involved in triglyceride homeostasis. PloS ONE, 5, e15188.
    • (2010) PloS ONE , vol.5
    • Yu, C.Y.1    Mayba, O.2    Lee, J.V.3    Tran, J.4    Harris, C.5    Speed, T.P.6    Wang, J.C.7
  • 49
    • 67749088181 scopus 로고    scopus 로고
    • Direct effect of glucocorticoids on lipolysis in adipocytes
    • Xu, C., He, J., Jiang, H., Zu, L., Zhai, W., Pu, S. and Xu, G. (2009) Direct effect of glucocorticoids on lipolysis in adipocytes. Mol. Endocrinol., 23, 1161-1170.
    • (2009) Mol. Endocrinol. , vol.23 , pp. 1161-1170
    • Xu, C.1    He, J.2    Jiang, H.3    Zu, L.4    Zhai, W.5    Pu, S.6    Xu, G.7
  • 50
    • 68149089755 scopus 로고    scopus 로고
    • Fluocinolone inhibits VEGF expression via glucocorticoid receptor in human retinal pigment epithelial (ARPE-19) cells and TNF-alpha-induced angiogenesis in chick chorioallantoic membrane (CAM)
    • Ayalasomayajula, S.P., Ashton, P. and Kompella, U.B. (2009) Fluocinolone inhibits VEGF expression via glucocorticoid receptor in human retinal pigment epithelial (ARPE-19) cells and TNF-alpha-induced angiogenesis in chick chorioallantoic membrane (CAM). J. Ocul. Pharmacol. Ther., 25, 97-103.
    • (2009) J. Ocul. Pharmacol. Ther. , vol.25 , pp. 97-103
    • Ayalasomayajula, S.P.1    Ashton, P.2    Kompella, U.B.3
  • 51
    • 4444289382 scopus 로고    scopus 로고
    • Negative glucocorticoid receptor response elements and their role in glucocorticoid action
    • Dostert, A. and Heinzel, T. (2004) Negative glucocorticoid receptor response elements and their role in glucocorticoid action. Curr. Pharm. Des., 10, 2807-2816.
    • (2004) Curr. Pharm. Des. , vol.10 , pp. 2807-2816
    • Dostert, A.1    Heinzel, T.2
  • 52
    • 24744448423 scopus 로고    scopus 로고
    • Preventing local regeneration of glucocorticoids by 11beta-hydroxysteroid dehydrogenase type 1 enhances angiogenesis
    • Small, G.R., Hadoke, P.W., Sharif, I., Dover, A.R., Armour, D., Kenyon, C.J., Gray, G.A. and Walker, B.R. (2005) Preventing local regeneration of glucocorticoids by 11beta-hydroxysteroid dehydrogenase type 1 enhances angiogenesis. Proc. Natl. Acad. Sci. U.S.A., 102, 12165-12170. Kidney Diseases
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 12165-12170
    • Small, G.R.1    Hadoke, P.W.2    Sharif, I.3    Dover, A.R.4    Armour, D.5    Kenyon, C.J.6    Gray, G.A.7    Walker, B.R.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.