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Volumn 9, Issue 1, 2016, Pages 1-17

Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits

Author keywords

DNA methylation; Enhancer; Epigenetics; Networks; Transcription factor

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR GATA 3;

EID: 84994429939     PISSN: None     EISSN: 17568935     Source Type: Journal    
DOI: 10.1186/s13072-016-0102-4     Document Type: Article
Times cited : (15)

References (39)
  • 1
    • 84938923353 scopus 로고    scopus 로고
    • Inferring regulatory element landscapes and transcription factor networks from cancer methylomes
    • Yao L, Shen H, Laird PW, Farnham PJ, Berman BP. Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. Genome Biol. 2015;16:105.
    • (2015) Genome Biol , vol.16 , pp. 105
    • Yao, L.1    Shen, H.2    Laird, P.W.3    Farnham, P.J.4    Berman, B.P.5
  • 3
    • 79951516056 scopus 로고    scopus 로고
    • A unique chromatin signature uncovers early developmental enhancers in humans
    • 1:CAS:528:DC%2BC3cXhsFKlsr%2FO
    • Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J. A unique chromatin signature uncovers early developmental enhancers in humans. Nature. 2011;470(7333):279-83.
    • (2011) Nature , vol.470 , Issue.7333 , pp. 279-283
    • Rada-Iglesias, A.1    Bajpai, R.2    Swigut, T.3    Brugmann, S.A.4    Flynn, R.A.5    Wysocka, J.6
  • 4
    • 84874816208 scopus 로고    scopus 로고
    • DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes
    • Aran D, Sabato S, Hellman A. DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes. Genome Biol. 2013;14(3):R21.
    • (2013) Genome Biol , vol.14 , Issue.3 , pp. R21
    • Aran, D.1    Sabato, S.2    Hellman, A.3
  • 5
    • 84900391269 scopus 로고    scopus 로고
    • Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells
    • Rhie SK, Hazelett DJ, Coetzee SG, Yan C, Noushmehr H, Coetzee GA. Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells. BMC Genom. 2014;15:331.
    • (2014) BMC Genom , vol.15 , pp. 331
    • Rhie, S.K.1    Hazelett, D.J.2    Coetzee, S.G.3    Yan, C.4    Noushmehr, H.5    Coetzee, G.A.6
  • 6
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium
    • ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57-74.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 57-74
  • 7
    • 84923362619 scopus 로고    scopus 로고
    • Integrative analysis of 111 reference human epigenomes
    • Roadmap Epigenomics Consortium
    • Roadmap Epigenomics Consortium. Integrative analysis of 111 reference human epigenomes. Nature. 2015;19:317-30.
    • (2015) Nature , vol.19 , pp. 317-330
  • 8
    • 84960185948 scopus 로고    scopus 로고
    • Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells
    • 1:CAS:528:DC%2BC28XhsFSisLjM
    • Tak YG, Hung Y, Yao L, Grimmer MR, Do A, Bhakta MS, O’Geen H, Segal DJ, Farnham PJ. Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells. Nucleic Acids Res. 2016;44(9):4123-33.
    • (2016) Nucleic Acids Res , vol.44 , Issue.9 , pp. 4123-4133
    • Tak, Y.G.1    Hung, Y.2    Yao, L.3    Grimmer, M.R.4    Do, A.5    Bhakta, M.S.6    O’Geen, H.7    Segal, D.J.8    Farnham, P.J.9
  • 11
    • 84908207355 scopus 로고    scopus 로고
    • Identifying and mitigating bias in next-generation sequencing methods for chromatin biology
    • 1:CAS:528:DC%2BC2cXhsFOltbfL
    • Meyer CA, Liu XS. Identifying and mitigating bias in next-generation sequencing methods for chromatin biology. Nat Rev Genet. 2014;15(11):709-21.
    • (2014) Nat Rev Genet , vol.15 , Issue.11 , pp. 709-721
    • Meyer, C.A.1    Liu, X.S.2
  • 12
    • 84924601067 scopus 로고    scopus 로고
    • Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics
    • 1:CAS:528:DC%2BC2MXjs1Omtr0%3D
    • Farlik M, Sheffield NC, Nuzzo A, Datlinger P, Schonegger A, Klughammer J, Bock C. Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics. Cell Rep. 2015;10(8):1386-97.
    • (2015) Cell Rep , vol.10 , Issue.8 , pp. 1386-1397
    • Farlik, M.1    Sheffield, N.C.2    Nuzzo, A.3    Datlinger, P.4    Schonegger, A.5    Klughammer, J.6    Bock, C.7
  • 13
    • 84907196865 scopus 로고    scopus 로고
    • Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
    • 1:CAS:528:DC%2BC2cXhsFaksLjL
    • Taberlay PC, Statham AL, Kelly TK, Clark SJ, Jones PA. Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer. Genome Res. 2014;24(9):1421-32.
    • (2014) Genome Res , vol.24 , Issue.9 , pp. 1421-1432
    • Taberlay, P.C.1    Statham, A.L.2    Kelly, T.K.3    Clark, S.J.4    Jones, P.A.5
  • 14
    • 84946195510 scopus 로고    scopus 로고
    • Network: the molecular taxonomy of primary prostate cancer
    • Cancer Genome Atlas Research
    • Cancer Genome Atlas Research. Network: the molecular taxonomy of primary prostate cancer. Cell. 2015;163(4):1011-25.
    • (2015) Cell , vol.163 , Issue.4 , pp. 1011-1025
  • 16
    • 84865773113 scopus 로고    scopus 로고
    • Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3
    • 1:CAS:528:DC%2BC38Xhtl2msb3J
    • Frietze S, Wang R, Yao L, Tak YG, Ye Z, Gaddis M, Witt H, Farnham PJ, Jin VX. Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3. Genome Biol. 2012;13(9):R52.
    • (2012) Genome Biol , vol.13 , Issue.9 , pp. R52
    • Frietze, S.1    Wang, R.2    Yao, L.3    Tak, Y.G.4    Ye, Z.5    Gaddis, M.6    Witt, H.7    Farnham, P.J.8    Jin, V.X.9
  • 17
    • 84871995408 scopus 로고    scopus 로고
    • GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility
    • 1:CAS:528:DC%2BC3sXnvV2lsA%3D%3D
    • Theodorou V, Stark R, Menon S, Carroll JS. GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility. Genome Res. 2013;23(1):12-22.
    • (2013) Genome Res , vol.23 , Issue.1 , pp. 12-22
    • Theodorou, V.1    Stark, R.2    Menon, S.3    Carroll, J.S.4
  • 21
    • 84873169147 scopus 로고    scopus 로고
    • CaMKK2: a novel target for shaping the androgen-regulated tumor ecosystem
    • 1:CAS:528:DC%2BC3sXitVGhtb0%3D
    • Racioppi L. CaMKK2: a novel target for shaping the androgen-regulated tumor ecosystem. Trends Mol Med. 2013;19(2):83-8.
    • (2013) Trends Mol Med , vol.19 , Issue.2 , pp. 83-88
    • Racioppi, L.1
  • 22
    • 84937010751 scopus 로고    scopus 로고
    • The transcription factor ZNF395 is required for the maximal hypoxic induction of proinflammatory cytokines in U87-MG cells
    • Herwartz C, Castillo-Juarez P, Schroder L, Barron BL, Steger G. The transcription factor ZNF395 is required for the maximal hypoxic induction of proinflammatory cytokines in U87-MG cells. Mediat Inflamm. 2015;2015:804264.
    • (2015) Mediat Inflamm , vol.2015 , pp. 804264
    • Herwartz, C.1    Castillo-Juarez, P.2    Schroder, L.3    Barron, B.L.4    Steger, G.5
  • 23
    • 84884508501 scopus 로고    scopus 로고
    • The hypoxia-inducible transcription factor ZNF395 is controlled by IkB kinase-signaling and activates genes involved in the innate immune response and cancer
    • 1:CAS:528:DC%2BC3sXhsFekurfN
    • Jordanovski D, Herwartz C, Pawlowski A, Taute S, Frommolt P, Steger G. The hypoxia-inducible transcription factor ZNF395 is controlled by IkB kinase-signaling and activates genes involved in the innate immune response and cancer. PLoS ONE. 2013;8(9):e74911.
    • (2013) PLoS ONE , vol.8 , Issue.9 , pp. e74911
    • Jordanovski, D.1    Herwartz, C.2    Pawlowski, A.3    Taute, S.4    Frommolt, P.5    Steger, G.6
  • 24
    • 34547215963 scopus 로고    scopus 로고
    • Identification and characterization of renal cell carcinoma gene markers
    • Dalgin GS, Holloway DT, Liou LS, DeLisi C. Identification and characterization of renal cell carcinoma gene markers. Cancer Inform. 2007;3:65-92.
    • (2007) Cancer Inform , vol.3 , pp. 65-92
    • Dalgin, G.S.1    Holloway, D.T.2    Liou, L.S.3    DeLisi, C.4
  • 25
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • 1:STN:280:DyaK28%2FjvFSjsg%3D%3D
    • 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
  • 29
    • 34447130861 scopus 로고    scopus 로고
    • Positive cross-regulatory loop ties GATA-3 to estrogen receptor alpha expression in breast cancer
    • 1:CAS:528:DC%2BD2sXnsVyqtbc%3D
    • Eeckhoute J, Keeton EK, Lupien M, Krum SA, Carroll JS, Brown M. Positive cross-regulatory loop ties GATA-3 to estrogen receptor alpha expression in breast cancer. Cancer Res. 2007;67(13):6477-83.
    • (2007) Cancer Res , vol.67 , Issue.13 , pp. 6477-6483
    • Eeckhoute, J.1    Keeton, E.K.2    Lupien, M.3    Krum, S.A.4    Carroll, J.S.5    Brown, M.6
  • 32
    • 84904722693 scopus 로고    scopus 로고
    • Prostate cancer metastasis-driving genes: hurdles and potential approaches in their identification
    • Chiang YT, Gout PW, Collins CC, Wang Y. Prostate cancer metastasis-driving genes: hurdles and potential approaches in their identification. Asian J Androl. 2014;16(4):545-8.
    • (2014) Asian J Androl , vol.16 , Issue.4 , pp. 545-548
    • Chiang, Y.T.1    Gout, P.W.2    Collins, C.C.3    Wang, Y.4
  • 33
    • 80052753295 scopus 로고    scopus 로고
    • Biology and clinical relevance of the micropthalmia family of transcription factors in human cancer
    • 1:CAS:528:DC%2BC3MXhtlWisLfN
    • Haq R, Fisher DE. Biology and clinical relevance of the micropthalmia family of transcription factors in human cancer. J Clin Oncol. 2011;29(25):3474-82.
    • (2011) J Clin Oncol , vol.29 , Issue.25 , pp. 3474-3482
    • Haq, R.1    Fisher, D.E.2
  • 34
    • 84899547426 scopus 로고    scopus 로고
    • RNA sequencing reveals upregulation of RUNX1-RUNX1T1 gene signatures in clear cell renal cell carcinoma
    • Xiong Z, Yu H, Ding Y, Feng C, Wei H, Tao S, Huang D, Zheng SL, Sun J, Xu J, et al. RNA sequencing reveals upregulation of RUNX1-RUNX1T1 gene signatures in clear cell renal cell carcinoma. Biomed Res Int. 2014;2014:450621.
    • (2014) Biomed Res Int , vol.2014 , pp. 450621
    • Xiong, Z.1    Yu, H.2    Ding, Y.3    Feng, C.4    Wei, H.5    Tao, S.6    Huang, D.7    Zheng, S.L.8    Sun, J.9    Xu, J.10
  • 35
    • 84964316069 scopus 로고    scopus 로고
    • Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes
    • Blattler A, Yao L, Witt H, Guo Y, Nicolet CM, Berman BP, Farnham PJ. Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes. Genome Biol. 2014;15(9):469.
    • (2014) Genome Biol , vol.15 , Issue.9 , pp. 469
    • Blattler, A.1    Yao, L.2    Witt, H.3    Guo, Y.4    Nicolet, C.M.5    Berman, B.P.6    Farnham, P.J.7
  • 39
    • 79953300078 scopus 로고    scopus 로고
    • FIMO: scanning for occurrences of a given motif
    • 1:CAS:528:DC%2BC3MXkt1yqs74%3D
    • Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011;27(7):1017-8.
    • (2011) Bioinformatics , vol.27 , Issue.7 , pp. 1017-1018
    • Grant, C.E.1    Bailey, T.L.2    Noble, W.S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.