메뉴 건너뛰기




Volumn 22, Issue 11, 2012, Pages 2278-2289

Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control

Author keywords

[No Author keywords available]

Indexed keywords

HOX PROTEIN; MEIS1 PROTEIN; PROTEIN; TRANSCRIPTION FACTOR NKX6.1; TRANSCRIPTION FACTOR POU; UNCLASSIFIED DRUG;

EID: 84868307469     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.139717.112     Document Type: Article
Times cited : (14)

References (63)
  • 2
    • 45449095883 scopus 로고    scopus 로고
    • The role of the cerebellum in schizophrenia
    • Andreasen NC, Pierson R. 2008. The role of the cerebellum in schizophrenia. Biol Psychiatry 64:81-88.
    • (2008) Biol Psychiatry , vol.64 , pp. 81-88
    • Andreasen, N.C.1    Pierson, R.2
  • 3
    • 24344508790 scopus 로고    scopus 로고
    • Brain structures and receptors involved in alertness
    • Aston-Jones G. 2005. Brain structures and receptors involved in alertness. Sleep Med (Suppl 1) 6: S3-S7.
    • (2005) Sleep Med , vol.6 , Issue.SUPPL. 1
    • Aston-Jones, G.1
  • 4
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey TL, Elkan C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2:28-36.
    • (1994) Proc Int Conf Intell Syst Mol Biol , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 5
    • 0031901903 scopus 로고    scopus 로고
    • Methods and statistics for combining motif match scores
    • Bailey TL, Gribskov M. 1998. Methods and statistics for combining motif match scores. J Comput Biol 5:211-221.
    • (1998) J Comput Biol , vol.5 , pp. 211-221
    • Bailey, T.L.1    Gribskov, M.2
  • 6
    • 0019811465 scopus 로고
    • Expression of a b-globin gene is enhanced by remote SV40 DNA sequences
    • Banerji J, Rusconi S, Schaffner W. 1981. Expression of a b-globin gene is enhanced by remote SV40 DNA sequences. Cell 27:299-308.
    • (1981) Cell , vol.27 , pp. 299-308
    • Banerji, J.1    Rusconi, S.2    Schaffner, W.3
  • 7
    • 18944391430 scopus 로고    scopus 로고
    • Expression of estrogen-receptor related receptors in amphioxus and zebrafish: Implications for the evolution of posterior brain segmentation at the invertebrate-to-vertebrate transition
    • Bardet PL, Schubert M, Horard B, Holland LZ, Laudet V, Holland ND, Vanacker JM. 2005. Expression of estrogen-receptor related receptors in amphioxus and zebrafish: Implications for the evolution of posterior brain segmentation at the invertebrate-to-vertebrate transition. Evol Dev 7:223-233.
    • (2005) Evol Dev , vol.7 , pp. 223-233
    • Bardet, P.L.1    Schubert, M.2    Horard, B.3    Holland, L.Z.4    Laudet, V.5    Holland, N.D.6    Vanacker, J.M.7
  • 8
    • 66149186985 scopus 로고    scopus 로고
    • Genomic location analysis by ChIP-Seq
    • Barski A, Zhao K. 2009. Genomic location analysis by ChIP-Seq. J Cell Biochem 107:11-18.
    • (2009) J Cell Biochem , vol.107 , pp. 11-18
    • Barski, A.1    Zhao, K.2
  • 9
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, 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
  • 11
    • 77951203799 scopus 로고    scopus 로고
    • Nkx6.1 and nkx6.2 regulate a-and b-cell formation in zebrafish by acting on pancreatic endocrine progenitor cells
    • Binot AC, Manfroid I, Flasse L, Winandy M, Motte P, Martial JA, Peers B, Voz ML. 2010. Nkx6.1 and nkx6.2 regulate a-and b-cell formation in zebrafish by acting on pancreatic endocrine progenitor cells. Dev Biol 340:397-407.
    • (2010) Dev Biol , vol.340 , pp. 397-407
    • Binot, A.C.1    Manfroid, I.2    Flasse, L.3    Winandy, M.4    Motte, P.5    Martial, J.A.6    Peers, B.7    Voz, M.L.8
  • 14
    • 79551655285 scopus 로고    scopus 로고
    • Functional and mechanistic diversity of distal transcription enhancers
    • Bulger M, Groudine M. 2011. Functional and mechanistic diversity of distal transcription enhancers. Cell 144:327-339.
    • (2011) Cell , vol.144 , pp. 327-339
    • Bulger, M.1    Groudine, M.2
  • 15
    • 10644236354 scopus 로고    scopus 로고
    • Homeodomain transcription factors in the development of subsets of hindbrain reticulospinal neurons
    • Cepeda-Nieto AC, Pfaff SL, Varela-Echavarria A. 2005. Homeodomain transcription factors in the development of subsets of hindbrain reticulospinal neurons. Mol Cell Neurosci 28:30-41.
    • (2005) Mol Cell Neurosci , vol.28 , pp. 30-41
    • Cepeda-Nieto, A.C.1    Pfaff, S.L.2    Varela-Echavarria, A.3
  • 16
    • 79955702502 scopus 로고    scopus 로고
    • LIBSVM: A library for support vector machines
    • article 27. doi:10.1145/1961189.1961199
    • Chang C-C, Lin C-J. 2011. LIBSVM: A library for support vector machines. ACM Trans Intell Syst Technol 2: article 27. doi:10.1145/1961189.1961199.
    • (2011) ACM Trans Intell Syst Technol , vol.2
    • Chang, C.-C.1    Lin, C.-J.2
  • 17
    • 80051968181 scopus 로고    scopus 로고
    • Needles in stacks of needles: Finding disease-causal variants in a wealth of genomic data
    • Cooper GM, Shendure J. 2011. Needles in stacks of needles: Finding disease-causal variants in a wealth of genomic data. Nat Rev Genet 12:628-640.
    • (2011) Nat Rev Genet , vol.12 , pp. 628-640
    • Cooper, G.M.1    Shendure, J.2
  • 19
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816.
    • (2007) Nature , vol.447 , pp. 799-816
  • 20
    • 79955550445 scopus 로고    scopus 로고
    • A user's guide to the encyclopedia of DNA elements (ENCODE)
    • The ENCODE Project Consortium doi:10.1371/journal.pbio.1001046
    • The ENCODE Project Consortium. 2011. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9: e1001046. doi:10.1371/journal.pbio. 1001046.
    • (2011) PLoS Biol , vol.9
  • 22
    • 33645833857 scopus 로고    scopus 로고
    • Conservation of RET regulatory function from human to zebrafish without sequence similarity
    • Fisher S, Grice EA, Vinton RM, Bessling SL, McCallion AS. 2006. Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science 312:276-279.
    • (2006) Science , vol.312 , pp. 276-279
    • Fisher, S.1    Grice, E.A.2    Vinton, R.M.3    Bessling, S.L.4    McCallion, A.S.5
  • 23
    • 83355166918 scopus 로고    scopus 로고
    • Structural basis for partial redundancy in a class of transcription factors, the LIM homeodomain proteins, in neural cell type specification
    • Gadd MS, Bhati M, Jeffries CM, Langley DB, Trewhella J, Guss JM, Matthews JM. 2011. Structural basis for partial redundancy in a class of transcription factors, the LIM homeodomain proteins, in neural cell type specification. J Biol Chem 286:42971-42980.
    • (2011) J Biol Chem , vol.286 , pp. 42971-42980
    • Gadd, M.S.1    Bhati, M.2    Jeffries, C.M.3    Langley, D.B.4    Trewhella, J.5    Guss, J.M.6    Matthews, J.M.7
  • 24
    • 0742265328 scopus 로고    scopus 로고
    • The origin and evolution of the nervous system
    • Ghysen A. 2003. The origin and evolution of the nervous system. Int J Dev Biol 47:555-562.
    • (2003) Int J Dev Biol , vol.47 , pp. 555-562
    • Ghysen, A.1
  • 25
    • 0036633114 scopus 로고    scopus 로고
    • To ERR in the estrogen pathway
    • Giguere V. 2002. To ERR in the estrogen pathway. Trends Endocrinol Metab 13:220-225.
    • (2002) Trends Endocrinol Metab , vol.13 , pp. 220-225
    • Giguere, V.1
  • 26
    • 13444304173 scopus 로고    scopus 로고
    • Chance caught on the wing: Cis-regulatory evolution and the origin of pigment patterns in Drosophila
    • Gompel N, Prud'homme B, Wittkopp PJ, Kassner VA, Carroll SB. 2005. Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila. Nature 433:481-487.
    • (2005) Nature , vol.433 , pp. 481-487
    • Gompel, N.1    Prud'Homme, B.2    Wittkopp, P.J.3    Kassner, V.A.4    Carroll, S.B.5
  • 27
    • 0036161259 scopus 로고    scopus 로고
    • Gene selection for cancer classification using support vector machines
    • Guyon I, Weston J, Barnhill S, Vapnik V. 2002. Gene selection for cancer classification using support vector machines. Mach Learn 46:389-422.
    • (2002) Mach Learn , vol.46 , pp. 389-422
    • Guyon, I.1    Weston, J.2    Barnhill, S.3    Vapnik, V.4
  • 28
    • 79955027617 scopus 로고    scopus 로고
    • Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart
    • He A, Kong SW, Ma Q, Pu WT. 2011. Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart. Proc Natl Acad Sci 108:5632-5637.
    • (2011) Proc Natl Acad Sci , vol.108 , pp. 5632-5637
    • He, A.1    Kong, S.W.2    Ma, Q.3    Pu, W.T.4
  • 34
    • 39949084307 scopus 로고    scopus 로고
    • The POU homeobox protein Oct-1 regulates radial glia formation downstream of Notch signaling
    • Kiyota T, Kato A, Altmann CR, Kato Y. 2008. The POU homeobox protein Oct-1 regulates radial glia formation downstream of Notch signaling. Dev Biol 315:579-592.
    • (2008) Dev Biol , vol.315 , pp. 579-592
    • Kiyota, T.1    Kato, A.2    Altmann, C.R.3    Kato, Y.4
  • 35
    • 83055181959 scopus 로고    scopus 로고
    • Discriminative prediction of mammalian enhancers from DNA sequence
    • Lee D, Karchin R, Beer MA. 2011. Discriminative prediction of mammalian enhancers from DNA sequence. Genome Res 21:2167-2180.
    • (2011) Genome Res , vol.21 , pp. 2167-2180
    • Lee, D.1    Karchin, R.2    Beer, M.A.3
  • 37
    • 34547569191 scopus 로고    scopus 로고
    • STAMP: A web tool for exploring DNA-binding motif similarities
    • Mahony S, Benos PV. 2007. STAMP: A web tool for exploring DNA-binding motif similarities. Nucleic Acids Res 35: W253-W258.
    • (2007) Nucleic Acids Res , vol.35
    • Mahony, S.1    Benos, P.V.2
  • 40
    • 39049147650 scopus 로고    scopus 로고
    • Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b
    • McGaughey DM, Vinton RM, Huynh J, Al-Saif A, Beer MA, McCallion AS. 2008. Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b. Genome Res 18:252-260.
    • (2008) Genome Res , vol.18 , pp. 252-260
    • McGaughey, D.M.1    Vinton, R.M.2    Huynh, J.3    Al-Saif, A.4    Beer, M.A.5    McCallion, A.S.6
  • 41
    • 36949023082 scopus 로고    scopus 로고
    • A nucleosome-guided map of transcription factor binding sites in yeast
    • doi:10.1371/journal.pcbi.0030215
    • Narlikar L, Gordan R, Hartemink AJ. 2007. A nucleosome-guided map of transcription factor binding sites in yeast. PLoS Comput Biol 3: e215. doi:10.1371/journal.pcbi.0030215.
    • (2007) PLoS Comput Biol , vol.3
    • Narlikar, L.1    Gordan, R.2    Hartemink, A.J.3
  • 43
    • 19444361832 scopus 로고    scopus 로고
    • Expression of Nkx6 genes in the hindbrain and gut of the developing mouse
    • Nelson SB, Janiesch C, Sander M. 2005. Expression of Nkx6 genes in the hindbrain and gut of the developing mouse. J Histochem Cytochem 53:787-790.
    • (2005) J Histochem Cytochem , vol.53 , pp. 787-790
    • Nelson, S.B.1    Janiesch, C.2    Sander, M.3
  • 46
    • 0041827087 scopus 로고    scopus 로고
    • Complementary roles for Nkx6 and Nkx2 class proteins in the establishment of motoneuron identity in the hindbrain
    • Pattyn A, Vallstedt A, Dias JM, Sander M, Ericson J. 2003. Complementary roles for Nkx6 and Nkx2 class proteins in the establishment of motoneuron identity in the hindbrain. Development 130:4149-4159.
    • (2003) Development , vol.130 , pp. 4149-4159
    • Pattyn, A.1    Vallstedt, A.2    Dias, J.M.3    Sander, M.4    Ericson, J.5
  • 50
    • 0036794646 scopus 로고    scopus 로고
    • On the generalisation of soft margin algorithms
    • Shawe-Taylor J, Cristianini N. 2002. On the generalisation of soft margin algorithms. IEEE Trans Inf Theory 48:2721-2735.
    • (2002) IEEE Trans Inf Theory , vol.48 , pp. 2721-2735
    • Shawe-Taylor, J.1    Cristianini, N.2
  • 52
    • 0030472176 scopus 로고    scopus 로고
    • Class III POU genes of zebrafish are predominantly expressed in the central nervous system
    • Spaniol P, Bornmann C, Hauptmann G, Gerster T. 1996. Class III POU genes of zebrafish are predominantly expressed in the central nervous system. Nucleic Acids Res 24:4874-4881.
    • (1996) Nucleic Acids Res , vol.24 , pp. 4874-4881
    • Spaniol, P.1    Bornmann, C.2    Hauptmann, G.3    Gerster, T.4
  • 54
    • 33748695399 scopus 로고    scopus 로고
    • Fast release clones: A high throughput expression analysis
    • Thisse B, Thisse C. 2004. Fast release clones: A high throughput expression analysis. In ZFIN Direct Data Submission (http://zfin.org).
    • (2004) ZFIN Direct Data Submission
    • Thisse, B.1    Thisse, C.2
  • 56
    • 80054091096 scopus 로고    scopus 로고
    • Pax genes during neural development and their potential role in neuroregeneration
    • Thompson JA, Ziman M. 2011. Pax genes during neural development and their potential role in neuroregeneration. Prog Neurobiol 95:334-351.
    • (2011) Prog Neurobiol , vol.95 , pp. 334-351
    • Thompson, J.A.1    Ziman, M.2
  • 57
    • 0033517107 scopus 로고    scopus 로고
    • Transcriptional targets shared by estrogen receptor-related receptors (ERRs) and estrogen receptor (ER) a, but not by ERb
    • Vanacker JM, Pettersson K, Gustafsson JA, Laudet V. 1999. Transcriptional targets shared by estrogen receptor-related receptors (ERRs) and estrogen receptor (ER) a, but not by ERb. EMBO J 18:4270-4279.
    • (1999) EMBO J , vol.18 , pp. 4270-4279
    • Vanacker, J.M.1    Pettersson, K.2    Gustafsson, J.A.3    Laudet, V.4
  • 61
    • 78149459363 scopus 로고    scopus 로고
    • Comparative genomic analysis reveals the evolutionary conservation of Pax gene family
    • Wang W, Zhong J, Wang YQ. 2010. Comparative genomic analysis reveals the evolutionary conservation of Pax gene family. Genes Genet Syst 85:193-206.
    • (2010) Genes Genet Syst , vol.85 , pp. 193-206
    • Wang, W.1    Zhong, J.2    Wang, Y.Q.3
  • 62
    • 0035176828 scopus 로고    scopus 로고
    • Zebrafish Meis functions to stabilize Pbx proteins and regulate hindbrain patterning
    • Waskiewicz AJ, Rikhof HA, Hernandez RE, Moens CB. 2001. Zebrafish Meis functions to stabilize Pbx proteins and regulate hindbrain patterning. Development 128:4139-4151.
    • (2001) Development , vol.128 , pp. 4139-4151
    • Waskiewicz, A.J.1    Rikhof, H.A.2    Hernandez, R.E.3    Moens, C.B.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.