메뉴 건너뛰기




Volumn 15, Issue 1, 2005, Pages 184-194

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR GATA 3;

EID: 12744253685     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.3007205     Document Type: Article
Times cited : (212)

References (41)
  • 2
    • 3042832819 scopus 로고    scopus 로고
    • Epithelial Bmpr1a regulates differentiation and proliferation in postnatal hair follicles and is essential for tooth development
    • Andl, T., Ahn, K., Kairo, A., Chu, E.Y., Wine-Lee, L., Reddy, S.T., Croft, N.J., Cebra-Thomas, J.A., Metzger, D., Chambon, P., et al. 2004. Epithelial Bmpr1a regulates differentiation and proliferation in postnatal hair follicles and is essential for tooth development. Development 131: 2257-2268.
    • (2004) Development , vol.131 , pp. 2257-2268
    • Andl, T.1    Ahn, K.2    Kairo, A.3    Chu, E.Y.4    Wine-Lee, L.5    Reddy, S.T.6    Croft, N.J.7    Cebra-Thomas, J.A.8    Metzger, D.9    Chambon, P.10
  • 5
    • 0037270315 scopus 로고    scopus 로고
    • AVID: A global alignment program
    • Bray, N., Dubchak, I., and Pachter, L. 2003. AVID: A global alignment program. Genome Res. 13: 97-102.
    • (2003) Genome Res. , vol.13 , pp. 97-102
    • Bray, N.1    Dubchak, I.2    Pachter, L.3
  • 6
    • 1642402120 scopus 로고    scopus 로고
    • The cardiac determination factor, Nkx2-5, is activated by mutual cofactors GATA-4 and Smad1/4 via a novel upstream enhancer
    • Brown III, C.O., Chi, X., Garcia-Gras, E., Shirai, M., Feng, X.H., and Schwartz, R.J. 2004. The cardiac determination factor, Nkx2-5, is activated by mutual cofactors GATA-4 and Smad1/4 via a novel upstream enhancer. J. Biol. Chem. 279: 10659-10669.
    • (2004) J. Biol. Chem. , vol.279 , pp. 10659-10669
    • Brown III, C.O.1    Chi, X.2    Garcia-Gras, E.3    Shirai, M.4    Feng, X.H.5    Schwartz, R.J.6
  • 8
    • 0035794208 scopus 로고    scopus 로고
    • A negative cis-element regulates the level of enhancement by hypersensitive site 2 of the β-globin locus control region
    • Elnitski, L., Li, J., Noguchi, C.T., Miller, W., and Hardison, R. 2001. A negative cis-element regulates the level of enhancement by hypersensitive site 2 of the β-globin locus control region. J. Biol. Chem. 276: 6289-6298.
    • (2001) J. Biol. Chem. , vol.276 , pp. 6289-6298
    • Elnitski, L.1    Li, J.2    Noguchi, C.T.3    Miller, W.4    Hardison, R.5
  • 9
    • 1542347048 scopus 로고    scopus 로고
    • Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional
    • Frazer, K.A., Tao, H., Osoegawa, K., de Jong, P.J., Chen, X., Doherty, M.F., and Cox, D.R. 2004. Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional. Genome Res. 14: 367-372.
    • (2004) Genome Res. , vol.14 , pp. 367-372
    • Frazer, K.A.1    Tao, H.2    Osoegawa, K.3    de Jong, P.J.4    Chen, X.5    Doherty, M.F.6    Cox, D.R.7
  • 12
    • 0037055269 scopus 로고    scopus 로고
    • Fugu and human sequence comparison identifies novel human genes and conserved non-coding sequences
    • Gilligan, P., Brenner, S., and Venkatesh, B. 2002. Fugu and human sequence comparison identifies novel human genes and conserved non-coding sequences. Gene 294: 35-44.
    • (2002) Gene , vol.294 , pp. 35-44
    • Gilligan, P.1    Brenner, S.2    Venkatesh, B.3
  • 16
    • 0141815478 scopus 로고    scopus 로고
    • Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
    • Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. 2003. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl. Acad. Sci. 100: 11484-11489.
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 11484-11489
    • Kent, W.J.1    Baertsch, R.2    Hinrichs, A.3    Miller, W.4    Haussler, D.5
  • 17
    • 0347914540 scopus 로고    scopus 로고
    • Conserved elements in Pax6 intron 7 involved in (auto)regulation and alternative transcription
    • Kleinjan, D.A., Seawright, A., Childs, A.J., and van Heyningen, V. 2004. Conserved elements in Pax6 intron 7 involved in (auto)regulation and alternative transcription. Dev. Biol. 265: 462-477.
    • (2004) Dev. Biol. , vol.265 , pp. 462-477
    • Kleinjan, D.A.1    Seawright, A.2    Childs, A.J.3    van Heyningen, V.4
  • 19
    • 0037147757 scopus 로고    scopus 로고
    • Expression of the transcription factors GATA3 and Pax2 during development of the mammalian inner ear
    • Lawoko-Kerali, G., Rivolta, M.N., and Holley, M. 2002. Expression of the transcription factors GATA3 and Pax2 during development of the mammalian inner ear. J. Comp Neurol. 442: 378-391.
    • (2002) J. Comp. Neurol. , vol.442 , pp. 378-391
    • Lawoko-Kerali, G.1    Rivolta, M.N.2    Holley, M.3
  • 22
    • 0034096902 scopus 로고    scopus 로고
    • Gata3 loss leads to embryonic lethality due to noradrenaline deficiency of the sympathetic nervous system
    • Lim, K.C., Lakshmanan, G., Crawford, S.E., Gu, Y., Grosveld, F., and Engel, J.D. 2000. Gata3 loss leads to embryonic lethality due to noradrenaline deficiency of the sympathetic nervous system. Nat. Genet. 25: 209-212.
    • (2000) Nat. Genet. , vol.25 , pp. 209-212
    • Lim, K.C.1    Lakshmanan, G.2    Crawford, S.E.3    Gu, Y.4    Grosveld, F.5    Engel, J.D.6
  • 23
    • 3242888285 scopus 로고    scopus 로고
    • rVISTA 2.0: Evolutionary analysis of transcription factor binding sites
    • Loots, G.G. and Ovcharenko, I. 2004. rVISTA 2.0: Evolutionary analysis of transcription factor binding sites. Nucleic Acids Res. 32: W217-W221.
    • (2004) Nucleic Acids Res. , vol.32
    • Loots, G.G.1    Ovcharenko, I.2
  • 24
    • 0034616398 scopus 로고    scopus 로고
    • Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons
    • Loots, G.G., Locksley, R.M., Blankespoor, C.M., Wang, Z.E., Miller, W., Rubin, E.M., and Frazer, K.A. 2000. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288: 136-140.
    • (2000) Science , vol.288 , pp. 136-140
    • Loots, G.G.1    Locksley, R.M.2    Blankespoor, C.M.3    Wang, Z.E.4    Miller, W.5    Rubin, E.M.6    Frazer, K.A.7
  • 25
    • 0036105591 scopus 로고    scopus 로고
    • rVista for comparative sequence-based discovery of functional transcription factor binding sites
    • Loots, G.G., Ovcharenko, I., Pachter, L., Dubchak, I., and Rubin, E.M. 2002. rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res. 12: 832-839.
    • (2002) Genome Res. , vol.12 , pp. 832-839
    • Loots, G.G.1    Ovcharenko, I.2    Pachter, L.3    Dubchak, I.4    Rubin, E.M.5
  • 27
    • 0142084743 scopus 로고    scopus 로고
    • Scanning human gene deserts for long-range enhancers
    • Nobrega, M.A., Ovcharenko, I., Afzal, V., and Rubin, E.M. 2003. Scanning human gene deserts for long-range enhancers. Science 302: 413.
    • (2003) Science , vol.302 , pp. 413
    • Nobrega, M.A.1    Ovcharenko, I.2    Afzal, V.3    Rubin, E.M.4
  • 28
    • 3042558659 scopus 로고    scopus 로고
    • eShadow: A tool for comparing closely related sequences
    • Ovcharenko, I., Boffelli, D., and Loots, G.G. 2004a. eShadow: A tool for comparing closely related sequences. Genome Res. 14: 1191-1198.
    • (2004) Genome Res. , vol.14 , pp. 1191-1198
    • Ovcharenko, I.1    Boffelli, D.2    Loots, G.G.3
  • 29
    • 1542347045 scopus 로고    scopus 로고
    • zPicture: Dynamic alignment and visualization tool for analyzing conservation profiles
    • Ovcharenko, I., Loots, G.G., Hardison, R.C., Miller, W., and Stubbs, L. 2004b. zPicture: Dynamic alignment and visualization tool for analyzing conservation profiles. Genome Res. 14: 472-477.
    • (2004) Genome Res. , vol.14 , pp. 472-477
    • Ovcharenko, I.1    Loots, G.G.2    Hardison, R.C.3    Miller, W.4    Stubbs, L.5
  • 31
    • 0036845822 scopus 로고    scopus 로고
    • Splitting pairs: The diverging fates of duplicated genes
    • Prince, V.E. and Pickett, F.B. 2002. Splitting pairs: The diverging fates of duplicated genes. Nat. Rev. Genet. 3: 827-837.
    • (2002) Nat. Rev. Genet. , vol.3 , pp. 827-837
    • Prince, V.E.1    Pickett, F.B.2
  • 32
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou, N. and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 33
    • 0141790017 scopus 로고    scopus 로고
    • Identification of cis-regulatory elements in the mouse Pax9/Nkx2-9 genomic region: Implication for evolutionary conserved synteny
    • Santagati, F., Abe, K., Schmidt, V., Schmitt-John, T., Suzuki, M., Yamamura, K., and Imai, K. 2003. Identification of cis regulatory elements in the mouse Pax9/Nkx2-9 genomic region: Implication for evolutionary conserved synteny. Genetics 165: 235-242.
    • (2003) Genetics , vol.165 , pp. 235-242
    • Santagati, F.1    Abe, K.2    Schmidt, V.3    Schmitt-John, T.4    Suzuki, M.5    Yamamura, K.6    Imai, K.7
  • 37
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 38
    • 0035971496 scopus 로고    scopus 로고
    • Distinct roles of Jun : Fos and Jun : ATF dimers in oncogenesis
    • van Dam, H. and Castellazzi, M. 2001. Distinct roles of Jun : Fos and Jun : ATF dimers in oncogenesis. Oncogene 20: 2453-2464.
    • (2001) Oncogene , vol.20 , pp. 2453-2464
    • van Dam, H.1    Castellazzi, M.2
  • 39
    • 0035167130 scopus 로고    scopus 로고
    • GATA3 and kidney development: Why case reports are still important
    • Van Esch, H. and Bilous, R.W. 2001. GATA3 and kidney development: Why case reports are still important. Nephrol. Dial. Transplant 16: 2130-2132.
    • (2001) Nephrol. Dial. Transplant. , vol.16 , pp. 2130-2132
    • Van Esch, H.1    Bilous, R.W.2
  • 41
    • 0029960055 scopus 로고    scopus 로고
    • TRANSFAC: A database on transcription factors and their DNA binding sites
    • Wingender, E., Dietze, P., Karas, H., and Knuppel, R. 1996. TRANSFAC: A database on transcription factors and their DNA binding sites. Nucleic Acids Res. 24: 238-241.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 238-241
    • Wingender, E.1    Dietze, P.2    Karas, H.3    Knuppel, R.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.