[1] Chatterjee S, Kraus P, Lufkin T. A symphony of inner ear developmental control genes. BMC Genet, 2010, 11: 68.<\p>
[2] Brown AS, Epstein DJ. Otic ablation of smoothened re-veals direct and indirect requirements for Hedgehog sig-naling in inner ear development. Development, 2011, 138(18): 3967–3976.<\p>
[3] Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li WZ, Lopez R, McWilliam R, Soding J, Thompson JD, Higgins DG. Fast, scalable generation of high-quality pro-tein multiple sequence alignments using Clustal Omega. Mol Syst Biol, 2011, 7(1): 539.<\p>
[4] Prestridge DS. Predicting Pol II promoter sequences using transcription factor binding sites. J Mol Biol, 1995, 249(5): 923–932.<\p>
[5] Knudsen S. Promoter2.0: for the recognition of PolII promoter sequences. Bioinformatics, 1999, 15(5): 356– 361.<\p>
[6] Sandelin A, Wasserman WW, Lenhard B. ConSite: web- based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res, 2004, 32(Suppl. 2): W249– W252.<\p>
[7] Messeguer X, Escudero R, Farre D, Núñez O, Martinez J, Alba MM. PROMO: detection of known transcription regulatory elements using species-tailored searches. Bio-informatics, 2002, 18(2): 333–334.<\p>
[8] Farré D, Roset R, Huerta M, Adsuara JE, Rosello L, Albà MM, Messeguer X. Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN. Nucleic Acids Res, 2003, 31(13): 3651–3653.<\p>
[9] Frith MC, Hansen U, Weng ZP. Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics, 2001, 17(10): 878–889.<\p>
[10] Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res, 2010, 38(Database issue): D105–D110.<\p>
[11] Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A. JASPAR, the open access database of transcription factor-binding pro-files: new content and tools in the 2008 update. Nucleic Acids Res, 2008, 36(Database issue): D102–D106.<\p>
[12] 陈鸿飞, 王进科. 转录因子相关数据库. 遗传, 2010, 32(10): 1009–1017.<\p>
[13] Longabaugh WJR, Davidson EH, Bolouri H. Computa-tional representation of developmental genetic regulatory networks. Dev Biol, 2005, 283(1): 1–16.<\p>
[14] Longabaugh WJ, Davidson EH, Bolouri H. Visualization, documentation, analysis, and communication of large- scale gene regulatory networks. Biochim Biophys Acta, 2009, 1789(4): 363–374.<\p>
[15] Grocott T, Tambalo M, Streit A. The peripheral sensory nervous system in the vertebrate head: a gene regulatory perspective. Dev Biol, 2012, 370(1): 3–23.<\p>
[16] Sato S, Ikeda K, Shioi G, Ochi H, Ogino H, Yajima H, Kawakami K. Conserved expression of mouse Six1 in the pre-placodal region (PPR) and identification of an enhan-cer for the rostral PPR. Dev Biol, 2010, 344(1): 158–171. <\p>
[17] Christophorou NAD, Bailey AP, Hanson S, Streit A. Acti-vation of Six1 target genes is required for sensory placode formation. Dev Biol, 2009, 336(2): 327–336.<\p>
[18] Burton Q, Cole LK, Mulheisen M, Chang W, Wu DK. The role of Pax2 in mouse inner ear development. Dev Biol, 2004, 272(1): 161–175.<\p>
[19] Bouchard M, de Caprona D, Busslinger M, Xu PX, Fritzsch B. Pax2 and Pax8 cooperate in mouse inner ear morphogenesis and innervation. BMC Dev Biol, 2010, 10(1): 89.<\p>
[20] Kwon HJ, Bhat N, Sweet EM, Cornell RA, Riley BB. Identification of early requirements for preplacodal ecto-derm and sensory organ development. PLoS Genet, 2010, 6(9): e1001133.<\p>
[21] Pieper M, Ahrens K, Rink E, Peter A, Schlosser G. Dif-ferential distribution of competence for panplacodal and neural crest induction to non-neural and neural ectoderm. Development, 2012, 139(6): 1175–1187.<\p>
[22] Bricaud O, Collazo A. The transcription factor six1 inhib-its neuronal and promotes hair cell fate in the developing zebrafish (Danio rerio) inner ear. J Neurosci, 2006, 26(41): 10438–10451.<\p>
[23] Steventon B, Mayor R, Streit A. Mutual repression be-tween Gbx2 and Otx2 in sensory placodes reveals a gen-eral mechanism for ectodermal patterning. Dev Biol, 2012, 367(1): 55–65.<\p>
[24] Chung IH, Han J, Iwata JY, Chai Y. Msx1 and Dlx5 func-tion synergistically to regulate frontal bone development. Genesis, 2010, 48(11): 645–655.<\p>
[25] Han J, Mayo J, Xu X, Li J, Bringas P Jr, Maas RL, Rubenstein JL, Chai Y. Indirect modulation of Shh sig-naling by Dlx5 affects the oral-nasal patterning of palate and rescues cleft palate in Msx1-null mice. Development, 2009, 136(24): 4225–4233.<\p>
[26] Sajan SA, Rubenstein JL, Warchol ME, Lovett M. Identi-fication of direct downstream targets of Dlx5 during early inner ear development. Hum Mol Genet, 2011, 20(7): 1262–1273.<\p>
[27] Hagglund AC, Dahl L, Carlsson L. Lhx2 is required for patterning and expansion of a distinct progenitor cell population committed to eye development. PLoS ONE, 2011, 6(8): e23387.<\p>
[28] Muranishi Y, Terada K, Furukawa T. An essential role for Rax in retina and neuroendocrine system development. Dev Growth Differ, 2012, 54(3): 341–348.<\p>
[29] Sakurai Y, Kurokawa D, Kiyonari H, Kajikawa E, Suda Y, Aizawa S. Otx2 and Otx1 protect diencephalon and mes-encephalon from caudalization into metencephalon during early brain regionalization. Dev Biol, 2010, 347(2): 392– 403.<\p>
[30] Nishihara D, Yajima I, Tabata H, Nakai M, Tsukiji N, Katahira T, Takeda K, Shibahara S, Nakamura H, Yama-moto H. Otx2 is involved in the regional specification of the developing retinal pigment epithelium by preventing the expression of sox2 and fgf8, factors that induce neural retina differentiation. PLoS ONE, 2012, 7(11): e48879.<\p>
[31] Larsen KB, Lutterodt M, Rath MF, Møller M. Expression of the homeobox genes PAX6, OTX2, and OTX1 in the early human fetal retina. Int J Dev Neurosci, 2009, 27(5): 485–492.<\p>
[32] Markitantova YV, Avdonin PP, Grigoryan EN, Zinov'eva RD. Identification of the Pitx1 embryogenesis regulatory gene in a regenerating newt retina. Dokl Biol Sci, 2010, 435(1): 421–424.<\p>
[33] Liu Y, Semina EV. Pitx2 Deficiency results in abnormal ocular and craniofacial development in zebrafish. PLoS ONE, 2012, 7(1): e30896.<\p>
[34] Star EN, Zhu M, Shi Z, Liu H, Pashmforoush M, Sauve Y, Bruneau BG, Chow RL. Regulation of retinal interneuron subtype identity by the Iroquois homeobox gene Irx6. Development, 2012, 139(24): 4644–4655.<\p>
[35] Feng L, Eisenstat DD, Chiba S, Ishizaki Y, Gan L, Shi-basaki K. Brn-3b inhibits generation of amacrine cells by binding to and negatively regulating DLX1/2 in develop-ing retina. Neuroscience, 2011, 195: 9–20.<\p>
[36] Rath MF, Bailey MJ, Kim JS, Coon SL, Klein DC, Møller M. Developmental and daily expression of the Pax4 and Pax6 homeobox genes in the rat retina: localization of Pax4 in photoreceptor cells. J Neurochem, 2009, 108(1): 285–294.<\p>
[37] Shim S, Kwan KY, Li MF, Lefebvre V, Šestan N. Cis-regulatory control of corticospinal system develop-ment and evolution. Nature, 2012, 486(7401): 74–79.<\p>
[38] Niu WZ, Zou YH, Shen CC, Zhang CL. Activation of postnatal neural stem cells requires nuclear receptor TLX. J Neurosci, 2011, 31(39): 13816–13828.<\p>
[39] Guner-Ataman B, Paffett-Lugassy N, Adams MS, Nevis KR, Jahangiri L, Obregon P, Kikuchi K, Poss KD, Burns CE, Burns CG. Zebrafish second heart field development relies on progenitor specification in anterior lateral plate mesoderm and nkx2.5 function. Development, 2013, 140(6): 1353–1363.<\p>
[40] Star EN, Zhu MY, Shi ZW, Liu HQ, Pashmforoush M, Sauve Y, Bruneau BG, Chow RL. Regulation of retinal in-terneuron subtype identity by the Iroquois homeobox gene Irx6. Development, 2012, 139(24): 4644–4655.<\p>
[41] Quina LA, Kuramoto T, Luquetti DV, Cox TC, Serikawa T, Turner EE. Deletion of a conserved regulatory element required for Hmx1 expression in craniofacial mesenchyme in the dumbo rat: a newly identified cause of congeni-tal ear malformation. Dis Model Mech, 2012, 5(6): 812– 822.<\p>
[42] Feng Y, Xu QL. Pivotal role of hmx2 and hmx3 in zebraf-ish inner ear and lateral line development. Dev Biol, 2010, 339(2): 507–518.<\p>
[43] Masuda M, Dulon D, Pak K, Mullen LM, Li Y, Erkman L, Ryan AF. Regulation of POU4F3 gene expression in hair cells by 5' DNA in mice. Neuroscience, 2011, 197: 48–64.<\p>
[44] Nandi S, Ioshikhes I. Optimizing the GATA-3 position weight matrix to improve the identification of novel bind-ing sites. BMC Genomics, 2012, 13(1): 416.<\p>
[45] 侯琳, 钱敏平, 朱云平, 邓明华. 转录因子结合位点生物信息学研究进展. 遗传, 2009, 35(4): 365–373.<\p>
[46] Khan MAF, Soto-Jimenez LM, Howe T, Streit A, Sosinsky A, Stern CD. Computational tools and resources for pre-diction and analysis of gene regulatory regions in the chick genome. Genesis, 2013, 51(5): 311–324.<\p>
[47] Oh YM, Kim JK, Choi S, Yoo JY. Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices. Nucleic Acids Res, 2012, 40(5): e38.<\p>
[48] Hannenhalli S. Eukaryotic transcription factor binding sites-modeling and integrative search methods. Bioinfor-matics, 2008, 24(11): 1325–1331.<\p>
[49] Habib N, Wapinski I, Margalit H, Regev A, Friedman N. A functional selection model explains evolutionary robust-ness despite plasticity in regulatory networks. Mol Sys Biol, 2012, 8(1): 619.<\p>
[50] Whitfield TW, Wang J, Collins PJ, Partridge EC, Aldred SF, Trinklein ND, Myers RM, Weng ZP. Functional analy-sis of transcription factor binding sites in human promot-ers. Genome Biol, 2012, 13(9): R50.<\p>
[51] Simcha D, Price ND, Geman D. The limits of de novo DNA motif discovery. PloS ONE, 2012, 7(11): e47836.<\p>
[52] Nurse P, Hayles J. The cell in an era of systems biology. Cell, 2011, 144(6): 850–854.<\p>
[53] Cheong R, Rhee A, Wang CJ, Nemenman I, Levchenko A. Information transduction capacity of noisy biochemical signaling network. Science, 2011, 334(6054): 354–358.<\p>
[54] Lander AD. Pattern, growth, and control. Cell, 2011, 144(6): 955–969.<\p>
[55] Barabási AL, Gulbahce N, Loscalzo J. Network medicine: a network-based approach to human disease. Nat Rev Genet, 2011, 12(1): 56–68.<\p> |