메뉴 건너뛰기




Volumn 13, Issue 1, 2012, Pages

AtPAN: An integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

EID: 84862806491     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-85     Document Type: Article
Times cited : (19)

References (37)
  • 1
    • 0036085047 scopus 로고    scopus 로고
    • PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences
    • 10.1093/nar/30.1.325, 99092, 11752327
    • Lescot M, Dehais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouze P, Rombauts S. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 2002, 30(1):325-327. 10.1093/nar/30.1.325, 99092, 11752327.
    • (2002) Nucleic Acids Res , vol.30 , Issue.1 , pp. 325-327
    • Lescot, M.1    Dehais, P.2    Thijs, G.3    Marchal, K.4    Moreau, Y.5    Van de Peer, Y.6    Rouze, P.7    Rombauts, S.8
  • 2
    • 79953231729 scopus 로고    scopus 로고
    • AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana
    • Bulow L, Brill Y, Hehl R. AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana. Database (Oxford) 2010, 2010:baq034.
    • (2010) Database (Oxford) , vol.2010
    • Bulow, L.1    Brill, Y.2    Hehl, R.3
  • 3
    • 58149200922 scopus 로고    scopus 로고
    • AthaMap, integrating transcriptional and post-transcriptional data
    • 10.1093/nar/gkn709, 2686474, 18842622, Database
    • Bulow L, Engelmann S, Schindler M, Hehl R. AthaMap, integrating transcriptional and post-transcriptional data. Nucleic Acids Res 2009, 37(Database):D983-986. 10.1093/nar/gkn709, 2686474, 18842622.
    • (2009) Nucleic Acids Res , vol.37
    • Bulow, L.1    Engelmann, S.2    Schindler, M.3    Hehl, R.4
  • 4
    • 60549111213 scopus 로고    scopus 로고
    • PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups
    • 10.1186/1471-2164-9-561, 2633311, 19036138
    • Chang WC, Lee TY, Huang HD, Huang HY, Pan RL. PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups. BMC Genomics 2008, 9:561. 10.1186/1471-2164-9-561, 2633311, 19036138.
    • (2008) BMC Genomics , vol.9 , pp. 561
    • Chang, W.C.1    Lee, T.Y.2    Huang, H.D.3    Huang, H.Y.4    Pan, R.L.5
  • 5
    • 78651339097 scopus 로고    scopus 로고
    • AGRIS: the Arabidopsis Gene Regulatory Information Server, an update
    • 10.1093/nar/gkq1120, 3013708, 21059685, Database
    • Yilmaz A, Mejia-Guerra MK, Kurz K, Liang X, Welch L, Grotewold E. AGRIS: the Arabidopsis Gene Regulatory Information Server, an update. Nucleic Acids Res 2011, 39(Database):D1118-1122. 10.1093/nar/gkq1120, 3013708, 21059685.
    • (2011) Nucleic Acids Res , vol.39
    • Yilmaz, A.1    Mejia-Guerra, M.K.2    Kurz, K.3    Liang, X.4    Welch, L.5    Grotewold, E.6
  • 6
    • 77954269901 scopus 로고    scopus 로고
    • The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
    • 10.1093/nar/gkq537, 2896186, 20576703, Web Server
    • Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res 2010, 38(Web Server):W214-220. 10.1093/nar/gkq537, 2896186, 20576703.
    • (2010) Nucleic Acids Res , vol.38
    • Warde-Farley, D.1    Donaldson, S.L.2    Comes, O.3    Zuberi, K.4    Badrawi, R.5    Chao, P.6    Franz, M.7    Grouios, C.8    Kazi, F.9    Lopes, C.T.10
  • 7
    • 77951879057 scopus 로고    scopus 로고
    • Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways
    • 10.1007/s10265-010-0333-6, 20383554
    • Obayashi T, Kinoshita K. Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways. J Plant Res 2010, 123(3):311-319. 10.1007/s10265-010-0333-6, 20383554.
    • (2010) J Plant Res , vol.123 , Issue.3 , pp. 311-319
    • Obayashi, T.1    Kinoshita, K.2
  • 8
    • 66649122827 scopus 로고    scopus 로고
    • Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks
    • 10.1104/pp.109.136028, 2689962, 19357200
    • Vandepoele K, Quimbaya M, Casneuf T, De Veylder L, Van de Peer Y. Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks. Plant Physiol 2009, 150(2):535-546. 10.1104/pp.109.136028, 2689962, 19357200.
    • (2009) Plant Physiol , vol.150 , Issue.2 , pp. 535-546
    • Vandepoele, K.1    Quimbaya, M.2    Casneuf, T.3    De Veylder, L.4    Van de Peer, Y.5
  • 12
    • 78651323089 scopus 로고    scopus 로고
    • PAIR: the predicted Arabidopsis interactome resource
    • 10.1093/nar/gkq938, 3013789, 20952401, Database
    • Lin M, Shen X, Chen X. PAIR: the predicted Arabidopsis interactome resource. Nucleic Acids Res 2011, 39(Database):D1134-1140. 10.1093/nar/gkq938, 3013789, 20952401.
    • (2011) Nucleic Acids Res , vol.39
    • Lin, M.1    Shen, X.2    Chen, X.3
  • 13
    • 78049485689 scopus 로고    scopus 로고
    • Combinatorial regulation of transcription factors and microRNAs
    • 10.1186/1752-0509-4-150, 3225826, 21059252
    • Su N, Wang Y, Qian M, Deng M. Combinatorial regulation of transcription factors and microRNAs. BMC Syst Biol 2010, 4:150. 10.1186/1752-0509-4-150, 3225826, 21059252.
    • (2010) BMC Syst Biol , vol.4 , pp. 150
    • Su, N.1    Wang, Y.2    Qian, M.3    Deng, M.4
  • 15
    • 38549116678 scopus 로고    scopus 로고
    • Ppdb: a plant promoter database
    • 2238996, 17947329, Database
    • Yamamoto YY, Obokata J. ppdb: a plant promoter database. Nucleic Acids Res 2008, 36(Database):D977-981. 2238996, 17947329.
    • (2008) Nucleic Acids Res , vol.36
    • Yamamoto, Y.Y.1    Obokata, J.2
  • 16
    • 78651317908 scopus 로고    scopus 로고
    • Entrez Gene: gene-centered information at NCBI
    • 10.1093/nar/gkq1237, 3013746, 21115458, Database
    • Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 2011, 39(Database):D52-57. 10.1093/nar/gkq1237, 3013746, 21115458.
    • (2011) Nucleic Acids Res , vol.39
    • Maglott, D.1    Ostell, J.2    Pruitt, K.D.3    Tatusova, T.4
  • 18
    • 0032918558 scopus 로고    scopus 로고
    • Plant cis-acting regulatory DNA elements (PLACE) database: 1999
    • 10.1093/nar/27.1.297, 148163, 9847208
    • Higo K, Ugawa Y, Iwamoto M, Korenaga T. Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 1999, 27(1):297-300. 10.1093/nar/27.1.297, 148163, 9847208.
    • (1999) Nucleic Acids Res , vol.27 , Issue.1 , pp. 297-300
    • Higo, K.1    Ugawa, Y.2    Iwamoto, M.3    Korenaga, T.4
  • 21
    • 79951562208 scopus 로고    scopus 로고
    • ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants
    • 10.1093/pcp/pcq203, 3037081, 21217125
    • Obayashi T, Nishida K, Kasahara K, Kinoshita K. ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. Plant Cell Physiol 2011, 52(2):213-219. 10.1093/pcp/pcq203, 3037081, 21217125.
    • (2011) Plant Cell Physiol , vol.52 , Issue.2 , pp. 213-219
    • Obayashi, T.1    Nishida, K.2    Kasahara, K.3    Kinoshita, K.4
  • 22
    • 0032964297 scopus 로고    scopus 로고
    • BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences
    • 10.1111/j.1574-6968.1999.tb13575.x, 10339815
    • Tatusova TA, Madden TL. BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 1999, 174(2):247-250. 10.1111/j.1574-6968.1999.tb13575.x, 10339815.
    • (1999) FEMS Microbiol Lett , vol.174 , Issue.2 , pp. 247-250
    • Tatusova, T.A.1    Madden, T.L.2
  • 23
    • 79955925871 scopus 로고    scopus 로고
    • Using unsupervised patterns to extract gene regulation relationships for network construction
    • 10.1371/journal.pone.0019633, 3091867, 21573008
    • Tang YT, Li SJ, Kao HY, Tsai SJ, Wang HC. Using unsupervised patterns to extract gene regulation relationships for network construction. Plos One 2011, 6(5):e19633. 10.1371/journal.pone.0019633, 3091867, 21573008.
    • (2011) Plos One , vol.6 , Issue.5
    • Tang, Y.T.1    Li, S.J.2    Kao, H.Y.3    Tsai, S.J.4    Wang, H.C.5
  • 24
    • 9944223769 scopus 로고    scopus 로고
    • A computational approach to discover differential cooperation of regulatory sites in functionally related genes in yeast genome
    • Huang HD, Horng JT, Chang CH, Tsou TS, Hong JY, Liu BJ. A computational approach to discover differential cooperation of regulatory sites in functionally related genes in yeast genome. J Inf Sci Eng 2004, 20(6):1141-1159.
    • (2004) J Inf Sci Eng , vol.20 , Issue.6 , pp. 1141-1159
    • Huang, H.D.1    Horng, J.T.2    Chang, C.H.3    Tsou, T.S.4    Hong, J.Y.5    Liu, B.J.6
  • 25
    • 70549112091 scopus 로고    scopus 로고
    • Integrated omics approaches in plant systems biology
    • 10.1016/j.cbpa.2009.09.022, 19837627
    • Fukushima A, Kusano M, Redestig H, Arita M, Saito K. Integrated omics approaches in plant systems biology. Curr Opin Chem Biol 2009, 13(5-6):532-538. 10.1016/j.cbpa.2009.09.022, 19837627.
    • (2009) Curr Opin Chem Biol , vol.13 , Issue.5-6 , pp. 532-538
    • Fukushima, A.1    Kusano, M.2    Redestig, H.3    Arita, M.4    Saito, K.5
  • 26
    • 37849020436 scopus 로고    scopus 로고
    • Decoding genes with coexpression networks and metabolomics-'majority report by precogs'
    • 10.1016/j.tplants.2007.10.006, 18160330
    • Saito K, Hirai MY, Yonekura-Sakakibara K. Decoding genes with coexpression networks and metabolomics-'majority report by precogs'. Trends Plant Sci 2008, 13(1):36-43. 10.1016/j.tplants.2007.10.006, 18160330.
    • (2008) Trends Plant Sci , vol.13 , Issue.1 , pp. 36-43
    • Saito, K.1    Hirai, M.Y.2    Yonekura-Sakakibara, K.3
  • 27
    • 1842716859 scopus 로고    scopus 로고
    • A novel subgroup of bZIP proteins functions as transcriptional activators in hypoosmolarity-responsive expression of the ProDH gene in Arabidopsis
    • 10.1093/pcp/pch036, 15047879
    • Satoh R, Fujita Y, Nakashima K, Shinozaki K, Yamaguchi-Shinozaki K. A novel subgroup of bZIP proteins functions as transcriptional activators in hypoosmolarity-responsive expression of the ProDH gene in Arabidopsis. Plant Cell Physiol 2004, 45(3):309-317. 10.1093/pcp/pch036, 15047879.
    • (2004) Plant Cell Physiol , vol.45 , Issue.3 , pp. 309-317
    • Satoh, R.1    Fujita, Y.2    Nakashima, K.3    Shinozaki, K.4    Yamaguchi-Shinozaki, K.5
  • 28
    • 77958612353 scopus 로고    scopus 로고
    • Mechanisms independent of abscisic acid (ABA) or proline feedback have a predominant role in transcriptional regulation of proline metabolism during low water potential and stress recovery
    • 10.1111/j.1365-3040.2010.02188.x, 20545884
    • Sharma S, Verslues PE. Mechanisms independent of abscisic acid (ABA) or proline feedback have a predominant role in transcriptional regulation of proline metabolism during low water potential and stress recovery. Plant Cell Environ 2010, 33(11):1838-1851. 10.1111/j.1365-3040.2010.02188.x, 20545884.
    • (2010) Plant Cell Environ , vol.33 , Issue.11 , pp. 1838-1851
    • Sharma, S.1    Verslues, P.E.2
  • 30
    • 29344472132 scopus 로고    scopus 로고
    • Role of abscisic acid (ABA) and Arabidopsis thaliana ABA-insensitive loci in low water potential-induced ABA and proline accumulation
    • 10.1016/j.envexpbot.2005.05.002, 16339784
    • Verslues PE, Bray EA. Role of abscisic acid (ABA) and Arabidopsis thaliana ABA-insensitive loci in low water potential-induced ABA and proline accumulation. J Exp Bot 2006, 57(1):201-212. 10.1016/j.envexpbot.2005.05.002, 16339784.
    • (2006) J Exp Bot , vol.57 , Issue.1 , pp. 201-212
    • Verslues, P.E.1    Bray, E.A.2
  • 32
    • 34547727206 scopus 로고    scopus 로고
    • JAZ repressor proteins are targets of the SCF(COI1) complex during jasmonate signalling
    • 10.1038/nature05960, 17637677
    • Thines B, Katsir L, Melotto M, Niu Y, Mandaokar A, Liu G, Nomura K, He SY, Howe GA, Browse J. JAZ repressor proteins are targets of the SCF(COI1) complex during jasmonate signalling. Nature 2007, 448(7154):661-665. 10.1038/nature05960, 17637677.
    • (2007) Nature , vol.448 , Issue.7154 , pp. 661-665
    • Thines, B.1    Katsir, L.2    Melotto, M.3    Niu, Y.4    Mandaokar, A.5    Liu, G.6    Nomura, K.7    He, S.Y.8    Howe, G.A.9    Browse, J.10
  • 33
    • 23944502834 scopus 로고    scopus 로고
    • Jasmonate-responsive gene expression
    • Pauw B, Memelink J. Jasmonate-responsive gene expression. J Plant Growth Regul 2004, 23(3):200-210.
    • (2004) J Plant Growth Regul , vol.23 , Issue.3 , pp. 200-210
    • Pauw, B.1    Memelink, J.2
  • 34
    • 0033575710 scopus 로고    scopus 로고
    • A novel jasmonate- and elicitor-responsive element in the periwinkle secondary metabolite biosynthetic gene Str interacts with a jasmonate- and elicitor-inducible AP2-domain transcription factor, ORCA2
    • 10.1093/emboj/18.16.4455, 1171520, 10449411
    • Menke FL, Champion A, Kijne JW, Memelink J. A novel jasmonate- and elicitor-responsive element in the periwinkle secondary metabolite biosynthetic gene Str interacts with a jasmonate- and elicitor-inducible AP2-domain transcription factor, ORCA2. EMBO J 1999, 18(16):4455-4463. 10.1093/emboj/18.16.4455, 1171520, 10449411.
    • (1999) EMBO J , vol.18 , Issue.16 , pp. 4455-4463
    • Menke, F.L.1    Champion, A.2    Kijne, J.W.3    Memelink, J.4
  • 35
    • 0035121285 scopus 로고    scopus 로고
    • The jasmonate-inducible AP2/ERF-domain transcription factor ORCA3 activates gene expression via interaction with a jasmonate-responsive promoter element
    • 10.1046/j.1365-313x.2001.00932.x, 11169181
    • van der Fits L, Memelink J. The jasmonate-inducible AP2/ERF-domain transcription factor ORCA3 activates gene expression via interaction with a jasmonate-responsive promoter element. Plant J 2001, 25(1):43-53. 10.1046/j.1365-313x.2001.00932.x, 11169181.
    • (2001) Plant J , vol.25 , Issue.1 , pp. 43-53
    • van der Fits, L.1    Memelink, J.2
  • 36
    • 0037259469 scopus 로고    scopus 로고
    • ETHYLENE RESPONSE FACTOR1 integrates signals from ethylene and jasmonate pathways in plant defense
    • 10.1105/tpc.007468, 143489, 12509529
    • Lorenzo O, Piqueras R, Sanchez-Serrano JJ, Solano R. ETHYLENE RESPONSE FACTOR1 integrates signals from ethylene and jasmonate pathways in plant defense. Plant Cell 2003, 15(1):165-178. 10.1105/tpc.007468, 143489, 12509529.
    • (2003) Plant Cell , vol.15 , Issue.1 , pp. 165-178
    • Lorenzo, O.1    Piqueras, R.2    Sanchez-Serrano, J.J.3    Solano, R.4
  • 37
    • 0242628016 scopus 로고    scopus 로고
    • CrMYC1, a Catharanthus roseus elicitor- and jasmonate-responsive bHLH transcription factor that binds the G-box element of the strictosidine synthase gene promoter
    • 10.1093/jxb/erg275, 12966042
    • Chatel G, Montiel G, Pre M, Memelink J, Thiersault M, Saint-Pierre B, Doireau P, Gantet P. CrMYC1, a Catharanthus roseus elicitor- and jasmonate-responsive bHLH transcription factor that binds the G-box element of the strictosidine synthase gene promoter. J Exp Bot 2003, 54(392):2587-2588. 10.1093/jxb/erg275, 12966042.
    • (2003) J Exp Bot , vol.54 , Issue.392 , pp. 2587-2588
    • Chatel, G.1    Montiel, G.2    Pre, M.3    Memelink, J.4    Thiersault, M.5    Saint-Pierre, B.6    Doireau, P.7    Gantet, P.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.