-
1
-
-
33644876958
-
TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes
-
Matys, V., Kel-Margoulis, O. V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K. et al. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res., 34, D108-D110.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. D108-D110
-
-
Matys, V.1
Kel-Margoulis, O.V.2
Fricke, E.3
Liebich, I.4
Land, S.5
Barre-Dirrie, A.6
Reuter, I.7
Chekmenev, D.8
Krull, M.9
Hornischer, K.10
-
2
-
-
46049087782
-
The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
-
Wingender, E. (2008) The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Bioinformatics, 9, 326-333.
-
(2008)
Bioinformatics
, vol.9
, pp. 326-333
-
-
Wingender, E.1
-
3
-
-
84891808382
-
JASPAR 2014: An extensively expanded and updated open-access database of transcription factor binding profiles
-
Mathelier, A., Zhao, X., Zhang, A. W., Parcy, F., Worsley-Hunt, R., Arenillas, D. J., Buchman, S., Chen, C. Y., Chou, A., Ienasescu, H. et al. (2014) JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res., 42, D142-D147.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D142-D147
-
-
Mathelier, A.1
Zhao, X.2
Zhang, A.W.3
Parcy, F.4
Worsley-Hunt, R.5
Arenillas, D.J.6
Buchman, S.7
Chen, C.Y.8
Chou, A.9
Ienasescu, H.10
-
4
-
-
0032918558
-
Plant cis-acting regulatory DNA elements (PLACE) database: 1999
-
Higo, K., Ugawa, Y., Iwamoto, M. and Korenaga, T. (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res., 27, 297-300.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 297-300
-
-
Higo, K.1
Ugawa, Y.2
Iwamoto, M.3
Korenaga, T.4
-
5
-
-
84907908639
-
AthaMap web tools for the analysis of transcriptional and posttranscriptional regulation of gene expression in Arabidopsis thaliana
-
Hehl, R. and Bulow, L. (2014) AthaMap web tools for the analysis of transcriptional and posttranscriptional regulation of gene expression in Arabidopsis thaliana. Methods Mol. Biol., 1158, 139-156.
-
(2014)
Methods Mol. Biol.
, vol.1158
, pp. 139-156
-
-
Hehl, R.1
Bulow, L.2
-
6
-
-
0036085047
-
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences
-
Lescot, M., Dehais, P., Thijs, G., Marchal, K., Moreau, Y., de Peer, Y., Rouze, P. and Rombauts, S. (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res., 30, 325-327.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 325-327
-
-
Lescot, M.1
Dehais, P.2
Thijs, G.3
Marchal, K.4
Moreau, Y.5
De Peer, Y.6
Rouze, P.7
Rombauts, S.8
-
7
-
-
84862806491
-
AtPAN: An integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana
-
Chen, Y. A., Wen, Y. C. and Chang, W. C. (2012) AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana. BMC Genomics, 13, 85.
-
(2012)
BMC Genomics
, vol.13
, pp. 85
-
-
Chen, Y.A.1
Wen, Y.C.2
Chang, W.C.3
-
8
-
-
78651339097
-
AGRIS: The arabidopsis gene regulatory information server, an update
-
Yilmaz, A., Mejia-Guerra, M. K., Kurz, K., Liang, X., Welch, L. and Grotewold, E. (2011) AGRIS: the Arabidopsis Gene Regulatory Information Server, an update. Nucleic Acids Res., 39, D1118-D1122.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D1118-D1122
-
-
Yilmaz, A.1
Mejia-Guerra, M.K.2
Kurz, K.3
Liang, X.4
Welch, L.5
Grotewold, E.6
-
9
-
-
60549111213
-
PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups
-
Chang, W. C., Lee, T. Y., Huang, H. D., Huang, H. Y. and Pan, R. L. (2008) PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups. BMC Genomics, 9, 561.
-
(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
-
10
-
-
33750882505
-
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
-
Berger, M. F., Philippakis, A. A., Qureshi, A. M., He, F. S., Estep, P. W. 3rd and Bulyk, M. L. (2006) Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat. Biotechnol., 24, 1429-1435.
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 1429-1435
-
-
Berger, M.F.1
Philippakis, A.A.2
Qureshi, A.M.3
He, F.S.4
Estep, P.W.5
Bulyk, M.L.6
-
11
-
-
84946068207
-
UniPROBE, update 2015: New tools and content for the online database of protein-binding microarray data on protein-DNA interactions
-
Hume, M. A., Barrera, L. A., Gisselbrecht, S. S. and Bulyk, M. L. (2015) UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Res., 43, D117-D122.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D117-D122
-
-
Hume, M.A.1
Barrera, L.A.2
Gisselbrecht, S.S.3
Bulyk, M.L.4
-
12
-
-
79955036679
-
Experimental strategies for studying transcription factor-DNA binding specificities
-
Geertz, M. and Maerkl, S. J. (2010) Experimental strategies for studying transcription factor-DNA binding specificities. Brief. Funct. Genomic., 9, 362-373.
-
(2010)
Brief. Funct. Genomic.
, vol.9
, pp. 362-373
-
-
Geertz, M.1
Maerkl, S.J.2
-
13
-
-
84893861206
-
DNA-binding specificities of plant transcription factors and their potential to define target genes
-
Franco-Zorrilla, J. M., Lopez-Vidriero, I., Carrasco, J. L., Godoy, M., Vera, P. and Solano, R. (2014) DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc. Natl. Acad. Sci. U. S. A., 111, 2367-2372.
-
(2014)
Proc. Natl. Acad. Sci. U. S. A.
, vol.111
, pp. 2367-2372
-
-
Franco-Zorrilla, J.M.1
Lopez-Vidriero, I.2
Carrasco, J.L.3
Godoy, M.4
Vera, P.5
Solano, R.6
-
14
-
-
84907413210
-
Determination and inference of eukaryotic transcription factor sequence specificity
-
Weirauch, M. T., Yang, A., Albu, M., Cote, A. G., Montenegro-Montero, A., Drewe, P., Najafabadi, H. S., Lambert, S. A., Mann, I., Cook, K. et al. (2014) Determination and inference of eukaryotic transcription factor sequence specificity. Cell, 158, 1431-1443.
-
(2014)
Cell
, vol.158
, pp. 1431-1443
-
-
Weirauch, M.T.1
Yang, A.2
Albu, M.3
Cote, A.G.4
Montenegro-Montero, A.5
Drewe, P.6
Najafabadi, H.S.7
Lambert, S.A.8
Mann, I.9
Cook, K.10
-
15
-
-
84946069451
-
UniProt: A hub for protein information
-
The UniProt, Consortium. (2015) UniProt: a hub for protein information. Nucleic Acids Res., 43, D204-D212.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D204-D212
-
-
The UniProt, Consortium,1
-
16
-
-
0041853625
-
MATCHTM: A tool for searching transcription factor binding sites in DNA sequences
-
Kel, A. E., Gößling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O. V. and Wingender, E. (2003) MATCHTM: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res., 31, 3576-3579.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3576-3579
-
-
Kel, A.E.1
Gößling, E.2
Reuter, I.3
Cheremushkin, E.4
Kel-Margoulis, O.V.5
Wingender, E.6
-
17
-
-
0037208166
-
®: Transcriptional regulation, from patterns to profiles
-
®: transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 374-378
-
-
Matys, V.1
Fricke, E.2
Geffers, R.3
Gößling, E.4
Haubrock, M.5
Hehl, R.6
Hornischer, K.7
Karas, D.8
Kel, A.E.9
Kel-Margoulis, O.V.10
-
18
-
-
84945894356
-
EXPath: A database of comparative expression analysis inferring metabolic pathways for plants
-
Chien, C. H., Chow, C. N., Wu, N. Y., Chiang-Hsieh, Y. F., Hou, P. F. and Chang, W. C. (2015) EXPath: a database of comparative expression analysis inferring metabolic pathways for plants. BMC Genomics, 16(Suppl. 2), S6.
-
(2015)
BMC Genomics
, vol.16
, pp. S6
-
-
Chien, C.H.1
Chow, C.N.2
Wu, N.Y.3
Chiang-Hsieh, Y.F.4
Hou, P.F.5
Chang, W.C.6
-
19
-
-
34247200577
-
The AtGenExpress global stress expression data set: Protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses
-
Kilian, J., Whitehead, D., Horak, J., Wanke, D., Weinl, S., Batistic, O., D'Angelo, C., Bornberg-Bauer, E., Kudla, J. and Harter, K. (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J., 50, 347-363.
-
(2007)
Plant J.
, vol.50
, pp. 347-363
-
-
Kilian, J.1
Whitehead, D.2
Horak, J.3
Wanke, D.4
Weinl, S.5
Batistic, O.6
D'Angelo, C.7
Bornberg-Bauer, E.8
Kudla, J.9
Harter, K.10
-
20
-
-
84876576760
-
RiceXPro version 3.0: Expanding the informatics resource for rice transcriptome
-
Sato, Y., Takehisa, H., Kamatsuki, K., Minami, H., Namiki, N., Ikawa, H., Ohyanagi, H., Sugimoto, K., Antonio, B. A. and Nagamura, Y. (2013) RiceXPro version 3.0: expanding the informatics resource for rice transcriptome. Nucleic Acids Res., 41, D1206-D1213.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D1206-D1213
-
-
Sato, Y.1
Takehisa, H.2
Kamatsuki, K.3
Minami, H.4
Namiki, N.5
Ikawa, H.6
Ohyanagi, H.7
Sugimoto, K.8
Antonio, B.A.9
Nagamura, Y.10
-
21
-
-
84862234802
-
The Arabidopsis Information Resource (TAIR): Improved gene annotation and new tools
-
Lamesch, P., Berardini, T. Z., Li, D., Swarbreck, D., Wilks, C., Sasidharan, R., Muller, R., Dreher, K., Alexander, D. L., Garcia-Hernandez, M. et al. (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res., 40, D1202-D1210.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D1202-D1210
-
-
Lamesch, P.1
Berardini, T.Z.2
Li, D.3
Swarbreck, D.4
Wilks, C.5
Sasidharan, R.6
Muller, R.7
Dreher, K.8
Alexander, D.L.9
Garcia-Hernandez, M.10
-
22
-
-
84874236029
-
Rice Annotation Project Database (RAP-DB): An integrative and interactive database for rice genomics
-
Sakai, H., Lee, S. S., Tanaka, T., Numa, H., Kim, J., Kawahara, Y., Wakimoto, H., Yang, C. C., Iwamoto, M., Abe, T. et al. (2013) Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol., 54, e6.
-
(2013)
Plant Cell Physiol.
, vol.54
, pp. e6
-
-
Sakai, H.1
Lee, S.S.2
Tanaka, T.3
Numa, H.4
Kim, J.5
Kawahara, Y.6
Wakimoto, H.7
Yang, C.C.8
Iwamoto, M.9
Abe, T.10
-
23
-
-
80053515344
-
MaizeGDB: Curation and outreach go hand-in-hand
-
Schaeffer, M. L., Harper, L. C., Gardiner, J. M., Andorf, C. M., Campbell, D. A., Cannon, E. K., Sen, T. Z. and Lawrence, C. J. (2011) MaizeGDB: curation and outreach go hand-in-hand. Database: J. Biol. Databases Curation, bar022.
-
(2011)
Database: J. Biol. Databases Curation
, pp. bar022
-
-
Schaeffer, M.L.1
Harper, L.C.2
Gardiner, J.M.3
Andorf, C.M.4
Campbell, D.A.5
Cannon, E.K.6
Sen, T.Z.7
Lawrence, C.J.8
-
24
-
-
84912124204
-
A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana
-
Heyndrickx, K. S., Van de Velde, J., Wang, C., Weigel, D. and Vandepoele, K. (2014) A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana. Plant Cell, 26, 3894-3910.
-
(2014)
Plant Cell
, vol.26
, pp. 3894-3910
-
-
Heyndrickx, K.S.1
Van De Velde, J.2
Wang, C.3
Weigel, D.4
Vandepoele, K.5
-
25
-
-
34447506667
-
Quantifying similarity between motifs
-
Gupta, S., Stamatoyannopoulos, J. A., Bailey, T. L. and Noble, W. S. (2007) Quantifying similarity between motifs. Genome Biol., 8, R24.
-
(2007)
Genome Biol.
, vol.8
, pp. R24
-
-
Gupta, S.1
Stamatoyannopoulos, J.A.2
Bailey, T.L.3
Noble, W.S.4
-
26
-
-
84941145210
-
The BioGRID interaction database: 2015 update
-
Chatr-Aryamontri, A., Breitkreutz, B. J., Oughtred, R., Boucher, L., Heinicke, S., Chen, D., Stark, C., Breitkreutz, A., Kolas, N., O'Donnell, L. et al. (2015) The BioGRID interaction database: 2015 update. Nucleic Acids Res., 43, D470-D478.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D470-D478
-
-
Chatr-Aryamontri, A.1
Breitkreutz, B.J.2
Oughtred, R.3
Boucher, L.4
Heinicke, S.5
Chen, D.6
Stark, C.7
Breitkreutz, A.8
Kolas, N.9
O'Donnell, L.10
-
27
-
-
84860918589
-
MINT, the molecular interaction database: 2012 update
-
Licata, L., Briganti, L., Peluso, D., Perfetto, L., Iannuccelli, M., Galeota, E., Sacco, F., Palma, A., Nardozza, A. P., Santonico, E. et al. (2012) MINT, the molecular interaction database: 2012 update. Nucleic Acids Res., 40, D857-D861.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D857-D861
-
-
Licata, L.1
Briganti, L.2
Peluso, D.3
Perfetto, L.4
Iannuccelli, M.5
Galeota, E.6
Sacco, F.7
Palma, A.8
Nardozza, A.P.9
Santonico, E.10
-
28
-
-
78651323089
-
PAIR: The predicted Arabidopsis interactome resource
-
Lin, M., Shen, X. and Chen, X. (2011) PAIR: the predicted Arabidopsis interactome resource. Nucleic Acids Res., 39, D1134-D1140.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D1134-D1140
-
-
Lin, M.1
Shen, X.2
Chen, X.3
-
29
-
-
77956548953
-
CytoscapeWeb: An interactive web-based network browser
-
Lopes, C. T., Franz, M., Kazi, F., Donaldson, S. L., Morris, Q. and Bader, G. D. (2010) CytoscapeWeb: an interactive web-based network browser. Bioinformatics, 26, 2347-2348.
-
(2010)
Bioinformatics
, vol.26
, pp. 2347-2348
-
-
Lopes, C.T.1
Franz, M.2
Kazi, F.3
Donaldson, S.L.4
Morris, Q.5
Bader, G.D.6
-
30
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
31
-
-
84872436186
-
Plant responses to stresses: Role of ascorbate peroxidase in the antioxidant protection
-
Caverzan, A., Passaia, G., Rosa, S. B., Ribeiro, C. W., Lazzarotto, F. and Margis-Pinheiro, M. (2012) Plant responses to stresses: Role of ascorbate peroxidase in the antioxidant protection. Genet. Mol. Biol., 35, 1011-1019.
-
(2012)
Genet. Mol. Biol.
, vol.35
, pp. 1011-1019
-
-
Caverzan, A.1
Passaia, G.2
Rosa, S.B.3
Ribeiro, C.W.4
Lazzarotto, F.5
Margis-Pinheiro, M.6
-
32
-
-
33646346645
-
The heat stress transcription factor HsfA2 serves as a regulatory amplifier of a subset of genes in the heat stress response in Arabidopsis
-
Schramm, F., Ganguli, A., Kiehlmann, E., Englich, G., Walch, D. and von Koskull-Doring, P. (2006) The heat stress transcription factor HsfA2 serves as a regulatory amplifier of a subset of genes in the heat stress response in Arabidopsis. Plant Mol. Biol., 60, 759-772.
-
(2006)
Plant Mol. Biol.
, vol.60
, pp. 759-772
-
-
Schramm, F.1
Ganguli, A.2
Kiehlmann, E.3
Englich, G.4
Walch, D.5
Von Koskull-Doring, P.6
-
33
-
-
0142060793
-
The novel MYB protein EARLY-PHYTOCHROME-RESPONSIVE1 is a component of a slave circadian oscillator in Arabidopsis
-
Kuno, N., Moller, S. G., Shinomura, T., Xu, X., Chua, N. H. and Furuya, M. (2003) The novel MYB protein EARLY-PHYTOCHROME-RESPONSIVE1 is a component of a slave circadian oscillator in Arabidopsis. Plant Cell, 15, 2476-2488.
-
(2003)
Plant Cell
, vol.15
, pp. 2476-2488
-
-
Kuno, N.1
Moller, S.G.2
Shinomura, T.3
Xu, X.4
Chua, N.H.5
Furuya, M.6
-
34
-
-
68249143317
-
The role of WRKY transcription factors in plant immunity
-
Pandey, S. P. and Somssich, I. E. (2009) The role of WRKY transcription factors in plant immunity. Plant Physiol., 150, 1648-1655.
-
(2009)
Plant Physiol.
, vol.150
, pp. 1648-1655
-
-
Pandey, S.P.1
Somssich, I.E.2
-
35
-
-
33845736874
-
The transcription factors WRKY11 and WRKY17 act as negative regulators of basal resistance in Arabidopsis thaliana
-
Journot-Catalino, N., Somssich, I. E., Roby, D. and Kroj, T. (2006) The transcription factors WRKY11 and WRKY17 act as negative regulators of basal resistance in Arabidopsis thaliana. Plant Cell, 18, 3289-3302.
-
(2006)
Plant Cell
, vol.18
, pp. 3289-3302
-
-
Journot-Catalino, N.1
Somssich, I.E.2
Roby, D.3
Kroj, T.4
|