-
1
-
-
0036273511
-
Cell signaling during cold, drought, and salt stress
-
Xiong L, Schumaker KS, Zhu JK, (2002) Cell signaling during cold, drought, and salt stress. Plant Cell 14: S165-S183.
-
(2002)
Plant Cell
, vol.14
-
-
Xiong, L.1
Schumaker, K.S.2
Zhu, J.K.3
-
2
-
-
33846798370
-
Gene networks involved in drought stress response and tolerance
-
Shinozaki K, Yamaguchi-Shinozaki K, (2007) Gene networks involved in drought stress response and tolerance. J Exp Bot 58: 221-227.
-
(2007)
J Exp Bot
, vol.58
, pp. 221-227
-
-
Shinozaki, K.1
Yamaguchi-Shinozaki, K.2
-
3
-
-
0742305866
-
Network biology: understanding the cell's functional organization
-
Barabasi AL, Oltvai ZN, (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101-113.
-
(2004)
Nat Rev Genet
, vol.5
, pp. 101-113
-
-
Barabasi, A.L.1
Oltvai, Z.N.2
-
4
-
-
70449657085
-
STARNET 2: a Web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data
-
Jupiter D, Chen H, VanBuren V, (2009) STARNET 2: a Web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data. BMC Bioinformatics 10: 332.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 332
-
-
Jupiter, D.1
Chen, H.2
VanBuren, V.3
-
5
-
-
70349215646
-
RiceArrayNet: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice
-
Lee TH, Kim YK, Pham TT, Song SI, Kim JK, et al. (2009) RiceArrayNet: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice. Plant Physiol 151: 16-33.
-
(2009)
Plant Physiol
, vol.151
, pp. 16-33
-
-
Lee, T.H.1
Kim, Y.K.2
Pham, T.T.3
Song, S.I.4
Kim, J.K.5
-
6
-
-
24744468755
-
From single genes to co-expression networks: extracting knowledge from barley functional genomics
-
Faccioli P, Provero P, Herrmann C, Stanca AM, Morcia C, et al. (2005) From single genes to co-expression networks: extracting knowledge from barley functional genomics. Plant Mol Biol 58: 739-750.
-
(2005)
Plant Mol Biol
, vol.58
, pp. 739-750
-
-
Faccioli, P.1
Provero, P.2
Herrmann, C.3
Stanca, A.M.4
Morcia, C.5
-
7
-
-
35948931439
-
An Arabidopsis gene network based on the graphical Gaussian model
-
Ma S, Gong Q, Bohnert HJ, (2007) An Arabidopsis gene network based on the graphical Gaussian model. Genome Res 17: 1614-1625.
-
(2007)
Genome Res
, vol.17
, pp. 1614-1625
-
-
Ma, S.1
Gong, Q.2
Bohnert, H.J.3
-
8
-
-
77956679288
-
Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network
-
Atias O, Chor B, Chamovitz DA, (2009) Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network. BMC Syst Biol 3: 86.
-
(2009)
BMC Syst Biol
, vol.3
, pp. 86
-
-
Atias, O.1
Chor, B.2
Chamovitz, D.A.3
-
9
-
-
71749094192
-
Arabidopsis gene co-expression network and its functional modules
-
Mao L, Van Hemert JL, Dash S, Dickerson JA, (2009) Arabidopsis gene co-expression network and its functional modules. BMC Bioinformatics 10: 346.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 346
-
-
Mao, L.1
van Hemert, J.L.2
Dash, S.3
Dickerson, J.A.4
-
10
-
-
51549093662
-
CressExpress: a tool for large-scale mining of expression data from Arabidopsis
-
Srinivasasainagendra V, Page GP, Mehta T, Coulibaly I, Loraine AE, (2008) CressExpress: a tool for large-scale mining of expression data from Arabidopsis. Plant Physiol 147: 1004-1016.
-
(2008)
Plant Physiol
, vol.147
, pp. 1004-1016
-
-
Srinivasasainagendra, V.1
Page, G.P.2
Mehta, T.3
Coulibaly, I.4
Loraine, A.E.5
-
11
-
-
58149197587
-
ATTED-II provides coexpressed gene networks for Arabidopsis
-
Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K, (2009) ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Res 37: D987-D991.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Obayashi, T.1
Hayashi, S.2
Saeki, M.3
Ohta, H.4
Kinoshita, K.5
-
12
-
-
77956674928
-
The association of multiple interacting genes with specific phenotypes in rice using gene coexpression networks
-
Ficklin SP, Luo F, Feltus FA, (2010) The association of multiple interacting genes with specific phenotypes in rice using gene coexpression networks. Plant Physiol 154: 13-24.
-
(2010)
Plant Physiol
, vol.154
, pp. 13-24
-
-
Ficklin, S.P.1
Luo, F.2
Feltus, F.A.3
-
13
-
-
76349125292
-
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana
-
Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY, (2010) Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat Biotechnol 28: 149-156.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 149-156
-
-
Lee, I.1
Ambaru, B.2
Thakkar, P.3
Marcotte, E.M.4
Rhee, S.Y.5
-
14
-
-
73249138596
-
Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm
-
Mutwil M, Usadel B, Schutte M, Loraine A, Ebenhoh O, et al. (2010) Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm. Plant Physiol 152: 29-43.
-
(2010)
Plant Physiol
, vol.152
, pp. 29-43
-
-
Mutwil, M.1
Usadel, B.2
Schutte, M.3
Loraine, A.4
Ebenhoh, O.5
-
15
-
-
34249697574
-
Approaches for extracting practical information from gene co-expression networks in plant biology
-
Aoki K, Ogata Y, Shibata D, (2007) Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol 48: 381-390.
-
(2007)
Plant Cell Physiol
, vol.48
, pp. 381-390
-
-
Aoki, K.1
Ogata, Y.2
Shibata, D.3
-
16
-
-
61849113253
-
Graph clustering via a discrete uncoupling process
-
Dongen SV, (2008) Graph clustering via a discrete uncoupling process. SIAM J on Matrix Analysis and Applications 30: 121-141.
-
(2008)
SIAM J on Matrix Analysis and Applications
, vol.30
, pp. 121-141
-
-
Dongen, S.V.1
-
17
-
-
23944458138
-
A general framework for weighted gene co-expression network analysis
-
Zhang B, Horvath S, (2005) A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 4: Article17.
-
(2005)
Stat Appl Genet Mol Biol
, vol.4
-
-
Zhang, B.1
Horvath, S.2
-
18
-
-
0034069495
-
Gene ontology: tool for the unification of biology
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. Nat Genet 25: 25-29.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
-
20
-
-
0034028259
-
Molecular responses to dehydration and low temperature: differences and cross-talk between two stress signaling pathways
-
Shinozaki K, Yamaguchi-Shinozaki K, (2000) Molecular responses to dehydration and low temperature: differences and cross-talk between two stress signaling pathways. Curr Opin Plant Biol 3: 217-223.
-
(2000)
Curr Opin Plant Biol
, vol.3
, pp. 217-223
-
-
Shinozaki, K.1
Yamaguchi-Shinozaki, K.2
-
21
-
-
33846067713
-
Genome-scale identification and analysis of LEA genes in rice (Oryza sativa L.)
-
Wang X, Zhu H, Jin G, Liu H, Wu W, et al. (2007) Genome-scale identification and analysis of LEA genes in rice (Oryza sativa L.). Plant Sci 172: 414-420.
-
(2007)
Plant Sci
, vol.172
, pp. 414-420
-
-
Wang, X.1
Zhu, H.2
Jin, G.3
Liu, H.4
Wu, W.5
-
22
-
-
33646932116
-
Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture
-
Li L, Wang X, Xia M, Stolc V, Su N, et al. (2005) Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. Genome Biol 6: R52.
-
(2005)
Genome Biol
, vol.6
-
-
Li, L.1
Wang, X.2
Xia, M.3
Stolc, V.4
Su, N.5
-
23
-
-
24944497900
-
A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription
-
Jiao Y, Jia P, Wang X, Su N, Yu S, et al. (2005) A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription. Plant Cell 17: 1641-1657.
-
(2005)
Plant Cell
, vol.17
, pp. 1641-1657
-
-
Jiao, Y.1
Jia, P.2
Wang, X.3
Su, N.4
Yu, S.5
-
24
-
-
84856599882
-
Q-TARO:QTL Annotation Rice Online Database
-
Yonemaru J, Yamamoto T, Fukuoka S, Uga Y, Hori K, et al. (2010) Q-TARO:QTL Annotation Rice Online Database. Rice 3: 194-203.
-
(2010)
Rice
, vol.3
, pp. 194-203
-
-
Yonemaru, J.1
Yamamoto, T.2
Fukuoka, S.3
Uga, Y.4
Hori, K.5
-
25
-
-
0033787106
-
Mapping QTLs for root traits in a recombinant inbred population from two indica ecotypes in rice
-
Ali ML, Pathan MS, Zhang J, Bai G, Sarkarung S, et al. (2000) Mapping QTLs for root traits in a recombinant inbred population from two indica ecotypes in rice. Theor Appl Genet 101: 756-766.
-
(2000)
Theor Appl Genet
, vol.101
, pp. 756-766
-
-
Ali, M.L.1
Pathan, M.S.2
Zhang, J.3
Bai, G.4
Sarkarung, S.5
-
26
-
-
26444589213
-
Genetic analysis for drought resistance of rice at reproductive stage in field with different types of soil
-
Yue B, Xiong L, Xue W, Xing Y, Luo L, et al. (2005) Genetic analysis for drought resistance of rice at reproductive stage in field with different types of soil. Theor Appl Genet 111: 1127-1136.
-
(2005)
Theor Appl Genet
, vol.111
, pp. 1127-1136
-
-
Yue, B.1
Xiong, L.2
Xue, W.3
Xing, Y.4
Luo, L.5
-
27
-
-
0033212943
-
A proline-, threonine-, and glycine-rich protein down-regulated by drought is localized in the cell wall of xylem elements
-
Harrak H, Chamberland H, Plante M, Bellemare G, Lafontaine JG, et al. (1999) A proline-, threonine-, and glycine-rich protein down-regulated by drought is localized in the cell wall of xylem elements. Plant Physiol 121: 557-564.
-
(1999)
Plant Physiol
, vol.121
, pp. 557-564
-
-
Harrak, H.1
Chamberland, H.2
Plante, M.3
Bellemare, G.4
Lafontaine, J.G.5
-
28
-
-
77649168721
-
A general co-expression network-based approach to gene expression analysis: comparison and applications
-
Ruan J, Dean AK, Zhang W, (2010) A general co-expression network-based approach to gene expression analysis: comparison and applications. BMC Syst Biol 4: 8.
-
(2010)
BMC Syst Biol
, vol.4
, pp. 8
-
-
Ruan, J.1
Dean, A.K.2
Zhang, W.3
-
29
-
-
59449095428
-
Identification of OsbZIP72 as a positive regulator of ABA response and drought tolerance in rice
-
Lu G, Gao C, Zheng X, Han B, (2009) Identification of OsbZIP72 as a positive regulator of ABA response and drought tolerance in rice. Planta 229: 605-615.
-
(2009)
Planta
, vol.229
, pp. 605-615
-
-
Lu, G.1
Gao, C.2
Zheng, X.3
Han, B.4
-
30
-
-
57749087852
-
Characterization of OsbZIP23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice
-
Xiang Y, Tang N, Du H, Ye H, Xiong L, (2008) Characterization of OsbZIP23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice. Plant Physiol 148: 1938-1952.
-
(2008)
Plant Physiol
, vol.148
, pp. 1938-1952
-
-
Xiang, Y.1
Tang, N.2
Du, H.3
Ye, H.4
Xiong, L.5
-
31
-
-
67650175458
-
Overexpression of the transcription factor AP37 in rice improves grain yield under drought conditions
-
Oh SJ, Kim YS, Kwon CW, Park HK, Jeong JS, et al. (2009) Overexpression of the transcription factor AP37 in rice improves grain yield under drought conditions. Plant Physiol 150: 1368-1379.
-
(2009)
Plant Physiol
, vol.150
, pp. 1368-1379
-
-
Oh, S.J.1
Kim, Y.S.2
Kwon, C.W.3
Park, H.K.4
Jeong, J.S.5
-
32
-
-
34249819663
-
F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress
-
Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, et al. (2007) F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 143: 1467-1483.
-
(2007)
Plant Physiol
, vol.143
, pp. 1467-1483
-
-
Jain, M.1
Nijhawan, A.2
Arora, R.3
Agarwal, P.4
Ray, S.5
-
33
-
-
79952299493
-
Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance
-
Lenka SK, Katiyar A, Chinnusamy V, Bansal KC, (2011) Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance. Plant Biotechnol J 9: 315-327.
-
(2011)
Plant Biotechnol J
, vol.9
, pp. 315-327
-
-
Lenka, S.K.1
Katiyar, A.2
Chinnusamy, V.3
Bansal, K.C.4
-
34
-
-
0033592931
-
A bZIP factor, TRAB1, interacts with VP1 and mediates abscisic acid-induced transcription
-
Hobo T, Kowyama Y, Hattori T, (1999) A bZIP factor, TRAB1, interacts with VP1 and mediates abscisic acid-induced transcription. Proc Natl Acad Sci USA 96: 15348-15353.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 15348-15353
-
-
Hobo, T.1
Kowyama, Y.2
Hattori, T.3
-
35
-
-
0034695679
-
ABFs, a family of ABA-responsive element binding factors
-
Choi HI, Hong JH, Ha JO, Kang JY, Kim SY, (2000) ABFs, a family of ABA-responsive element binding factors. J Biol Chem 275: 1723-1730.
-
(2000)
J Biol Chem
, vol.275
, pp. 1723-1730
-
-
Choi, H.I.1
Hong, J.H.2
Ha, J.O.3
Kang, J.Y.4
Kim, S.Y.5
-
36
-
-
40949165379
-
A bZIP transcription factor, OsABI5, is involved in rice fertility and stress tolerance
-
Zou M, Guan Y, Ren H, Zhang F, Chen F, (2008) A bZIP transcription factor, OsABI5, is involved in rice fertility and stress tolerance. Plant Mol Biol 66: 675-683.
-
(2008)
Plant Mol Biol
, vol.66
, pp. 675-683
-
-
Zou, M.1
Guan, Y.2
Ren, H.3
Zhang, F.4
Chen, F.5
-
37
-
-
79959898336
-
ABA-mediated transcriptional regulation in response to osmotic stress in plants
-
Fujita Y, Fujita M, Shinozaki K, Yamaguchi-Shinozaki K, (2011) ABA-mediated transcriptional regulation in response to osmotic stress in plants. J Plant Res 124: 509-525.
-
(2011)
J Plant Res
, vol.124
, pp. 509-525
-
-
Fujita, Y.1
Fujita, M.2
Shinozaki, K.3
Yamaguchi-Shinozaki, K.4
-
38
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
Bolstad BM, Irizarry RA, Astrand M, Speed TP, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
-
(2003)
Bioinformatics
, vol.19
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
39
-
-
33846101405
-
The TIGR Rice Genome Annotation Resource: improvements and new features
-
Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, et al. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35: D883-D887.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Ouyang, S.1
Zhu, W.2
Hamilton, J.3
Lin, H.4
Campbell, M.5
-
40
-
-
38449101120
-
Integration of biological networks and gene expression data using Cytoscape
-
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2: 2366-2382.
-
(2007)
Nat Protoc
, vol.2
, pp. 2366-2382
-
-
Cline, M.S.1
Smoot, M.2
Cerami, E.3
Kuchinsky, A.4
Landys, N.5
-
41
-
-
77954299992
-
agriGO: a GO analysis toolkit for the agricultural community
-
Du Z, Zhou X, Ling Y, Zhang Z, Su Z, (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38: W64-70.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Du, Z.1
Zhou, X.2
Ling, Y.3
Zhang, Z.4
Su, Z.5
-
42
-
-
0034628901
-
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
-
Hughes JD, Estep PW, Tavazoie S, Church GM, (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 296: 1205-1214.
-
(2000)
J Mol Biol
, vol.296
, pp. 1205-1214
-
-
Hughes, J.D.1
Estep, P.W.2
Tavazoie, S.3
Church, G.M.4
-
43
-
-
0032918558
-
Plant cis-acting regulatory DNA elements (PLACE) database: 1999
-
Higo K, Ugawa Y, Iwamoto M, 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
-
44
-
-
33646907417
-
AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks
-
Palaniswamy SK, James S, Sun H, Lamb RS, Davuluri RV, et al. (2006) AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks. Plant Physiol 40: 818-829.
-
(2006)
Plant Physiol
, vol.40
, pp. 818-829
-
-
Palaniswamy, S.K.1
James, S.2
Sun, H.3
Lamb, R.S.4
Davuluri, R.V.5
|