-
1
-
-
33744805096
-
Development and implementation of an algorithm for detection of protein complexes in large interaction networks
-
Altaf-Ul-Amin M, Shinbo Y, Mihara K, Kurokawa K, Kanaya S (2006) Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics 7: 207
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 207
-
-
Altaf-Ul-Amin, M.1
Shinbo, Y.2
Mihara, K.3
Kurokawa, K.4
Kanaya, S.5
-
2
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (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
-
3
-
-
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
-
4
-
-
77956679288
-
Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network
-
AtiasO, Chor B, ChamovitzDA(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
-
5
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
Barabási 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
-
-
Barabási, A.L.1
Oltvai, Z.N.2
-
6
-
-
41149138077
-
Structural and functional genomics of tomato
-
Barone A, ChiusanoML, ErcolanoMR, Giuliano G, Grandillo S, Frusciante L (2008) Structural and functional genomics of tomato. Int J Plant Genomics 2008: 820274
-
(2008)
Int J Plant Genomics
, vol.2008
, pp. 820274
-
-
Barone, A.1
Chiusano, M.L.2
Ercolano, M.R.3
Giuliano, G.4
Grandillo, S.5
Frusciante, L.6
-
7
-
-
78651339534
-
NCBI GEO: Archive for functional genomics data sets-10 years on
-
Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, et al (2011) NCBI GEO: archive for functional genomics data sets-10 years on. Nucleic Acids Res 39: D1005-D1010
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Barrett, T.1
Troup, D.B.2
Wilhite, S.E.3
Ledoux, P.4
Evangelista, C.5
Kim, I.F.6
Tomashevsky, M.7
Marshall, K.A.8
Phillippy, K.H.9
Sherman, P.M.10
-
8
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57: 289-300
-
(1995)
J R Stat Soc B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
9
-
-
78651327629
-
The Sol Genomics Network (solgenomics. net): Growing tomatoes using Perl
-
Bombarely A, Menda N, Tecle IY, Buels RM, Strickler S, Fischer-York T, Pujar A, Leto J, Gosselin J, Mueller LA (2011) The Sol Genomics Network (solgenomics. net): growing tomatoes using Perl. Nucleic Acids Res 39: D1149-D1155
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Bombarely, A.1
Menda, N.2
Tecle, I.Y.3
Buels, R.M.4
Strickler, S.5
Fischer-York, T.6
Pujar, A.7
Leto, J.8
Gosselin, J.9
Mueller, L.A.10
-
11
-
-
77950537784
-
Source to sink: Regulation of carotenoid biosynthesis in plants
-
Cazzonelli CI, Pogson BJ (2010) Source to sink: regulation of carotenoid biosynthesis in plants. Trends Plant Sci 15: 266-274
-
(2010)
Trends Plant Sci
, vol.15
, pp. 266-274
-
-
Cazzonelli, C.I.1
Pogson, B.J.2
-
12
-
-
0031200962
-
A gene fusion at a homeobox locus: Alterations in leaf shape and implications for morphological evolution
-
Chen JJ, Janssen BJ, Williams A, Sinha N (1997) A gene fusion at a homeobox locus: alterations in leaf shape and implications for morphological evolution. Plant Cell 9: 1289-1304
-
(1997)
Plant Cell
, vol.9
, pp. 1289-1304
-
-
Chen, J.J.1
Janssen, B.J.2
Williams, A.3
Sinha, N.4
-
13
-
-
77954311470
-
Differential co-expression framework to quantify goodness of biclusters and compare biclustering algorithms
-
Chia BK, Karuturi RK (2010) Differential co-expression framework to quantify goodness of biclusters and compare biclustering algorithms. Algorithms Mol Biol 5: 23
-
(2010)
Algorithms Mol Biol
, vol.5
, pp. 23
-
-
Chia, B.K.1
Karuturi, R.K.2
-
14
-
-
28944444652
-
Differential coexpression analysis using microarray data and its application to human cancer
-
Choi JK, Yu U, Yoo OJ, Kim S (2005) Differential coexpression analysis using microarray data and its application to human cancer. Bioinformatics 21: 4348-4355
-
(2005)
Bioinformatics
, vol.21
, pp. 4348-4355
-
-
Choi, J.K.1
Yu, U.2
Yoo, O.J.3
Kim, S.4
-
15
-
-
43349094507
-
The igraph software package for complex network research
-
Csardi G, Nepusz T (2006) The igraph software package for complex network research. InterJournal Complex Systems 1695. http://igraph. sf.net
-
(2006)
InterJournal Complex Systems
, vol.1695
-
-
Csardi, G.1
Nepusz, T.2
-
16
-
-
77953913791
-
From 'differential expression' to 'differential networking': Identification of dysfunctional regulatory networks in diseases
-
de la Fuente A (2010) From 'differential expression' to 'differential networking': identification of dysfunctional regulatory networks in diseases. Trends Genet 26: 326-333
-
(2010)
Trends Genet
, vol.26
, pp. 326-333
-
-
de la Fuente, A.1
-
17
-
-
34548550573
-
Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process
-
Elo LL, Järvenpää H, Oresic M, Lahesmaa R, Aittokallio T (2007) Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. Bioinformatics 23: 2096-2103
-
(2007)
Bioinformatics
, vol.23
, pp. 2096-2103
-
-
Elo, L.L.1
Järvenpää, H.2
Oresic, M.3
Lahesmaa, R.4
Aittokallio, T.5
-
18
-
-
78651325241
-
Tomato Functional Genomics Database: A comprehensive resource and analysis package for tomato functional genomics
-
Fei Z, Joung JG, Tang X, Zheng Y, HuangM, Lee JM, McQuinn R, Tieman DM, Alba R, Klee HJ, et al (2011) Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics. Nucleic Acids Res 39: D1156-D1163
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Fei, Z.1
Joung, J.G.2
Tang, X.3
Zheng, Y.4
Huang, M.5
Lee, J.M.6
McQuinn, R.7
Tieman, D.M.8
Alba, R.9
Klee, H.J.10
-
19
-
-
76349097837
-
Characterizing gene coexpression modules in Oryza sativa based on a graph-clustering approach
-
Fukushima A, Kanaya S, Arita M (2009a) Characterizing gene coexpression modules in Oryza sativa based on a graph-clustering approach. Plant Biotechnol 26: 485-493
-
(2009)
Plant Biotechnol
, vol.26
, pp. 485-493
-
-
Fukushima, A.1
Kanaya, S.2
Arita, M.3
-
20
-
-
70549112091
-
Integrated omics approaches in plant systems biology
-
Fukushima A, KusanoM, Redestig H, Arita M, Saito K (2009b) Integrated omics approaches in plant systems biology. Curr Opin Chem Biol 13: 532-538
-
(2009)
Curr Opin Chem Biol
, vol.13
, pp. 532-538
-
-
Fukushima, A.1
Kusano, M.2
Redestig, H.3
Arita, M.4
Saito, K.5
-
21
-
-
78650676139
-
Metabolomic correlation-network modules in Arabidopsis based on a graphclustering approach
-
Fukushima A, Kusano M, Redestig H, Arita M, Saito K (2011) Metabolomic correlation-network modules in Arabidopsis based on a graphclustering approach. BMC Syst Biol 5: 1
-
(2011)
BMC Syst Biol
, vol.5
, pp. 1
-
-
Fukushima, A.1
Kusano, M.2
Redestig, H.3
Arita, M.4
Saito, K.5
-
22
-
-
39249083203
-
Abscisic acid deficiency in the tomato mutant high-pigment 3 leading to increased plastid number and higher fruit lycopene content
-
Galpaz N, Wang Q, Menda N, Zamir D, Hirschberg J (2008) Abscisic acid deficiency in the tomato mutant high-pigment 3 leading to increased plastid number and higher fruit lycopene content. Plant J 53: 717-730
-
(2008)
Plant J
, vol.53
, pp. 717-730
-
-
Galpaz, N.1
Wang, Q.2
Menda, N.3
Zamir, D.4
Hirschberg, J.5
-
24
-
-
33645756545
-
-
Springer, New York
-
Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W (2005) Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Springer, New York
-
(2005)
Bioinformatics and Computational Biology Solutions Using R and Bioconductor
-
-
Gentleman, R.1
Carey, V.2
Dudoit, S.3
Irizarry, R.4
Huber, W.5
-
25
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80
-
(2004)
Genome Biol
, vol.5
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
Dettling, M.5
Dudoit, S.6
Ellis, B.7
Gautier, L.8
Ge, Y.9
Gentry, J.10
-
26
-
-
70449358722
-
A methodology for the analysis of differential coexpression across the human lifespan
-
Gillis J, Pavlidis P (2009) A methodology for the analysis of differential coexpression across the human lifespan. BMC Bioinformatics 10: 306
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 306
-
-
Gillis, J.1
Pavlidis, P.2
-
27
-
-
0029029817
-
Molecular genetic analysis of the ripening-inhibitor and non-ripening loci of tomato: A first step in genetic map-based cloning of fruit ripening genes
-
Giovannoni JJ, Noensie EN, Ruezinsky DM, Lu X, Tracy SL, Ganal MW, Martin GB, Pillen K, Alpert K, Tanksley SD (1995) Molecular genetic analysis of the ripening-inhibitor and non-ripening loci of tomato: a first step in genetic map-based cloning of fruit ripening genes. Mol Gen Genet 248: 195-206
-
(1995)
Mol Gen Genet
, vol.248
, pp. 195-206
-
-
Giovannoni, J.J.1
Noensie, E.N.2
Ruezinsky, D.M.3
Lu, X.4
Tracy, S.L.5
Ganal, M.W.6
Martin, G.B.7
Pillen, K.8
Alpert, K.9
Tanksley, S.D.10
-
28
-
-
34147133691
-
Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis
-
Gutiérrez RA, Lejay LV, Dean A, Chiaromonte F, Shasha DE, Coruzzi GM (2007) Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol 8: R7
-
(2007)
Genome Biol
, vol.8
-
-
Gutiérrez, R.A.1
Lejay, L.V.2
Dean, A.3
Chiaromonte, F.4
Shasha, D.E.5
Coruzzi, G.M.6
-
29
-
-
50649114261
-
Annotating genes of known and unknown function by large-scale coexpression analysis
-
Horan K, Jang C, Bailey-Serres J, Mittler R, Shelton C, Harper JF, Zhu JK, Cushman JC, Gollery M, Girke T (2008) Annotating genes of known and unknown function by large-scale coexpression analysis. Plant Physiol 147: 41-57
-
(2008)
Plant Physiol
, vol.147
, pp. 41-57
-
-
Horan, K.1
Jang, C.2
Bailey-Serres, J.3
Mittler, R.4
Shelton, C.5
Harper, J.F.6
Zhu, J.K.7
Cushman, J.C.8
Gollery, M.9
Girke, T.10
-
30
-
-
44349092469
-
Metabolite annotations based on the integration of mass spectral information
-
Iijima Y, Nakamura Y, Ogata Y, Tanaka K, Sakurai N, Suda K, Suzuki T, Suzuki H, Okazaki K, Kitayama M, et al (2008) Metabolite annotations based on the integration of mass spectral information. Plant J 54: 949-962
-
(2008)
Plant J
, vol.54
, pp. 949-962
-
-
Iijima, Y.1
Nakamura, Y.2
Ogata, Y.3
Tanaka, K.4
Sakurai, N.5
Suda, K.6
Suzuki, T.7
Suzuki, H.8
Okazaki, K.9
Kitayama, M.10
-
31
-
-
0142121516
-
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
-
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264
-
(2003)
Biostatistics
, vol.4
, pp. 249-264
-
-
Irizarry, R.A.1
Hobbs, B.2
Collin, F.3
Beazer-Barclay, Y.D.4
Antonellis, K.J.5
Scherf, U.6
Speed, T.P.7
-
32
-
-
79955467281
-
Metabolomics data reveal a crucial role of cytosolic glutamine synthetase 1;1 in coordinating metabolic balance in rice
-
Kusano M, TabuchiM, Fukushima A, Funayama K, Diaz C, KobayashiM, Hayashi N, Tsuchiya YN, Takahashi H, Kamata A, et al (2011) Metabolomics data reveal a crucial role of cytosolic glutamine synthetase 1;1 in coordinating metabolic balance in rice. Plant J 66: 456-466
-
(2011)
Plant J
, vol.66
, pp. 456-466
-
-
Kusano, M.1
Tabuchi, M.2
Fukushima, A.3
Funayama, K.4
Diaz, C.5
Kobayashi, M.6
Hayashi, N.7
Tsuchiya, Y.N.8
Takahashi, H.9
Kamata, A.10
-
33
-
-
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
-
34
-
-
54349096842
-
Modifying the DPClus algorithm for identifying protein complexes based on new topological structures
-
Li M, Chen JE, Wang JX, Hu B, Chen G (2008) Modifying the DPClus algorithm for identifying protein complexes based on new topological structures. BMC Bioinformatics 9: 398
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 398
-
-
Li, M.1
Chen, J.E.2
Wang, J.X.3
Hu, B.4
Chen, G.5
-
35
-
-
34248329496
-
Convergent evolution in the BAHD family of acyl transferases: Identification and characterization of anthocyanin acyl transferases from Arabidopsis thaliana
-
Luo J, Nishiyama Y, Fuell C, Taguchi G, Elliott K, Hill L, Tanaka Y, Kitayama M, Yamazaki M, Bailey P, et al (2007) Convergent evolution in the BAHD family of acyl transferases: identification and characterization of anthocyanin acyl transferases from Arabidopsis thaliana. Plant J 50: 678-695
-
(2007)
Plant J
, vol.50
, pp. 678-695
-
-
Luo, J.1
Nishiyama, Y.2
Fuell, C.3
Taguchi, G.4
Elliott, K.5
Hill, L.6
Tanaka, Y.7
Kitayama, M.8
Yamazaki, M.9
Bailey, P.10
-
36
-
-
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
-
37
-
-
24044440971
-
BiNGO: A Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks
-
Maere S, Heymans K, Kuiper M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics 21: 3448-3449
-
(2005)
Bioinformatics
, vol.21
, pp. 3448-3449
-
-
Maere, S.1
Heymans, K.2
Kuiper, M.3
-
40
-
-
77953230084
-
ORTom: A multi-species approach based on conserved co-expression to identify putative functional relationships among genes in tomato
-
Miozzi L, Provero P, Accotto GP (2010) ORTom: a multi-species approach based on conserved co-expression to identify putative functional relationships among genes in tomato. Plant Mol Biol 73: 519-532
-
(2010)
Plant Mol Biol
, vol.73
, pp. 519-532
-
-
Miozzi, L.1
Provero, P.2
Accotto, G.P.3
-
41
-
-
33747137944
-
A liquid chromatography-mass spectrometry-based metabolome database for tomato
-
Moco S, Bino RJ, Vorst O, Verhoeven HA, de Groot J, van Beek TA, Vervoort J, de Vos CH (2006) A liquid chromatography-mass spectrometry-based metabolome database for tomato. Plant Physiol 141: 1205-1218
-
(2006)
Plant Physiol
, vol.141
, pp. 1205-1218
-
-
Moco, S.1
Bino, R.J.2
Vorst, O.3
Verhoeven, H.A.4
de Groot, J.5
van Beek, T.A.6
Vervoort, J.7
de Vos, C.H.8
-
42
-
-
32044454046
-
Metabolomic networks in plants: Transitions from pattern recognition to biological interpretation
-
Morgenthal K, Weckwerth W, Steuer R (2006) Metabolomic networks in plants: transitions from pattern recognition to biological interpretation. Biosystems 83: 108-117
-
(2006)
Biosystems
, vol.83
, pp. 108-117
-
-
Morgenthal, K.1
Weckwerth, W.2
Steuer, R.3
-
43
-
-
27244454556
-
The SOL Genomics Network: A comparative resource for Solanaceae biology and beyond
-
Mueller LA, Solow TH, Taylor N, Skwarecki B, Buels R, Binns J, Lin C, Wright MH, Ahrens R, Wang Y, et al (2005) The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond. Plant Physiol 138: 1310-1317
-
(2005)
Plant Physiol
, vol.138
, pp. 1310-1317
-
-
Mueller, L.A.1
Solow, T.H.2
Taylor, N.3
Skwarecki, B.4
Buels, R.5
Binns, J.6
Lin, C.7
Wright, M.H.8
Ahrens, R.9
Wang, Y.10
-
44
-
-
79955581503
-
PlaNet: Combined sequence and expression comparisons across plant networks derived from seven species
-
Mutwil M, Klie S, Tohge T, Giorgi FM, Wilkins O, Campbell MM, Fernie AR, Usadel B, Nikoloski Z, Persson S (2011) PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. Plant Cell 23: 895-910
-
(2011)
Plant Cell
, vol.23
, pp. 895-910
-
-
Mutwil, M.1
Klie, S.2
Tohge, T.3
Giorgi, F.M.4
Wilkins, O.5
Campbell, M.M.6
Fernie, A.R.7
Usadel, B.8
Nikoloski, Z.9
Persson, S.10
-
45
-
-
79951562208
-
ATTED-II updates: Condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants
-
Obayashi T, Nishida K, Kasahara K, Kinoshita K (2011) ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. Plant Cell Physiol 52: 213-219
-
(2011)
Plant Cell Physiol
, vol.52
, pp. 213-219
-
-
Obayashi, T.1
Nishida, K.2
Kasahara, K.3
Kinoshita, K.4
-
46
-
-
77952799294
-
CoP: A database for characterizing co-expressed gene modules with biological information in plants
-
Ogata Y, Suzuki H, Sakurai N, Shibata D (2010) CoP: a database for characterizing co-expressed gene modules with biological information in plants. Bioinformatics 26: 1267-1268
-
(2010)
Bioinformatics
, vol.26
, pp. 1267-1268
-
-
Ogata, Y.1
Suzuki, H.2
Sakurai, N.3
Shibata, D.4
-
47
-
-
77951137933
-
Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module
-
Ozaki S, Ogata Y, Suda K, Kurabayashi A, Suzuki T, Yamamoto N, Iijima Y, Tsugane T, Fujii T, Konishi C, et al (2010) Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module. DNA Res 17: 105-116
-
(2010)
DNA Res
, vol.17
, pp. 105-116
-
-
Ozaki, S.1
Ogata, Y.2
Suda, K.3
Kurabayashi, A.4
Suzuki, T.5
Yamamoto, N.6
Iijima, Y.7
Tsugane, T.8
Fujii, T.9
Konishi, C.10
-
48
-
-
78651284406
-
ArrayExpress update: An archive of microarray and high-throughput sequencing-based functional genomics experiments
-
Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, et al (2011) ArrayExpress update: an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res 39: D1002-D1004
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Parkinson, H.1
Sarkans, U.2
Kolesnikov, N.3
Abeygunawardena, N.4
Burdett, T.5
Dylag, M.6
Emam, I.7
Farne, A.8
Hastings, E.9
Holloway, E.10
-
49
-
-
20844445318
-
Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets
-
Persson S, Wei H, Milne J, Page GP, Somerville CR (2005) Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc Natl Acad Sci USA 102: 8633-8638
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 8633-8638
-
-
Persson, S.1
Wei, H.2
Milne, J.3
Page, G.P.4
Somerville, C.R.5
-
50
-
-
37849020436
-
Decoding genes with coexpression networks and metabolomics: 'majority report by precogs'
-
Saito K, Hirai MY, Yonekura-Sakakibara K (2008) Decoding genes with coexpression networks and metabolomics: 'majority report by precogs.' Trends Plant Sci 13: 36-43
-
(2008)
Trends Plant Sci
, vol.13
, pp. 36-43
-
-
Saito, K.1
Hirai, M.Y.2
Yonekura-Sakakibara, K.3
-
51
-
-
78651340558
-
KaPPA-View4: A metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data
-
Sakurai N, Ara T, Ogata Y, Sano R, Ohno T, Sugiyama K, Hiruta A, Yamazaki K, Yano K, Aoki K, et al (2011) KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data. Nucleic Acids Res 39: D677-D684
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Sakurai, N.1
Ara, T.2
Ogata, Y.3
Sano, R.4
Ohno, T.5
Sugiyama, K.6
Hiruta, A.7
Yamazaki, K.8
Yano, K.9
Aoki, K.10
-
52
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504
-
(2003)
Genome Res
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
53
-
-
75949127736
-
Metabolic networks: How to identify key components in the regulation of metabolism and growth
-
Stitt M, Sulpice R, Keurentjes J (2010) Metabolic networks: how to identify key components in the regulation of metabolism and growth. Plant Physiol 152: 428-444
-
(2010)
Plant Physiol
, vol.152
, pp. 428-444
-
-
Stitt, M.1
Sulpice, R.2
Keurentjes, J.3
-
54
-
-
45449097447
-
Fdrtool: A versatile R package for estimating local and tail area-based false discovery rates
-
Strimmer K (2008) fdrtool: a versatile R package for estimating local and tail area-based false discovery rates. Bioinformatics 24: 1461-1462
-
(2008)
Bioinformatics
, vol.24
, pp. 1461-1462
-
-
Strimmer, K.1
-
55
-
-
0141993704
-
A gene-coexpression network for global discovery of conserved genetic modules
-
Stuart JM, Segal E, Koller D, Kim SK (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302: 249-255
-
(2003)
Science
, vol.302
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
Kim, S.K.4
-
56
-
-
74549181321
-
Arabidopsis auxin response factor6 and 8 regulate jasmonic acid biosynthesis and floral organ development via repression of class 1 KNOX genes
-
Tabata R, Ikezaki M, Fujibe T, Aida M, Tian CE, Ueno Y, Yamamoto KT, Machida Y, Nakamura K, Ishiguro S (2010) Arabidopsis auxin response factor6 and 8 regulate jasmonic acid biosynthesis and floral organ development via repression of class 1 KNOX genes. Plant Cell Physiol 51: 164-175
-
(2010)
Plant Cell Physiol
, vol.51
, pp. 164-175
-
-
Tabata, R.1
Ikezaki, M.2
Fujibe, T.3
Aida, M.4
Tian, C.E.5
Ueno, Y.6
Yamamoto, K.T.7
Machida, Y.8
Nakamura, K.9
Ishiguro, S.10
-
57
-
-
12144291195
-
MAPMAN: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
-
Thimm O, Bläsing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY, Stitt M (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37: 914-939
-
(2004)
Plant J
, vol.37
, pp. 914-939
-
-
Thimm, O.1
Bläsing, O.2
Gibon, Y.3
Nagel, A.4
Meyer, S.5
Krüger, P.6
Selbig, J.7
Müller, L.A.8
Rhee, S.Y.9
Stitt, M.10
-
58
-
-
77954396635
-
Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function
-
Tohge T, Fernie AR (2010) Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function. Nat Protoc 5: 1210-1227
-
(2010)
Nat Protoc
, vol.5
, pp. 1210-1227
-
-
Tohge, T.1
Fernie, A.R.2
-
59
-
-
25444512061
-
HDBStat!: A platform-independent software suite for statistical analysis of high dimensional biology data
-
Trivedi P, Edwards JW, Wang J, Gadbury GL, Srinivasasainagendra V, Zakharkin SO, Kim K, Mehta T, Brand JP, Patki A, et al (2005) HDBStat!: a platform-independent software suite for statistical analysis of high dimensional biology data. BMC Bioinformatics 6: 86
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 86
-
-
Trivedi, P.1
Edwards, J.W.2
Wang, J.3
Gadbury, G.L.4
Srinivasasainagendra, V.5
Zakharkin, S.O.6
Kim, K.7
Mehta, T.8
Brand, J.P.9
Patki, A.10
-
60
-
-
70449115789
-
Co-expression tools for plant biology: Opportunities for hypothesis generation and caveats
-
Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ (2009) Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ 32: 1633-1651
-
(2009)
Plant Cell Environ
, vol.32
, pp. 1633-1651
-
-
Usadel, B.1
Obayashi, T.2
Mutwil, M.3
Giorgi, F.M.4
Bassel, G.W.5
Tanimoto, M.6
Chow, A.7
Steinhauser, D.8
Persson, S.9
Provart, N.J.10
-
61
-
-
0035984046
-
Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing
-
Van der Hoeven R, Ronning C, Giovannoni J, Martin G, Tanksley S (2002) Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing. Plant Cell 14: 1441-1456
-
(2002)
Plant Cell
, vol.14
, pp. 1441-1456
-
-
van der Hoeven, R.1
Ronning, C.2
Giovannoni, J.3
Martin, G.4
Tanksley, S.5
-
63
-
-
34247504045
-
Tomato linalool synthase is induced in trichomes by jasmonic acid
-
van Schie CC, Haring MA, Schuurink RC (2007) Tomato linalool synthase is induced in trichomes by jasmonic acid. Plant Mol Biol 64: 251-263
-
(2007)
Plant Mol Biol
, vol.64
, pp. 251-263
-
-
van Schie, C.C.1
Haring, M.A.2
Schuurink, R.C.3
-
64
-
-
0037066465
-
AMADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus
-
Vrebalov J, Ruezinsky D, Padmanabhan V, White R, Medrano D, Drake R, SchuchW, Giovannoni J (2002) AMADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science 296: 343-346
-
(2002)
Science
, vol.296
, pp. 343-346
-
-
Vrebalov, J.1
Ruezinsky, D.2
Padmanabhan, V.3
White, R.4
Medrano, D.5
Drake, R.6
Schuch, W.7
Giovannoni, J.8
-
65
-
-
78649679994
-
Recent advances in clustering methods for protein interaction networks
-
Wang J, LiM, Deng Y, Pan Y (2010) Recent advances in clustering methods for protein interaction networks. BMC Genomics (Suppl 3) 11: S10
-
(2010)
BMC Genomics
, vol.11
, Issue.SUPPL. 3
-
-
Wang, J.1
Li, M.2
Deng, Y.3
Pan, Y.4
-
66
-
-
34547649056
-
CoXpress: Differential co-expression in gene expression data
-
Watson M (2006) CoXpress: differential co-expression in gene expression data. BMC Bioinformatics 7: 509
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 509
-
-
Watson, M.1
-
67
-
-
2442647715
-
Differential metabolic networks unravel the effects of silent plant phenotypes
-
Weckwerth W, Loureiro ME, Wenzel K, Fiehn O (2004) Differential metabolic networks unravel the effects of silent plant phenotypes. Proc Natl Acad Sci USA 101: 7809-7814
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 7809-7814
-
-
Weckwerth, W.1
Loureiro, M.E.2
Wenzel, K.3
Fiehn, O.4
-
68
-
-
84355166610
-
Two glycosyltransferases involved in anthocyanin modification delineated by transcriptome independent component analysis in Arabidopsis thaliana
-
Yonekura-Sakakibara K, Fukushima A, Nakabayashi R, Hanada K, Matsuda F, Sugawara S, Inoue E, Kuromori T, Ito T, Shinozaki K, et al (2012) Two glycosyltransferases involved in anthocyanin modification delineated by transcriptome independent component analysis in Arabidopsis thaliana. Plant J 69: 154-167
-
(2012)
Plant J
, vol.69
, pp. 154-167
-
-
Yonekura-Sakakibara, K.1
Fukushima, A.2
Nakabayashi, R.3
Hanada, K.4
Matsuda, F.5
Sugawara, S.6
Inoue, E.7
Kuromori, T.8
Ito, T.9
Shinozaki, K.10
-
69
-
-
57749089675
-
Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis
-
Yonekura-Sakakibara K, Tohge T, Matsuda F, Nakabayashi R, Takayama H, Niida R, Watanabe-Takahashi A, Inoue E, Saito K (2008) Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis. Plant Cell 20: 2160-2176
-
(2008)
Plant Cell
, vol.20
, pp. 2160-2176
-
-
Yonekura-Sakakibara, K.1
Tohge, T.2
Matsuda, F.3
Nakabayashi, R.4
Takayama, H.5
Niida, R.6
Watanabe-Takahashi, A.7
Inoue, E.8
Saito, K.9
-
70
-
-
34447502537
-
Identification of a flavonol 7-O-rhamnosyltransferase gene determining flavonoid pattern in Arabidopsis by transcriptome coexpression analysis and reverse genetics
-
Yonekura-Sakakibara K, Tohge T, Niida R, Saito K (2007) Identification of a flavonol 7-O-rhamnosyltransferase gene determining flavonoid pattern in Arabidopsis by transcriptome coexpression analysis and reverse genetics. J Biol Chem 282: 14932-14941
-
(2007)
J Biol Chem
, vol.282
, pp. 14932-14941
-
-
Yonekura-Sakakibara, K.1
Tohge, T.2
Niida, R.3
Saito, K.4
-
71
-
-
0000234892
-
Flavonoids content of tomato plants for the study of the nutritional status
-
Zornoza P, Esteban RM (1984) Flavonoids content of tomato plants for the study of the nutritional status. Plant Soil 82: 269-271
-
(1984)
Plant Soil
, vol.82
, pp. 269-271
-
-
Zornoza, P.1
Esteban, R.M.2
|