-
1
-
-
33745626459
-
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
-
Alexa, A., Rahnenführer, J., and Lengauer, T. (2006). Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22: 1600-1607.
-
(2006)
Bioinformatics
, vol.22
, pp. 1600-1607
-
-
Alexa, A.1
Rahnenführer, J.2
Lengauer, T.3
-
2
-
-
0042768158
-
Genome-wide insertional mutagenesis of Arabidopsis thaliana
-
Alonso, J.M., et al. (2003). Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301: 653-657.
-
(2003)
Science
, vol.301
, pp. 653-657
-
-
Alonso, J.M.1
-
3
-
-
0000196110
-
Distribution of the kurtosis statistic b2 for normal samples
-
Anscombe, F.J., and Glynn, W.J. (1983). Distribution of the kurtosis statistic b2 for normal samples. Biometrika 70: 227-234.
-
(1983)
Biometrika
, vol.70
, pp. 227-234
-
-
Anscombe, F.J.1
Glynn, W.J.2
-
4
-
-
38549110664
-
Update of ASRP: The Arabidopsis Small RNA Project database
-
(Database issue)
-
Backman, T.W., Sullivan, C.M., Cumbie, J.S., Miller, Z.A., Chapman, E.J., Fahlgren, N., Givan, S.A., Carrington, J.C., and Kasschau, K.D. (2008). Update of ASRP: The Arabidopsis Small RNA Project database. Nucleic Acids Res. 36(Database issue): D982-D985.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Backman, T.W.1
Sullivan, C.M.2
Cumbie, J.S.3
Miller, Z.A.4
Chapman, E.J.5
Fahlgren, N.6
Givan, S.A.7
Carrington, J.C.8
Kasschau, K.D.9
-
5
-
-
0347447343
-
A gene expression map of the Arabidopsis root
-
Birnbaum, K., Shasha, D.E., Wang, J.Y., Jung, J.W., Lambert, G.M., Galbraith, D.W., and Benfey, P.N. (2003). A gene expression map of the Arabidopsis root. Science 302: 1956-1960.
-
(2003)
Science
, vol.302
, pp. 1956-1960
-
-
Birnbaum, K.1
Shasha, D.E.2
Wang, J.Y.3
Jung, J.W.4
Lambert, G.M.5
Galbraith, D.W.6
Benfey, P.N.7
-
6
-
-
38149109010
-
A high-resolution root spatiotemporal map reveals dominant expression patterns
-
Brady, S.M., Orlando, D.A., Lee, J.Y., Wang, J.Y., Koch, J., Dinneny, J.R., Mace, D., Ohler, U., and Benfey, P.N. (2007). A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 318: 801-806.
-
(2007)
Science
, vol.318
, pp. 801-806
-
-
Brady, S.M.1
Orlando, D.A.2
Lee, J.Y.3
Wang, J.Y.4
Koch, J.5
Dinneny, J.R.6
Mace, D.7
Ohler, U.8
Benfey, P.N.9
-
7
-
-
5044245707
-
Gene co-expression network topology provides a framework for molecular characterization of cellular state
-
Carter, S.L., Brechbühler, C.M., Griffin, M., and Bond, A.T. (2004). Gene co-expression network topology provides a framework for molecular characterization of cellular state. Bioinformatics 20: 2242-2250.
-
(2004)
Bioinformatics
, vol.20
, pp. 2242-2250
-
-
Carter, S.L.1
Brechbühler, C.M.2
Griffin, M.3
Bond, A.T.4
-
8
-
-
0036772151
-
Expression profiling of the whole Arabidopsis shaggy-like kinase multigene family by real-time reverse transcriptase-polymerase chain reaction
-
Charrier, B., Champion, A., Henry, Y., and Kreis, M. (2002). Expression profiling of the whole Arabidopsis shaggy-like kinase multigene family by real-time reverse transcriptase-polymerase chain reaction. Plant Physiol. 130: 577-590.
-
(2002)
Plant Physiol
, vol.130
, pp. 577-590
-
-
Charrier, B.1
Champion, A.2
Henry, Y.3
Kreis, M.4
-
9
-
-
41349117788
-
Finding community structure in very large networks
-
Clauset, A., Newman, M.E., and Moore, C. (2004). Finding community structure in very large networks. Physiol. Rev. E Stat. Nonlin. Soft Matter Phys. 70: 066111.
-
(2004)
Physiol. Rev. E Stat. Nonlin. Soft Matter Phys
, vol.70
, pp. 066111
-
-
Clauset, A.1
Newman, M.E.2
Moore, C.3
-
10
-
-
79955680277
-
Analysis of anther transcriptomes to identify genes contributing to meiosis and male gametophyte development in rice
-
Deveshwar, P., Bovill, W.D., Sharma, R., Able, J.A., and Kapoor, S. (2011). Analysis of anther transcriptomes to identify genes contributing to meiosis and male gametophyte development in rice. BMC Plant Biol. 11: 78.
-
(2011)
BMC Plant Biol
, vol.11
, pp. 78
-
-
Deveshwar, P.1
Bovill, W.D.2
Sharma, R.3
Able, J.A.4
Kapoor, S.5
-
11
-
-
53749100493
-
Drought induction of Arabidopsis 9-cis-epoxycarotenoid dioxygenase occurs in vascular parenchyma cells
-
Endo, A., et al. (2008). Drought induction of Arabidopsis 9-cis-epoxycarotenoid dioxygenase occurs in vascular parenchyma cells. Plant Physiol. 147: 1984-1993.
-
(2008)
Plant Physiol
, vol.147
, pp. 1984-1993
-
-
Endo, A.1
-
12
-
-
0032946556
-
Detecting selective expression of genes and proteins
-
Greller, L.D., and Tobin, F.L. (1999). Detecting selective expression of genes and proteins. Genome Res. 9: 282-296.
-
(1999)
Genome Res
, vol.9
, pp. 282-296
-
-
Greller, L.D.1
Tobin, F.L.2
-
13
-
-
77952534179
-
Comparison of scores for bimodality of gene expression distributions and genomewide evaluation of the prognostic relevance of high-scoring genes
-
Hellwig, B., Hengstler, J.G., Schmidt, M., Gehrmann, M.C., Schormann, W., and Rahnenführer, J. (2010). Comparison of scores for bimodality of gene expression distributions and genomewide evaluation of the prognostic relevance of high-scoring genes. BMC Bioinformatics 11: 276.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 276
-
-
Hellwig, B.1
Hengstler, J.G.2
Schmidt, M.3
Gehrmann, M.C.4
Schormann, W.5
Rahnenführer, J.6
-
14
-
-
58749109023
-
Genevestigator v3: A reference expression database for the metaanalysis of transcriptomes
-
Hruz, T., Laule, O., Szabo, G., Wessendorp, F., Bleuler, S., Oertle, L., Widmayer, P., Gruissem, W., and Zimmermann, P. (2008). Genevestigator v3: A reference expression database for the metaanalysis of transcriptomes. Adv. Bioinforma. 2008: 420747.
-
(2008)
Adv. Bioinforma
, vol.2008
, pp. 420747
-
-
Hruz, T.1
Laule, O.2
Szabo, G.3
Wessendorp, F.4
Bleuler, S.5
Oertle, L.6
Widmayer, P.7
Gruissem, W.8
Zimmermann, P.9
-
15
-
-
59149095771
-
A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies
-
Jiao, Y., et al. (2009). A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat. Genet. 41: 258-263.
-
(2009)
Nat. Genet
, vol.41
, pp. 258-263
-
-
Jiao, Y.1
-
16
-
-
0035671395
-
Building a multicellular organism
-
Kaiser, D. (2001). Building a multicellular organism. Annu. Rev. Genet. 35: 103-123.
-
(2001)
Annu. Rev. Genet
, vol.35
, pp. 103-123
-
-
Kaiser, D.1
-
17
-
-
63549132294
-
A systems approach uncovers restrictions for signal interactions regulating genomewide responses to nutritional cues in Arabidopsis
-
Krouk, G., Tranchina, D., Lejay, L., Cruikshank, A.A., Shasha, D., Coruzzi, G.M., and Gutiérrez, R.A. (2009). A systems approach uncovers restrictions for signal interactions regulating genomewide responses to nutritional cues in Arabidopsis. PLoS Comput. Biol. 5: e1000326.
-
(2009)
PLoS Comput. Biol
, vol.5
-
-
Krouk, G.1
Tranchina, D.2
Lejay, L.3
Cruikshank, A.A.4
Shasha, D.5
Coruzzi, G.M.6
Gutiérrez, R.A.7
-
18
-
-
0037507299
-
NADPH oxidase AtrbohD and AtrbohF genes function in ROS-dependent ABA signaling in Arabidopsis
-
Kwak, J.M., Mori, I.C., Pei, Z.M., Leonhardt, N., Torres, M.A., Dangl, J.L., Bloom, R.E., Bodde, S., Jones, J.D., and Schroeder, J.I. (2003). NADPH oxidase AtrbohD and AtrbohF genes function in ROS-dependent ABA signaling in Arabidopsis. EMBO J. 22: 2623-2633.
-
(2003)
EMBO J
, vol.22
, pp. 2623-2633
-
-
Kwak, J.M.1
Mori, I.C.2
Pei, Z.M.3
Leonhardt, N.4
Torres, M.A.5
Dangl, J.L.6
Bloom, R.E.7
Bodde, S.8
Jones, J.D.9
Schroeder, J.I.10
-
19
-
-
76349125292
-
Rational association of genes with traits using a genomescale gene network for Arabidopsis thaliana
-
Lee, I., Ambaru, B., Thakkar, P., Marcotte, E.M., and Rhee, S.Y. (2010). Rational association of genes with traits using a genomescale 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
-
20
-
-
33745961113
-
Detecting and profiling tissue-selective genes
-
Liang, S., Li, Y., Be, X., Howes, S., and Liu, W. (2006). Detecting and profiling tissue-selective genes. Physiol. Genomics 26: 158-162.
-
(2006)
Physiol. Genomics
, vol.26
, pp. 158-162
-
-
Liang, S.1
Li, Y.2
Be, X.3
Howes, S.4
Liu, W.5
-
21
-
-
65249184459
-
Sumoylation of ABI5 by the Arabidopsis SUMO E3 ligase SIZ1 negatively regulates abscisic acid signaling
-
Miura, K., Lee, J., Jin, J.B., Yoo, C.Y., Miura, T., and Hasegawa, P.M. (2009). Sumoylation of ABI5 by the Arabidopsis SUMO E3 ligase SIZ1 negatively regulates abscisic acid signaling. Proc. Natl. Acad. Sci. USA 106: 5418-5423.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 5418-5423
-
-
Miura, K.1
Lee, J.2
Jin, J.B.3
Yoo, C.Y.4
Miura, T.5
Hasegawa, P.M.6
-
22
-
-
21144455484
-
The Arabidopsis SUMO E3 ligase SIZ1 controls phosphate deficiency responses
-
Miura, K., Rus, A., Sharkhuu, A., Yokoi, S., Karthikeyan, A.S., Raghothama, K.G., Baek, D., Koo, Y.D., Jin, J.B., Bressan, R.A., Yun, D.J., and Hasegawa, P.M. (2005). The Arabidopsis SUMO E3 ligase SIZ1 controls phosphate deficiency responses. Proc. Natl. Acad. Sci. USA 102: 7760-7765.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 7760-7765
-
-
Miura, K.1
Rus, A.2
Sharkhuu, A.3
Yokoi, S.4
Karthikeyan, A.S.5
Raghothama, K.G.6
Baek, D.7
Koo, Y.D.8
Jin, J.B.9
Bressan, R.A.10
Yun, D.J.11
Hasegawa, P.M.12
-
23
-
-
79955581503
-
PlaNet: Combined sequence and expression comparisons across plant networks derived from seven species
-
Mutwil, M., Klie, S., Tohge, T., Giorgi, F.M., Wilkins, O., Campbell, M.M., Fernie, A.R., Usadel, B., Nikoloski, Z., and 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
-
24
-
-
48449091196
-
Gene- CAT-novel webtools that combine BLAST and co-expression analyses
-
Mutwil, M., Obro, J., Willats, W.G., and Persson, S. (2008). Gene- CAT-novel webtools that combine BLAST and co-expression analyses. Nucleic Acids Res. 36: W320-W326.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Mutwil, M.1
Obro, J.2
Willats, W.G.3
Persson, S.4
-
25
-
-
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., and 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
-
26
-
-
33745474841
-
Gprotein complex mutants are hypersensitive to abscisic acid regulation of germination and postgermination development
-
Pandey, S., Chen, J.G., Jones, A.M., and Assmann, S.M. (2006). Gprotein complex mutants are hypersensitive to abscisic acid regulation of germination and postgermination development. Plant Physiol. 141: 243-256.
-
(2006)
Plant Physiol
, vol.141
, pp. 243-256
-
-
Pandey, S.1
Chen, J.G.2
Jones, A.M.3
Assmann, S.M.4
-
27
-
-
77953244611
-
Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein action
-
Pandey, S., Wang, R.S., Wilson, L., Li, S., Zhao, Z., Gookin, T.E., Assmann, S.M., and Albert, R. (2010). Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein action. Mol. Syst. Biol. 6: 372.
-
(2010)
Mol. Syst. Biol
, vol.6
, pp. 372
-
-
Pandey, S.1
Wang, R.S.2
Wilson, L.3
Li, S.4
Zhao, Z.5
Gookin, T.E.6
Assmann, S.M.7
Albert, R.8
-
28
-
-
78650647272
-
Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana
-
Pop, A., Huttenhower, C., Iyer-Pascuzzi, A., Benfey, P.N., and Troyanskaya, O.G. (2010). Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. BMC Syst. Biol. 4: 180.
-
(2010)
BMC Syst. Biol
, vol.4
, pp. 180
-
-
Pop, A.1
Huttenhower, C.2
Iyer-Pascuzzi, A.3
Benfey, P.N.4
Troyanskaya, O.G.5
-
29
-
-
34548856552
-
Near linear time algorithm to detect community structures in large-scale networks
-
Raghavan, U.N., Albert, R., and Kumara, S. (2007). Near linear time algorithm to detect community structures in large-scale networks. Physiol. Rev. E Stat. Nonlin. Soft Matter Phys. 76: 036106.
-
(2007)
Physiol. Rev. E Stat. Nonlin. Soft Matter Phys
, vol.76
, pp. 036106
-
-
Raghavan, U.N.1
Albert, R.2
Kumara, S.3
-
30
-
-
58549103327
-
The origins of multicellularity and the early history of the genetic toolkit for animal development
-
Rokas, A. (2008). The origins of multicellularity and the early history of the genetic toolkit for animal development. Annu. Rev. Genet. 42: 235-251.
-
(2008)
Annu. Rev. Genet
, vol.42
, pp. 235-251
-
-
Rokas, A.1
-
31
-
-
16244362244
-
A gene expression map of Arabidopsis thaliana development
-
Schmid, M., Davison, T.S., Henz, S.R., Pape, U.J., Demar, M., Vingron, M., Schölkopf, B., Weigel, D., and Lohmann, J.U. (2005). A gene expression map of Arabidopsis thaliana development. Nat. Genet. 37: 501-506.
-
(2005)
Nat. Genet
, vol.37
, pp. 501-506
-
-
Schmid, M.1
Davison, T.S.2
Henz, S.R.3
Pape, U.J.4
Demar, M.5
Vingron, M.6
Schölkopf, B.7
Weigel, D.8
Lohmann, J.U.9
-
32
-
-
51549093662
-
CressExpress: A tool for large-scale mining of expression data from Arabidopsis
-
Srinivasasainagendra, V., Page, G.P., Mehta, T., Coulibaly, I., and Loraine, A.E. (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
-
33
-
-
0141993704
-
A genecoexpression network for global discovery of conserved genetic modules
-
Stuart, J.M., Segal, E., Koller, D., and Kim, S.K. (2003). A genecoexpression 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
-
34
-
-
11144358198
-
A gene atlas of the mouse and human proteinencoding transcriptomes
-
Su, A.I., et al. (2004). A gene atlas of the mouse and human proteinencoding transcriptomes. Proc. Natl. Acad. Sci. USA 101: 6062-6067.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 6062-6067
-
-
Su, A.I.1
-
35
-
-
33748708623
-
PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer
-
Teschendorff, A.E., Naderi, A., Barbosa-Morais, N.L., and Caldas, C. (2006). PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer. Bioinformatics 22: 2269-2275.
-
(2006)
Bioinformatics
, vol.22
, pp. 2269-2275
-
-
Teschendorff, A.E.1
Naderi, A.2
Barbosa-Morais, N.L.3
Caldas, C.4
-
36
-
-
78651472654
-
Tissue-specific disallowance of housekeeping genes: The other face of cell differentiation
-
Thorrez, L., et al. (2011). Tissue-specific disallowance of housekeeping genes: The other face of cell differentiation. Genome Res. 21: 95-105.
-
(2011)
Genome Res
, vol.21
, pp. 95-105
-
-
Thorrez, L.1
-
37
-
-
22044437388
-
The Botany Array Resource: E-Northerns, expression angling, and promoter analyses
-
Toufighi, K., Brady, S.M., Austin, R., Ly, E., and Provart, N.J. (2005). The Botany Array Resource: e-Northerns, expression angling, and promoter analyses. Plant J. 43: 153-163.
-
(2005)
Plant J
, vol.43
, pp. 153-163
-
-
Toufighi, K.1
Brady, S.M.2
Austin, R.3
Ly, E.4
Provart, N.J.5
-
38
-
-
1642287458
-
Universality and flexibility in gene expression from bacteria to human
-
Ueda, H.R., Hayashi, S., Matsuyama, S., Yomo, T., Hashimoto, S., Kay, S.A., Hogenesch, J.B., and Iino, M. (2004). Universality and flexibility in gene expression from bacteria to human. Proc. Natl. Acad. Sci. USA 101: 3765-3769.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 3765-3769
-
-
Ueda, H.R.1
Hayashi, S.2
Matsuyama, S.3
Yomo, T.4
Hashimoto, S.5
Kay, S.A.6
Hogenesch, J.B.7
Iino, M.8
-
39
-
-
70449115789
-
Co-expression tools for plant biology: Opportunities for hypothesis generation and caveats
-
Usadel, B., Obayashi, T., Mutwil, M., Giorgi, F.M., Bassel, G.W., Tanimoto, M., Chow, A., Steinhauser, D., Persson, S., and Provart, N.J. (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
-
40
-
-
78650596675
-
CalS7 encodes a callose synthase responsible for callose deposition in the phloem
-
Xie, B., Wang, X., Zhu, M., Zhang, Z., and Hong, Z. (2011). CalS7 encodes a callose synthase responsible for callose deposition in the phloem. Plant J. 65: 1-14.
-
(2011)
Plant J
, vol.65
, pp. 1-14
-
-
Xie, B.1
Wang, X.2
Zhu, M.3
Zhang, Z.4
Hong, Z.5
-
41
-
-
2442526837
-
Just-in-time transcription program in metabolic pathways
-
Zaslaver, A., Mayo, A.E., Rosenberg, R., Bashkin, P., Sberro, H., Tsalyuk, M., Surette, M.G., and Alon, U. (2004). Just-in-time transcription program in metabolic pathways. Nat. Genet. 36: 486-491.
-
(2004)
Nat. Genet
, vol.36
, pp. 486-491
-
-
Zaslaver, A.1
Mayo, A.E.2
Rosenberg, R.3
Bashkin, P.4
Sberro, H.5
Tsalyuk, M.6
Surette, M.G.7
Alon, U.8
-
42
-
-
62549094876
-
Functional proteomics of Arabidopsis thaliana guard cells uncovers new stomatal signaling pathways
-
Zhao, Z., Zhang, W., Stanley, B.A., and Assmann, S.M. (2008). Functional proteomics of Arabidopsis thaliana guard cells uncovers new stomatal signaling pathways. Plant Cell 20: 3210-3226.
-
(2008)
Plant Cell
, vol.20
, pp. 3210-3226
-
-
Zhao, Z.1
Zhang, W.2
Stanley, B.A.3
Assmann, S.M.4
|