CATMA: A Complete Arabidopsis transcriptome Microarray

CATMA publications

Citations

• When citing the CATMA GST repository as a whole, please refer to:

  Sclep, G., Allemeersch, J., Liechti, B., De Meyer, B. Beynon, J., Bhalerao, R., Moreau, Y., Nietfeld, W., Renou, J-P, Reymond, P., Hilson, P., Kuiper, M. (2007) CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes. BMC Bioinformatics Submitted

• When citing the use of GSTs in microarray or RNAi experiments, please refer to:

  Hilson, P., Allemeersch, J., Altmann, T., Aubourg, S., Avon, A., Beynon, J., Bhalerao, R., Bitton, F., Caboche, M., Cannoot, B., Chardakov, V., Cognet-Holliger, C. Colot, V., Crowe, M., Darimont, C., Durinck, S., Eickhoff, H., Falcon de Longevialle, A., Farmer, E.E., Grant, M., Kuiper, M.T.R., Lehrach, H., Léon, C., Leyva, A., Lundeberg, J., Lurin, C., Moreau, Y., Nietfeld, W., Paz-Ares, J., Reymond, P., Rouzé, P., Sandberg, G., Segura, M.D., Serizet, C., Tabrett, A., Taconnat, L., Thareau, V., Van Hummelen, P., Vercruysse, S., Vuylsteke, M., Weingartner, M., Weisbeek, P.J., Wirta, V., Wittink, F.R.A., Zabeau, M. and Small, I. (2004) Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: transcript profiling and reverse genetics applications. Genome Research 14 (10b), 2176-2189. (PubMed)

• When citing the CATMA GST database, please refer to:

  Crowe, M.L., Serizet, C., Thareau, V., Aubourg, S., Rouzé, P., Beynon, J.L., Hilson, P., Weisbeek, P., Van Hummelen, P., Reymond, P., Paz-Ares, J., Nietfeld, W. and Trick, M. (2003) CATMA - A complete Arabidopsis GST database. Nucleic Acids Res 31, 156-158. (PubMed)

• When citing the software used to design the GSTs, refer to:

  Thareau, V., Déhais, P., Serizet, C., Hilson, P., Rouzé, P. and Aubourg, S. (2003) Automatic design of gene-specific sequence tags for genome-wide functional studies. Bioinformatics 19, 2191-2198. (PubMed)

Other papers presenting CATMA microarray data

• Lurin, C., Andres, C., Aubourg, S., Bellaoui, M., Bitton, F., Bruyere, C., Caboche, M., Debast, C., Gualberto, J., Hoffmann, B., Lecharny, A., Le Ret, M., Martin-Magniette, M.L., Mireau, H., Peeters, N., Renou, J.P., Szurek, B., Taconnat, L. and Small, I. (2004) Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell 16, 2089-2103. (PubMed)


• Dieterle, M., Thomann, A., Renou, J.P., Parmentier, Y., Cognat, V., Lemonnier, G., Müller, R., Shen, W.-H., Kretsch, T. and Genschick, P. Molecular and functional characterization of Arabidopsis Cullin 3A. Plant Journal. 2005 Feb;41(3):386-99. (PubMed)


• Bertand, C., Benhamed, M., Li, Y.F., Ayadi, M., Lemonnier, G., Renou, J.P., Delarue, M. and Zhou, D.X. Arabidopsis HAF2 encoding TATA-binding (TBP)-associated factor TAF1, is required to integrate light signals to regulate gene expression and growth. Journal of Biological Chemistry. 2005 Jan 14;280(2):1465-73. (PubMed)


• Allemeersch, J., Durinck, S., Vanderhaeghen, R., Alard, P., Maes, R., Seeuws, K., Bogaert, T., Coddens, K., Deschouwer, K., Van Hummelen, P., Vuylsteke, M., Moreau, Y., Kwekkeboom, J., Wijfjes, A.H.M., May, S., Beynon, J., Hilson, P.* and Kuiper, M.T.R.* Benchmarking the CATMA microarray: a novel tool for Arabidopsis transcriptome analysis. Plant Physiology 2005 137, 588-601. (PubMed)


• Pineau C, Freydier A, Ranocha P, Jauneau A, Turner S, Lemonnier G, Renou JP, Tarkowski P, Sandberg G, Jouanin L, Sundberg B, Boudet AM, Goffner D and Pichon. Hca: an Arabidopsis mutant exhibiting unusual cambial activity and altered vascular patterning. Plant Journal. 2005 Oct 44(2), 271-289. (PubMed)


• Jammes F, Lecomte P, Almeida-Engler J, Bitton F, Martin-Magniette ML, Renou JP, Abad P and Favery B. Genome-wide expression profiling of the host response to root-knot nematode infection in Arabidopsis. Plant Joural. 2005 Nov 44 (3), 447-58. (PubMed)


• Vergnolle, C., Vaultier, M.N., Taconnat, L., Renou, J.P., Kader, J.C., Zachowski, A. and Ruelland E. (2005) The cold-induced early activation of phospholipase C and D pathways determine the response of two distinct clusters of genes in Arabidopsis cell suspensions. Plant Physiology 2005 Nov;139(3):1217-33. (PubMed)


• Abdulrazzak, N., Pollet, B., Ehlting, J., Larsen, K., Asnaghi, C., Ronseau, S., Proux, C., Erhardt, M., Seltzer, V., Renou, J.P., Ullmann, P., Pauly, M., Lapierre, C. and Werck-Reichhart, D. (2006) A coumaroyl-ester-3-hydroxylase insertion mutant reveals the existence of nonredundant meta-hydroxylation pathways and essential roles for phenolic precursors in cell expansion and plant growth. Plant Physiology 2006 Jan; 140(1):30-48. (PubMed)


• Guyomarc'h, S., Benhamed, M., Lemonnier, G., Renou, J.P., Zhou, D.X. and Delarue, M. (2006) MGOUN3: evidence for chromatin-mediated regulation of FLC expression. J of Exp Botany. 2006;57(9):2111-9. (PubMed)


• Ferrario-Mery, S., Besin, E., Pichon, O., Meyer, C. and Hodges, M. (2006) The regulatory PII protein controls arginine biosynthesis in Arabidopsis. FEBS Lett. 2006 Apr 3;580(8):2015-20. (PubMed)


• Herbette, S., Taconnat, L., Hugouvieux, V., Martin-Magniette, M.L., Cuine, S., Auroy, P., Richaud, P., Forestier, C., Bourguignon, J., Renou, J.P., Vavasseur, A. and Leonhart, N. (2006) Genome-wide transcriptome profiling of the early cadmium response of Arabidopsis roots and shoots. Biochimie. 2006 Jun 6; [Epub ahead of print] (PubMed)


• Manavella, P.A., Arce, A.L., Dezar, C.A., Bitton, F., Renou, J.P., Crespi, M. and Chan R. (2006) Analysis of transcriptional networks regulated by the sunflower Hahb-4 transcription factor in Arabidopsis revealed a conserved role in ethylene signaling. Plant Journal.2006 Oct;48(1):125-37. (PubMed)


• Masclaux-Daubresse C., Purdy S., Lemaitre T., Pourtau N., Taconnat L., Renou J.P. & Wingler A. (2006) Genetic variation suggests an interaction between cold acclimation and the metabolic regulation of leaf senescence. Plant Physiology. Jan;143(1):434-46. (Pubmed)


• Little, D., Gouhier-Darimont, C., Bruessow, F., and Reymond, P. (2007). Oviposition by Pierid Butterflies Triggers Defense Responses in Arabidopsis. Plant Physiol. 143, 784-800. (PubMed)


• Gagnot, S., Tamby, J.-P., Martin-Magniette, M.-L., Bitton, F., Taconnat, L., Balzergue, S., Aubourg, S., Renou, J.-P., Lecharny, A., Brunaud, V. (2007) CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform. Nucleic Acids Res 0: p. gkm757v1-gkm757 (Pubmed)


• Lim PO, Kim Y, Breeze E, Koo JC, Woo HR, Ryu JS, Park DH, Beynon J, Tabrett A, Buchanan-Wollaston V, Nam HG (2007) Overexpression of a chromatin architecture-controlling AT-hook protein extends leaf longevity and increases the post-harvest storage life of plants. The Plant Journal. 52, 1140­1153. (Pubmed)


• Ricaud L., Proux C., Renou J.P., Pichon O., Fochesato S., Ortet P., Montane M.H. (2007) ATM-Mediated Transcriptional and Developmental Responses to gamma-rays in Arabidopsis. PLoS ONE. May 9;2(5):e430. (Pubmed)


• Krinke O., Ruelland E., Valentova O., Vergnolle C., Renou J.P., Taconnat L., Flemr M., Burketova L., Zachowski A. (2007) Phosphatidylinositol 4-kinase Activation Is an Early Response to Salicylic Acid in Arabidopsis Suspension Cells. Plant Physiol. 144(3): 1347-59. (Pubmed)


• Hematy K., Sado P.E., Van Tuinen A., Rochange S., Desnos T., Balzergue S., Pelletier S., Renou J.P., Hofte H. (2007) A Receptor-like Kinase Mediates the Response of Arabidopsis Cells to the Inhibition of Cellulose Synthesis. Curr Biol. 2007 Jun 5;17(11):922-31. (Pubmed)


• Aubourg S., Martin-Magniette M.L., Brunaud V., Taconnat L., Bitton F., Balzergue S., Jullien P.E., Ingouff M., Thareau V., Schiex T., Lecharny A., Renou J.P. (2007) Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome. BMC Genomics. Nov 2;8(1):401 (Pubmed)


• Ramel F., Cabello-Hurtado F., Sulmon C., Taconnat L., Martin-Magniette M.L., Renou J.P., El Amrani A., Couée I., Gouesbet G. (2007) Transcriptome profiling reveals the apoptotic effects of the herbicide atrazine and large-scale protective effects of sucrose signaling in Arabidopsis thaliana plantlets. BMC Genomics. Dec 5;8(1):450 (Pubmed)


• Xu L., Zhao Z., Dong A., Soubigou-Taconnat L., Renou J.P., Steinmetz A. & Shen W.H. (2007) Di- and tri- but not mono-methylation on histone H3 lysine 36 marks active transcription in Arabidopsis thaliana Mol Cell Biol. 28(4):1348-60. (Pubmed)


• Cartriaux F., Contesto C., Gallou A., Desbrosses G., Taconnat L., Renou J.P. and Touraine B. (2008) Simultaneous interaction of Arabidopsis thaliana with Bradyrhizobium sp. ORS278 and Pseudomonas syringae pv tomato DC3000 leads to complex transcriptome changes. Mol Plant Microbe Interact. Feb;21(2):244-59. (Pubmed)


• Chávez Montes R.A., Ranocha P., Martinez Y., Minic Z., Jouanin L., Marquis M., Saulnier L., Fulton L.M., Cobbett C.S., Bitton F., Renou J.P. , Jauneau A. and Goffner D. (2008) Cell wall modifications in Arabidopsis thaliana plants with altered {alpha}-Larabinofuranosidase activity. Plant Physiol. 147(1):63-77. (Pubmed)


• Achard P., Renou J.P., Berthomé R., Harberd N.P. and Genschik P. (2008) Plant DELLAs regulate growth and survival of adversity via control of reactive oxygen species levels. Current Biology. 18(9):656-60. (Pubmed)


• Martin-Magniette M.L., Aubert J., Bar-Hen A., Elftieh S., Magniette F., Renou J.P. and Daudin J.J. (2008) Normalization for triple-target microarray experiments BMC bioinformatics. 9(1):216. (Pubmed)


• Mérigout P., Lelandais M., Bitton F., Renou J.P., Briand X., Meyer C. & Daniel-Vedele F. (2008) Physiological and transcriptomic aspects of urea uptake and assimilation in Arabidopsis plants. Plant Physiol. May08 [Epub ahead of print] (Pubmed)


• Castaings L., Camargo A., Pocholle D., Taconnat L., Renou J.P., Daniel-Vedele F., Fernandez E., Meyer C. & Krapp A. (2008) A nodulation-inception-like gene regulates nitrate assimilation in the non-legume Arabidopsis. Plant Journal. Sep 26. [Epub ahead of print] (Pubmed)
• Breeze E, Harrison H, Page T, Warner N, Shen C, Zhang C and Buchanan-Wollaston V (2008) Transcriptional regulation of plant senescence: from functional genomics to systems biology. Plant Biology. 10, 99-109. (Pubmed)



• Loizeau K., De Brouwer V., Gambonnet B., Yu A., Renou J.P., Van Der Straeten D., E. Lambert W., Rébeillé F. and Ravanel S. (2008) A genome-wide and metabolic analysis determined the adaptation of Arabidopsis cells to folate depletion induced by methotrexate. Plant Physiology. Oct 17. [Epub ahead of print] (Pubmed)


• Bouchabke-Coussa O, Quashie ML, Seoane-Redondo J, Fortabat MN, Gery C, Yu A, Linderme D, Trouverie J, Granier F, Teoule E, Durand-Tardif M. (2008) ESKIMO1 is a key gene involved in water economy as well as cold acclimation and salt tolerance. BMC Plant Biol. Dec 7;8(1):125. (Pubmed)


• Talaat Bashandy, Ludivine Taconnat, Jean-Pierre Renou, Yves Meyer, and Jean-Philippe Reichheld (2008) Accumulation of Flavonoids in an ntra ntrb Mutant Leads to Tolerance to UV-C. Mol Plant, Advance Access published on October 29, 2008; doi: doi:10.1093/mp/ssn065 (Pubmed)


• Matakiadis T, Alboresi A, Jikumaru Y, Tatematsu K, Pichon O, Renou JP, Kamiya Y, Nambara E, Truong HN. (2008) The Arabidopsis Abscisic Acid Catabolic Gene CYP707A2 Plays a Key Role in Nitrate Control of Seed Dormancy. Plant Physiology. Dec 12 .[Epub ahead of print] (Pubmed)


• Depuydt S, Trenkamp S, Fernie AR, Elftieh S, Renou JP, Vuylsteke M, Holsters M, Vereecke D. (2008) An integrated genomics approach to define niche establishment by Rhodococcus fascians. Plant Physiol. Dec 31. [Epub ahead of print] (Pubmed)


• Benhamed M., Martin-Magniette M.L., Taconnat L., Bitton F., Servet C., De Clercq R., De Meyer B., Buyschaert C., Rombauts S., Villarroel R., Aubourg S., Beynon J., Bhalerao R., Coupland G., Gruissem W., Menke F., Weigel D., Weisshaar B., Renou J.P., Dao-Xiu Zhou D.X. & Hilson P. (2008) Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5. Plant Journal. July 04. Epub ahead of print (Pubmed)


• Pitzschke A., Djamei A., Bitton F. and Hirt H. (2009) A Major Role of the MEKK1–MKK1/2–MPK4 Pathway in ROS Signalling. Molecular Plant, Advance Access published on January 6, 2009; doi: doi:10.1093/mp/ssn079. (Pubmed)


• Minic Z., Jamet E., San-Clemente H., Renou J.P., Rihouey C., PO Okinyo D., Proux C., Lerouge P. and Jouanin L. (2009) Transcriptomic analysis of Arabidopsis developing stems: a close-up on cell wall genes. BMC Plant Biol. 2009 Jan 16;9(1):6. [Epub ahead of print] (Pubmed)


• Besson-Bard A., Gravot A., Richaud P., Auroy P., Gaymard F., Taconnat L., Renou J.P., Pugin A. and Wendehenne D. (2009) A cadmium induced nitrite oxide production in Arabidopsis thaliana triggers upregulation of genes related to iron uptake and sets up resistance mechanisms through induction of a NAS4 dependant nicotianamide production. Plant Physiol. 2009 Jan 23. [Epub ahead of print] (Pubmed)


• Zhu, Y., Dong, A., Meyer, D., Pichon, O., Renou, J.P., Cao, K. and Shen WH. NRP1 and NRP2 encoding NUCLEOSOME ASSEMBLY PROTEIN 1-related proteins in Arabidopsis are required for maintaining postembryonic root growth. Plant Cell. In Press.

Other papers presenting CATMA microarray data in CATdb:

Selected posters

This is a selection of presention by members of the CATMA consortium describing various aspects of the CATMA project. All are Microsoft Powerpoint files.

Design and Databasing of Genome-wide Gene Specific Tags	Talk describing the design of the CATMA genes and GSTs given by Pierre Rouzé of University Ghent at the Plant GEMs meeting in Berlin in October 2002.
CATMA, the Complete Arabidopsis Transcriptome Micro Array	Talk describing the aims and progress of CATMA given by Jim Beynon of HRI at the GARNet meeting in York in September 2001
The Complete Arabidopsis Transcriptome MicroArray (CATMA) Project	A poster describing the whole CATMA project, presented at the GARNet meeting in York in September 2001
Design and Databasing for the Complete Arabidopsis Transcriptome MicroArray (CATMA) project	Description of the bioinformatics behind the CATMA project, presented at the JOBIM meeting in St Malo in June 2002

To download the posters to your hard drive for easier viewing, right-click on the link and select 'save link/target as'.