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NOTIFICATION: Permanent migration of all CSB.DB services and functionalities on 1.1.2016.
Herewith we inform you that all CSB.DB databases have been migrated at the beginning of 2016. This includes all gene correlation and expression databases, the GMD@CSB.DB module and all associated databases
The BestFit software, a tool for non-aqueous fractionation data analysis, will also be available by the Experimental Systems Biology Research Group headed by Dr. Patrick Giavalisco.
We thank all users, contributors, and collaborators of CSB.DB at the Max Planck Institute for their long-standing support.
Yours sincerely, the CSB.DB Curator and the CSB.DB Developmental Core Team
Matrices@CSB.DB: A.thaliana Matrix Information Page
This page provides background information about the Arabidopsis thaliana gene expression data matrices which are the basis for the co-response analyses. For further information about particular experiments follow the given link.
A.thaliana Matrices
To get information of your choice for the Arabidopsis thaliana gene expression data matrices use the links listed below.
Matrix nasc0271: Processing

Arabidopsis thaliana - Expression Data Matrix nasc0271 (m0271): Processing back to top

Transcript profiles of Matrix nasc0271 (m0271) were derived from the NASC's Affymetrix Facility (NASCArrays, Craigon et al., 2004) and originated from 22k oligonucleotide microarray technology (Affymetrix). The transcript profiling experiments of nasc0271 (m0271) covered miscellaneous treatments and characterisation of mutants. In order to reduce the number of missing data nasc0271 (m0271) was designed according to the following criteria. Each particular gene was well measured in at least 85% of the experiments (Detection Call: 'M' or 'P'). 15% of measurements were tolerated to be absent (Detection Call: 'A'). Negative transcript intensities were treated as missing value and genes with more than 5% missing values were ignored. To avoid overrepresentation of experimental conditions the chosen number of replicates per experimental condition was approximately equal. Matrix nasc0271 (m0271) comprised 51 experiments, which were described by 9694 genes. Normalised transcript intensities were log base 2 transformed. Co-Response analyses were performed on range normalised (genes) matrix.
Matrix nasc0271: Experiments

Arabidopsis thaliana - Expression Data Matrix nasc0271 (m0271): Experiment List back to top

CSB.DB ID SlideName Group Experiment (NASC) Type (NASC)
104 Shirr-Cal_REP3 1 Environmental Genomics of calcicole-calcifuge physiology Ecotype Analysis
106 Shirr-Col-REP3
110 Jones_A1-jones-WT1_SLD 10 The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue Mutant (chemical / radiation induced)
113 Jones_A4-jones-rh2_SLD
121 A2-WILLA-ISOX 11 Assembly of the cell wall pectic matrix Cell Treatment
122 A1-willa-CON-REP2
130 Deeken_A-1-Deeke-Tum_SLD_REP1 12 Agrobacterium tumefaciens-induced tumour development of Arabidopsis thaliana Treatment
131 Deeken_A-2-Deeke-Inf_SLD_REP1
143 HEGGIE_A1-CAG 13 Identification of genes controlling stomatal number in response to rising atmospheric carbon dioxide levels Carbon dioxide treatment
151 Vizcay Barrena_A2-Wilson-mlb 14 Analysis of anther development by analysing downstream genes controlled by MS1 Male sterility
153 Vizcay Barrena_A4-Wilson-leb
160 Bramke_A3-warre-S6C 15 Cold induced changes in gene expression: differences between the Arabidopsis thaliana wild type and freezing sensitive mutants Cold treatment
162 Bramke_A5-warre-S2C
164 Bramke_A1-warre-WTC
170 Villadsen_A-1-villa-zer_SLD 16 Identification of genes responsive to non-metabolised glucose analoges as an approach to hexokinase-independent glucose sensing in plants Hexokinase Signalling
175 Villadsen_A-6-villa-man_SLD
183 A5-Campb-321 17 Control of lignification Lignification
184 A12-Campb-328
186 A13-Campb-329
190 A17-Campb-333
193 A8-Campb-324
196 A3-Campb-319
214 Cornah_A2-cornah-irvl_SLD_REP1 18 Transcriptome analysis of glyoxylate cycle knock-out mutants in early stages of seedling development Effect of gene knock out
216 Cornah_A4-cornah-wsx_SLD_REP1
219 Cornah_A3-cornah-msx_SLD_REP2
221 Cornah_A1-cornah-icl_SLD_REP3
230 Ward_A1-WARD-ax3_SLD 19 Identification of genes differentially expressed in dormant versus active axillary shoot apical mersitems Mutant/Wildtype
231 Ward_A2-WARD-ax1_SLD
250 Yap_A1-AMF 20 Testing Arabidopsis for the presence of arbuscular mycorrhizal signalling pathways Treatment
251 Yap_A2-AMF
322 Murray_A2_ATH1 26 Identification of global gene expression in cir1 and cir1:ein2 plants Effect of gene knock out
431 A2-Rente-KKO-HO_SLD 32 The role of the OX1 protein kinase in H2O2 signal transduction Effect of gene knock out
433 A3-Rente-WS2-Control_SLD
450 A1-Greco-Bou 34 Higher order transcriptional regulation conferred by the bountiful gain_of_function mutant Effect of gene overexpression
451 A2-Greco-WT
461 Swidzinski Senescence ATH1 Replicate 1 35 Genes Involved in Plant Programmed Cell Death (PCD) Cell Treatment
463 Swidzinski Heat ATH1 Replicate 1
464 Swidzinski Control ATH1 Replicate 1
480 Urwin_A-1-Urwin-Con_SLD 36 Plant gene expression associated with susceptibility to nematodes Treatment
503 Honys_UNM1_SLD 5 Transcriptome analysis of Arabidopsis microgametogenesis Cell type
505 Honys_BCP1_SLD
551 Millenaar_A1-MILL-AIR-REP1 7 Ethylene induced hyponastic growth in Arabidopsis thaliana Hyponastic growth
553 Millenaar_A2-MILL-ETH-REP1
555 Millenaar_A3-MILL-LL-REP1
560 Short_A1-mcain-ozo 8 Functional Genomics of Ozone Stress in Arabidopsis Ozone treatment
561 Short_A2-mcain-con
562 A1-LLOYD-PHO_REP1 9 Transcriptome analysis of pho3 pho3 mutation

For suggestions and questions feel free to contact the CSB.DB curator.
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