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AtGenExpress
is a multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana. This large collaborative project will combine resources of gene expression patterns using Affymetrix GeneChip across the whole plant-life cycle.
Tools...
To find biological relationships among experiments available in public databases, correlations of transcriptome experiments were analyzed by module-based correlation approach, and then presented in networks.
AtCAST Ver2.06
This version is specific for transcriptome data about phytohormones.
AtMet(test) Ver0.01
JBrowse Ver1.12.1
Genome viewer with data focusing on exon combinations from RNA sequencing analysis under nutient deficiencies.
Tools under development (not open for public access)
AtCAST (Arabidopsis thaliana transcriptome profile correlation analysis tool) is a web-based database with tools to analyze microarray and RNA-seq data. AtCAST provides basic statistical analysis of differentially expressed genes, its visualization by plots, gene ontology term enrichment (GO) analysis and Experiment-Experiment relation analysis using automatically selected marker gene module. New features: GSES, fRMA normalization with R data package. Coming soon...
SlCAST Ver0.03beta
This version is for Tomato transcriptome data.
Contents...
Redman, JC, Haas BJ, Tanimoto G, Town CD. (2004) Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant Journal 38: 545-561
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU (2005) A gene expression map of Arabidopsis thaliana development. Nature Genetics 37: 501-506
Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D'Angelo C, Bornberg-Bauer E, Kudla J, Harter K (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant Journal 50: 347-363
Goda H, Sasaki E, Akiyama K, Maruyama-Nakashita A, Nakabayashi K, Li W, Ogawa M, Yamauchi u, Preston J, Aoki K, Kiba T, Takatsuto S, Fujioka S, Asami T, Nakano T, Kato H, Mizuno T, Sakakibara H, Yamaguchi S, Nambara E, Kamiya Y, Takahashi H, Hirai MY, Sakurai T, Shinozaki K, Saito K, Yoshida S, Shimada Y (2008) The AtGenExpress hormone- and chemical-treatment data set: Experimental design, data evaluation, model data analysis, and data access. Plant Journal 130: 1319-1334
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU (2005) A gene expression map of Arabidopsis thaliana development. Nature Genetics 37: 501-506
Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D'Angelo C, Bornberg-Bauer E, Kudla J, Harter K (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant Journal 50: 347-363
Goda H, Sasaki E, Akiyama K, Maruyama-Nakashita A, Nakabayashi K, Li W, Ogawa M, Yamauchi u, Preston J, Aoki K, Kiba T, Takatsuto S, Fujioka S, Asami T, Nakano T, Kato H, Mizuno T, Sakakibara H, Yamaguchi S, Nambara E, Kamiya Y, Takahashi H, Hirai MY, Sakurai T, Shinozaki K, Saito K, Yoshida S, Shimada Y (2008) The AtGenExpress hormone- and chemical-treatment data set: Experimental design, data evaluation, model data analysis, and data access. Plant Journal 130: 1319-1334