New function "Gene set enrichment search"
Normalization update using fRMA
A new function "Search experiments by differently expressed genes (DEGs)" added.
Statistic information page renewal with improved annotations
MA plot to show the selection of modules
93 RNA-seq experiments added.
Speed up of calculation (x10)
|2015.10.15||3.04||414 Microarray experiments added.|
A probrem about generating some pages in user analysis solved.
This was because of an update of RSQLite that is used via R scripts.
User analyses run on a job queueing system to prevent overflow..
Bug (Recognition of AGI code sometimes fails) fixed.
Input of Microsoft Excel files (.xls and .xlsx) is supported.
Bug (Input of user data from Windows fails) fixed.
Bug fixed. Released.
[Kakei Y and Shimada Y. (2015) AtCAST3.0 Update: A Web-Based Tool for Analysis of Transcriptome Data
by Searching Similarities in Gene Expression Profiles., Plant Cell Physiol., 56 (1): e7. ]
7000+ public microarray data were added.
AtCAST3.0 supports muilti-platform of DNA Microarray data, i.e. Affimetrix AG, ATH1
and Arabidopsis Gene 1.1 ST Array chips.
Input of RNA-seq count data is also supported.
GO term enrichment analysis of Modules is added.
UI and Visual design of network graph was changed.
|2012.8.17||2.06||Correlation experiment list fixed. UI fixed.|
|2012.5.21||2.04||Added the sort (by p-value or q-value) to results of t-test for each probe sets.|
[Sasaki E, Takahashi C, Asami T and Shimada Y. (2011) AtCAST, a tool for exploring gene expression
similarities among DNA microarray experiments using networks., Plant Cell Physiol., 52:169-180.]
|2009.7.23||2.00β||We released beta version of the new tool for analysing user own experiments.|