An R Package for Tissue Specific Genes Analysis
Copyright 2008 ©
Ye Chengyin, Wang Xusheng, Jun Zhu
Institute of Bioinformatics, Zhejiang University, China
TSGA is an R package used for microarray datasets analysis in purpose of identification of genes with overall treatments specificity and detection treatments with specific expression patterns for each gene. It improved ROKU method  by adding a gene expression filtration step. This software was written by ye which can be freely obtained from here.
The procedures included in TSGA for microarray data analysis are:
² Corrected Shannon Entropy Calculation for microarray data: the value indicates the overall specificity of each gene
² Specific Expression Patterns Detection, using an outlier detection-based method
² Principle Component Analysis (PCA) for the genes with high overall specificity
² Cluster analysis for genes and treatments
² Plotting for different results from above analysis
This package is suitable for microarray data of one-factor experimental design with multiple treatment levels.
Package and Manual Download
Supplementary Data Download
Error Messages and Troubleshooting:
If you have any questions with our software, please contact Jun Zhu, Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang 310029, China. Email: email@example.com.
 Kadota K, Ye J, Nakai Y, Terada T, Shimizu K: ROKU: a novel method for identification of tissue-specific genes. BMC Bioinformatics 2006, 7:294.
 Ye Chengyin, Wang Xusheng, Jun Zhu: TSGA: an R package for tissue specific genes analysis. submitted.