TAPPA

A software for pathway analysis with network structure.

supportData.zip needs to be unzipped to run TAPPA.

Citation

Shouguo Gao, Xujing Wang, TAPPA: topological analysis of pathway phenotype association, Bioinformatics, Volume 23, Issue 22, 15 November 2007, Pages 3100–3102. https://academic.oup.com/bioinformatics/article/23/22/3100/208693

2. Basic steps for analysis

Step 1. Dowload the software and unzip file, then click pathway.bat to start the program.

**Step 2.** Choose files for gene expression (EntrezID as the first column) and phenotype data, then click run.

**Step 3.** The result is shown in a table and can be saved in a text file. Choose one pathway and click "Display Pathway Diagram".

**Step 4.** The selected pathway appears, and genes are colored by their expression features.

**Step 5.** Use mouse to select the subpathway for information examination.

**Step 6.** Check the genes in the selected subpathway. Expression can be examined with "Show Expression" button, and gene annotation can be retrived with "Detail information" button.

Developers and Maintainers

• Shouguo Gao (shouguo.gao@nih.gov)