ANAT: A Tool for Constructing and Analyzing Functional Protein Networks

Nir Yosef, Einat Zalckvar, Assaf D. Rubinstein, Max Homilius, Nir Atias, Liram Vardi, Igor Berman, Hadas Zur, Adi Kimchi, Eytan Ruppin, Roded Sharan*

*To whom correspondence should be addressed. E-mail: roded{at}post.tau.ac.ilmpsnyder{at}stanford.edu

Supplementary Materials:

• Supplementary Text: Performance evaluation of the TLM network.
• Table S1: Network sizes, data sources, and gene identifier types.
• Table S2: Constraints used for the autophagy-apoptosis crosstalk network.
• ANAT Plugin File (AnatPlugin.zip).
• ANAT User Manual (ANAT_manual.pdf).
• Gene Identifiers: A compressed archive of text files containing all the gene identifiers used in ANAT’s database (Gene_identifiers.zip).
• Autophagy Input Files: A compressed archive of the files for creating the autophagy-apoptosis crosstalk network (Autophagy_input.zip).
• Autophagy Network Reports: A compressed archive of the HTML reports for the autophagy-apoptosis crosstalk network (AutophagyNetworkReports.zip).
• Autophagy-Apoptosis File: A compressed archive of the Cytoscape session file for the autophagy-apoptosis crosstalk networks (Autophagy-apoptosis.zip).

Instructions for downloading and decompressing files:

1. Create a temporary folder on your machine's hard drive.
2. Save the compressed archive to the temporary folder you created, using the links above.
3. Decompress the compressed file in the temporary folder using decompression software such as WinZip (Windows; www.winzip.com) or StuffIt Expander (Windows and Mac; www.stuffit.com).

© 2011 American Association for the Advancement of Science