Description of the EASE Archive

EASE Annotation File System Information

What is EASE?

The EASE algorithm and supplied resource files support the identification of prevalent biological roles within lists of genes. The algorithm was originally created at NIAID (http://david.abcc.ncifcrf.gov/ease/ease.jsp, Hosack et al. 2003) and currently has been implemented in TIGR's MultiExperiment Viewer (MeV, http://www.tm4.org/mev/). EASE in MeV can be used to find and score biological roles within lists of genes that have correlated or interesting expression patterns. The results are presented in a table and individual viewers display the expression of genes within the discovered biological roles.

What will this file system contain?

The file systems produced for the PFGRC arrays are specifically designed to support the EASE analysis for the loci in the associated annotation file (.ann file) for this array. The loci within the array are always linked to TIGR CMR Cellular Role information (http://cmr.jcvi.org/tigr-scripts/CMR/RoleIds.cgi), PFam protein families (http://pfam.sanger.ac.uk/), TIGRFam TIGR generated protein families (http://www.jcvi.org/cms/research/projects/tigrfams/overview/), and in many cases Gene Ontology (GO) terms (http://www.geneontology.org/index.shtml). The file systems are structured to work with the EASE implementation within MeV and they contain files that link the locus IDs in the annotation file to functional annotation. A text file is included that describes the production date for the file system as well as the nature of the contents and some tips on using the file system. The source of the annotation is the TIGR Comprehensive Microbial Resource (CMR, http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi).

How to Install and Use the File System

The file system supports EASE analysis within MeV. If MeV is not currently used, you should download MeV from http://www.tm4.org/mev/ and unzip the download into a new folder.
Download and unzip the ease file system and .ann file for your array type.The default ease folder within MeV's 'data' directory can be renamed or removed and replaced with the folder labeled 'ease' in the new file system. The ease folder will be one level into the provided file system in a folder labeled with the annotation file name with "_ease.zip" appended (e.g. B_anthraisis_ease.zip). This folder will also contain the README.txt file that describes the contents of the file system.
The documentation directory in the MeV folder contains the user's manual in PDF format. The table of contents has a section covering all analysis modules in MeV and you can refer to the section on EASE for detailed instructions. In general the process involves loading the expression data into MeV, applying a clustering or statistical method to the data to produce clusters of interest, saving the clusters to the cluster manager (MeV's cluster repository), and then applying the EASE algorithm to identify and score prevalent biological themes.

Information and Resources

TIGR MeV - TIGR MultiExperiment Viewer and TM4 Suite Download Pages
http://www.tm4.org/mev/

TIGR TM4 Development Team

Original EASE Reference
Hosack, D.A., G. Dennis Jr., B.T. Sherman, H.C. Lane, R.A. Lempicki. Identifying biological themes within lists of genes with EASE. Genome Biol., 4:R70-R70.8, 2003.

TIGR Comprehensive Microbial Resource (CMR) Reference
J.D. Peterson, L.A. Umayam, T.M. Dickinson, E.K. Hickey and O. White. The Comprehensive Microbial Resource. Nucleic Acids Research, 29:1 (2001), 123-125.