Convert your Genes to Themes with EASE...
EASE is a software package that provides tools to help answer the following questions given a "results list" of genes from a genome-scale assay such as a microarray, SAGE or proteomics experiment:
1. What are the biological themes of the gene list?
2. What is known about the genes on the list associated with each of these themes?
3. How can the biomedical literature and other databases associated with these genes be mined to find a publishable story to pursue?
EASE is a standalone software package that runs on Windows operating systems. It uses a system of text files for its data sources, so it can be easily customized for the needs of any researcher. EASE comes equipped with an automatic update process that can be launched to create the various data files directly from primary online data sources.
EASE addresses the three questions above as follows:
1. EASE performs a statistical analysis of gene categories in the gene list to find those that are the most over-represented. The user can pick from the standard Fisher exact probability, or a conservative variant thereof called the EASE score that favors robust categories. The most significant categories as assessed by EASE score are deemed "themes" of the gene list.
2. Part of the data installed by the automatic update process includes descriptive gene annotation. EASE returns the genes for any given category so that the user can then create an annotation table to learn about the biology of those genes.
EASE uses a system of URL configuration files so that the user can load a list of genes into various online tools without the hassle of having to convert their identifiers into gene symbols, etc. URL configurations are provided for MedMole, PubMatrix and XploreMed for literature mining, and Amigo, DAVID, KEGG and LocusLink for functional mining. The user can create new URL configuration files so that future tools can be leveraged just as easily.