Much of microarray and proteomic analysis involves finding groups of interesting genes/proteins.
Some examples of such groups are:
1. clusters of genes with similar expression behavior over a timecourse,
2. genes significantly up-regulated or down-regulated with some experimental treatment,
3. genes for which expression correlates with some other experimental parameter, and
4. groups of genes derived from Venn diagrams of various groupings such as those listed above.
There are many bioinformatics software packages to address the needs of finding these groups of genes, but surprisingly little to help the a researcher once an interesting group of genes has been identified. EASE is meant to help the researcher explore the biology of any given group of genes. Currently, three tools are implemented in EASE:
The link-out tool allows researchers to stay abreast of new online analysis tools as they become available. It is essentially a method of creating a custom URL based upon a given list of genes. The simple configuration schema allows researchers to set up EASE as an interface to their favorite online tools. This way, a given list can be loaded a single time and used to query any number of online tools without the hassle of having to manually reformat the same genelist for each tool.
The analysis tool discovers categories of genes that are over-represented in the chosen gene list compared to what is represented in the microarray or species genome as a whole. Such over-represented categories represent biological "themes" of a given list.
The annotation tool is used quickly generate a table of descriptive information for all of the genes in one shot, without the need to flip to a different website for each gene.
Together, these tools help the researcher to determine the biological significance of their results in the context of the experiment, and allow the researcher to find interesting stories to pursue from any list of genes derived by any method.
Alas, we are still a long way from implementing the "Just give me the Answer" button...