Frequently Asked Questions
1. What is Ease?
2. Why does EASE have some functions redundant to DAVID?
3. If I don't mind transmitting my gene lists over the Internet, should I bother downloading EASE?
4. How do I get help using EASE?
5. Why are the gene counts within various categories different between DAVID and EASE?
6. I'm studying an organism not represented in LocusLink / I don't agree with defining genes as LocusLink numbers. Can I still use EASE?
7. Why is Human data always included with the distributions?
8. Why not include all species data in a single distribution?
9. What if I find a bug / EASE doesn't work / EASE behaves strangely?
10. What do I do if I have a question that is not answered here or in the "Help" function of EASE?
What is EASE? EASE is a stand-alone application for use on Windows operating systems that enables local analysis of gene lists. EASE includes a function to automatically download and parse annotation from public sources into local files so that gene lists can be analyzed without transmission over the internet. EASE accepts a list of gene identifiers in a manner similar to DAVID and performs three basic functions for any given list of genes: annotation, customizable linking to online tools, and biological "theme" finding using gene category over-representation analysis.
Why does EASE have some functions redundant to DAVID? Some researchers are reluctant to transmit gene lists over the internet for reasons of confidentiality. EASE allows these researchers to analyze data without a connection to the internet. More importantly, we realize that we cannot possibly include every conceivable type of annotation for every possible way of referring to genes on DAVID. So EASE is available as a system that is easy to customize to your individual needs.
If I don't mind transmitting my gene lists over the Internet, should I bother downloading EASE? If you are only annotating lists consisting of accession types available on DAVID, probably not. On the other hand, you'll need to download EASE if you plan to use EASE functions not yet implemented in DAVID such as those involved with biological "theme" finding by category over-representation analysis or those involved with customizable linking of gene lists to online tools. Also, if you prefer to use a gene accession system (e.g. 'clone ID') outside of Genbank, RefSeq, Unigene, LocusLink or Affymetrix, EASE is useful. EASE can serve as a convenient interface to DAVID and any number of online tools though a simple system of specifying URLs. EASE is also customizable in ways that are not possible with an online tool like DAVID. For example, if a researcher has access to a proprietary system for classifying genes, this classification system can be easily incorporated into the category over-representation function of EASE.
How do I get help using EASE? After starting the program, there is a "help" button near the upper right corner of the main screen. Click it, and a new window with buttons for various help topics will appear.
Why are the gene counts within various categories different between DAVID and EASE? DAVID reports the number of accessions that belong to a given category, EASE reports the number of genes that belong to a given category. This difference occurs with accession systems such as Genbank that can have many accessions for the same gene. DAVID leaves the choice of what is to be counted up to the user; whatever is input is what gets counted. EASE, on the other hand, cannot simply use the accessions supplied by the user, since this might lead to a gene with multiple accessions receiving more that one "vote" in the over-representation analysis. So EASE converts all accessions to LocusLink numbers before reporting counts. This of course begs the question of whether a unique LocusLink number is the best way to define a single gene. This definition is not without problems, however we have found that it is superior to other methods such as using the gene symbol.
I'm studying an organism not represented in LocusLink / I don't agree with defining genes as LocusLink numbers. Can I still use EASE? Yes. EASE uses a system of simple tab-delimited files for everything it does including converting accessions into genes, linking genes to annotation, linking genes to classification schema, and specifying gene-conversion schema for online tool URL creation. You can use any "unique gene identifier" (case-sensitive) you like in these files, but you will have to create the files manually. This is akin to "tricking" EASE into using your preferred unique gene identifiers instead of LocusLink numbers. The big disadvantage of doing this is that the automated update function of EASE cannot be used; you'll have to manually update your files.
Why is Human data always included with the distributions?Many of the non-human species are poorly annotated in the public databases. For this reason, we include the best annotated species (human) for the purpose of enabling "Enhancement" of annotation and categorical data for these species with human annotation. To use enhancement, click the checkbox below the over-representation analysis button or the checkbox below the annotation button. Then be sure to select the enhancement methods you want to use because the default is none even if you have the enhancement checkbox checked. You can enhance your species annotation by including annotation from Homologenes, KEGG orthologs, or even genes from other species with the same gene symbol.
Why not include all species data in a single distribution?For efficiency reasons. The simple text-file schema used by EASE for its data files makes modification and enhancement easy for the broadest number of users. But this flexibility comes at a substantial price in terms of performance: EASE must read through an entire annotation file, even if it only needs to extract a single line of information. So we try to limit the amount of "uninformative data" for various users by making various distributions available. Note that you can have an "all species" version of EASE if you so desire- just download any of the distributions, launch the update function within EASE and select all of the species listed when prompted.
What if I find a bug / EASE doesn't work / EASE behaves strangely? Make sure you have the most recent version of EASE: Click here for the current version information. --the bug may be fixed in the current version. (You can find your version in the "window title" at the top of the EASE main window.) If you are using the latest version, we would appreciate an e-mail sent to email@example.com that lets us know about the bug you've found as well as the version of Microsoft Windows you are using. Your input is critical to us! We will fix the bug and notify you when the fixed version is available on DAVID.
What do I do if I have a question that is not answered here or in the "Help" function of EASE? E-mail your question to firstname.lastname@example.org and we'll get back to you ASAP. This will also help us to determine additional FAQs to post on this page.