Preview Release of EPConDB 4.1

Version 4.1 of the EPConDB website has been released for preview and comment.

Our main goal for EPConDB 4.1 is to increase the visibility, utility, and amount of the expression data we are presenting. In addition, we want to highlight connections to the BCBC reagents and look forward to new ways of presenting data.

This is a preview release, so please take a look and tell us what you think. EPConDB 4.1 is available by a link from the front page of the EPConDB 4.0 site.

The rest of this document describes the new data and features in EPConDB 4.1. Click on the images to see that part of the site in more detail.

EPConDB now has 37 pancreatic studies and a total of 23 non pancreatic public studies. Many of the non-pancreatic studies are from the DGAP project and provide important diabetes-related information.

In addition, we have further categorized the studies to help you find the ones you want. The front page now contains a pop-menu which lists the categories and provide an easy way to find studies.

We have begun to create high-level summaries of the studies in EPConDB. These are visible at the betacell.org site and at EPConDB. They describe the goal, experimental approach, results and conclusions of the study with extensive links out to the relevant genes, publications, microarrays and more. The betacell.org display includes all lists of differentiallly expressed genes found in the study. We also point you to related studies that may also be of interest.

New study summaries will be created on an on-going basis.

To make data from expression studies more useful, EPConDB 4.1 includes comparison profiles which display the fold-changes in a transcript's expression across studies. The comparison profiles are displayed graphically as bar charts and appear in several places in the website.

First, when you go to a DoTS transcript page a medium-sized image will appear at the top of the page. (example)

Second, if you click on that small image you will go to the 'Comparison Profile' page for the DoTS transcript. This page shows a larger version of the graph as well as details of the comparisons and studies used to generate the graph. (example)

Third, thumbnails images of the graphs can be displayed in any DoTS transcript query result. To see them follow these simple steps:

1. do any transcript query (example)
2. find the 'Add Column' pop-up menu above the table of results
3. choose 'Comparison Profiles' from the menu

We have made comparisons for all of the studies that have enough biological replicates to make calls with reasonable confidence. We will expand coverage to all studies over the next few months.

While EPConDB has long had the ability to browse through expression studies, it hasn't been possible to query for studies of interest. With EPConDB 4.1, you can now search for studies in which your gene does something interesting. Just enter the transcript ID and EPConDB will list all of the comparisons where your gene did something interesting. (example)

The EPConDB navbar now includes a 'Networks' entry which links to a page containing a network of the transcription factors and other genes involved in the development and function of pancreatic islet cells. The network is clickable; gene links lead to DTs for those gene and tissue or cell type links lead to lists of genes specific to those tissues.

All of the BCBC mice strains or antibodies related to a transcript are now shown at the top each transcript summary page. The table contains links to the full description at the betacell.org site.