ExpressDB Information Page

ExpressDB was originally a relational database containing yeast and E. coli RNA expression data. As of October, 2000 it contained more than 20 million pieces of information loaded from numerous published and in-house expression studies. Only a small number of datasets have been added since that time. A manuscript describing the database and the process of managing and analyzing expression data was published in Genome Research. You can find the abstract and a link to the article that was published here.

The original query interface for ExpressDB depended on a Sybase installation running on a machine that has become quite old and unreliable, and most recent interest we have heard from users has requested the ability to download the datasets rather than query them centrally. We have had to decommision the old machine, and we now offer the ability to download most of the datasets. A few datasets have not yet been set up for downloading, but they all can be in response to specific requests.

ExpressDB documentation and donwload interfaces

Estimated relative abundances (ERAs) for 213 yeast conditions in the database

Procedures used to generate this file are described in detail in the article. Note: ERAs computed for microarray-based experiments exhibit increased error due to the way they were calculated.

Private yeast and E. coli datasets

There are a few dataset produced locally that have never been made available to the public. Those Church lab members who know the password for the labonly portion of the website can download these using these links:

Supplemental materials for article

BIGED data model

In addition to ExpressDB, we worked on a Biomolecule Interaction Growth and Expression Database (BIGED) that we conceived as a general, integrated database for functional genomics. BIGED can manage more than just RNA expression data and maintains strain and condition information in structured, queriable form. The Total Biomolecule Expression and Interaction Database (TBEID) was an earlier version of BIGED that covered more kinds of experiments but had less sophisticated indexing of biological entities.

Please contact Wayne Rindone if you have any questions or comments.

Copyright (c) 2006 Wayne Rindone and the President and Fellows of Harvard University.