FUNCTIONAL BIOINFORMATICS: THE CELLULAR RESPONSE DATABASE

James Sorace^1,2,3, Kip Canfield¹, Steven Russell¹

1 Department of Information Systems, University of Maryland Baltimore County, ²The Department of Pathology and Laboratory Service Baltimore VA Medical Center, ³ Department of Pathology, University of Maryland at Baltimore School of Medicine, Baltimore, Maryland

Received 4/3/97 Accepted 10/24/97

4. RESULTS OF TRIAL QUERIES

In order to demonstrate the utility of the data model, data from several of the thalidomide references noted above (1,2), and from a set of studies describing a family of interferon (IFN) induced GTPase like molecules (8,9,10), have been entered into the prototype CRD. The GTPase family currently consists of four published sequences, which show significant sequence homology with one another (8,9,10,11,12). Their expression is known to be modulated by a wide variety of agents including LPS, and IFNs. For some members of this family, patterns of inhibition or lack of induction by cytokines or drugs have also been reported. Based on these data, we have developed several queries that include:

1. Find the pattern(s) of response and manuscript reference for a given test agent. An example of this query, using thalidomide as the test agent, is shown in table 3, Panel A. Source data can be found in figure 2 and table 1 of reference 1, and figure 2 of reference 2.

2. Find the target genes up regulated by a cytokine, and display the test cell population. An example of this query is shown in table 3. Panel B, for IFN-gamma. Source data may be found in the first figure of references 8,9 and 10.

3. Find conditions in which an agent down-regulates the expression of a gene. The data from this query is shown in table 3, Panel C. This illustrates that LPS inhibits the ability of IFN-gamma to induce the MG21 GTPase. Source data may be found in figure 5 of reference 9.

4. List all other agents which have been assayed in combination with a given test agent. table 3, Panel D, lists all agents and assays that are linked to thalidomide as a test agent. Source data may be found in tables 1 and 2 of reference 1 (assay numbers 1-5, and 33), and figure 2A of reference 2 (assay number 6).