For each human, mouse, or rat microarray resource (full details of which are included in Table ), including widely distributed clone sets [6
] and the commercially available Affymetrix GeneChips™ [11
], we loaded the clone or feature identifiers, as appropriate, into the RESOURCERER database, along with the associated GenBank accession numbers and other available annotation data, such as UniGene [19
] cluster IDs, if provided by the creators of the primary resources. The GenBank accession numbers are then used as keys to link these resources to the TC sequences in the appropriate TGI database, and through those, to the orthologs captured in TOGA; as the TGI and TOGA databases are updated, annotations based upon them are updated as well, providing the most current annotation possible.
Array resources currently represented in RESOURCERER, with the total number of elements in each
As all data are stored in a relational database, we are then able to make a variety of complex queries. For each represented microarray resource, RESOURCERER allows creation of a table of TGI-based annotation for each element of the set, including TC numbers, putative functional assignments, and links to orthologous TCs in the other species (Figure ). Further, one can use RESOURCERER to make comparisons between two resource sets derived from the same species, including identifying both the intersection and difference between those sets, with comparisons based on the appropriate species-specific TGI database, or UniGene identifiers, if available (see Table for details of the relationships between the different array resources accessed through RESOURCERER). Finally, by using TOGA, orthologous genes represented in these microarray resources can be identified, facilitating comparisons of gene expression patterns between species (Figure ).
Figure 1 An example of the data provided for the NIA mouse cDNA collection [8,9]. Annotation for individual microarray resource sets is provided by the TGI databases, including functional assignments (where available), links to the TCs for the species in question, (more ...)
The number of orthologous and/or corresponding genes shared between array resources across and/or within species, based on the TOGA and TGI databases
Figure 2 Using RESOURCERER, one can identify corresponding orthologous elements in various microarray resources, providing the information necessary to facilitate cross-species comparisons. Note that in this comparison between the NIA mouse cDNA collection [8,9] (more ...)
It is this final feature that provides the greatest utility in RESOURCERER. Mouse and rat are ideal organisms for comparative analysis of mammalian coding sequences. Mouse is the premier organism for the study of mammalian genetics and development, while rat has been extensively used for physiological and pharmacological studies. Mouse and rat genome projects, involving genetic and physical mapping, EST sequencing, and genomic sequencing, are underway and progressing rapidly. Consequently, there is a tremendous opportunity to understand disease processes in humans by comparing and contrasting gene expression profiles in both mice and rats, and linking these to patterns observed in human patients. RESOURCERER provides a crucial tool for making such comparisons. Already, RESOURCERER has been used to facilitate comparisons between patterns of expression observed in rodent models of tumor metastasis and those seen in patients (N.H. Lee, personal communication). As expression analysis programs continue to expand, comparison between experiments and experimental systems will be increasingly important. RESOURCERER plays the critical role of facilitating these comparisons.