RESOURCERER: a database for annotating and linking microarray resources within and across species - PubMed (original) (raw)

RESOURCERER: a database for annotating and linking microarray resources within and across species

J Tsai et al. Genome Biol. 2001.

Abstract

Microarray expression analysis is providing unprecedented data on gene expression in humans and mammalian model systems. Although such studies provide a tremendous resource for understanding human disease states, one of the significant challenges is cross-referencing the data derived from different species, across diverse expression analysis platforms, in order to properly derive inferences regarding gene expression and disease state. To address this problem, we have developed RESOURCERER, a microarray-resource annotation and cross-reference database built using the analysis of expressed sequence tags (ESTs) and gene sequences provided by the TIGR Gene Index (TGI) and TIGR Orthologous Gene Alignment (TOGA) databases [now called Eukaryotic Gene Orthologs (EGO)].

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Figures

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, links to orthologous TCs in other mammalian species, and UniGene [19] cluster IDs where available. Text in blue is hot-linked to various databases through the RESOURCERER website.

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] and the Operon human oligos [10], redundancy in the clone set is captured by multiple rows in the table.

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References

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2. 1. RESOURCERER http://pga.tigr.org/tigr-scripts/nhgi_scripts/resourcerer.pl
3. 1. Quackenbush J, Cho J, Lee Y, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana J, White J. The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acid Res. 2001;29:159–164. - PMC - PubMed
4. 1. TIGR Gene Indices http://www.tigr.org/tdb/tgi.shtml
5. 1. TIGR Orthologous Gene Alignment database http://www.tigr.org/tdb/tgi/ego/index.shtml [All references in this article to TOGA and TIGR Orthologous Gene Alignments have been changed to EGO and Eukaryotic Gene Orthologs, respectively].

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