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Using Genomica from GeneCards®
Genomica is an analysis and visualization tool for genomic data, which can integrate gene expression data, DNA sequence data, and gene and experiment annotation information. Genomica's standalone java application provides extensive functionality; a subset of these capabilities can be accessed online.
GeneCards interfaces with one of these online services, Gene Set Enrichment, which analyzes whether or not genes of interest are functionally related, by comparing them against an extensive compendium of heterogeneous genomic data (including transcription factor targets, gene ontology, cancer modules, and more).
After executing a search in GeneCards, the results page provides a Genomica button. Clicking on it causes the set of gene symbols found by the search to be translated to EntrezGene identifiers which are sent to the Genomica server for further analysis and visualization.
Initially, an intermediate Genomica page is shown, detailing the progress of the query, and its estimated execution time. Please be patient; the Genomica server is undergoing an upgrade, and queries may encounter temporary peaks in CPU usage, sometimes taking a bit longer than estimated.
The final Genomica results page shows a link to the input set identifiers, followed by a summary table listing the comparison annotation sets, and whether or not the probe set (e.g. the GeneCards genes found by the GeneCards search) is found to be enriched in each respective arena. Finally, the enriched annotations, with scores and details, are visualized for each of the found matches.