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June 01, 2009 (Vol. 29, No. 11)

Identifying New Gene-Expression Patterns

Analyzing XpressWay Human Expression Data with OmniViz Visual Analytics Software

  • Sensitive and Standardized Methodology

    The XpressWay gene-expression profiles are generated using quantitative real-time PCR, a method that allows detection of absolute mRNA levels in tissues. This technique is different from other methodologies such as chip-based assays, which measure relative abundance of mRNA.

    The target gene is multiplexed in the same well as GAPDH, which is used to confirm successful amplification. PCR amplification curves are analyzed to yield threshold values, and these are used to determine the starting mRNA copy number of both target and GAPDH genes by interpolation from a global standard curve. Rigorous pass/fail criteria are applied in order to ensure the quality of the data.

  • Gene Annotation

    XpressWay gene-expression data is provided with BioWisdom annotation around gene synonyms, disease, and process information. The provision of gene synonyms ensures that the user can find the gene of interest, and also facilitates connections to other data sources. For example, it is possible to send the synonyms out to PubMed in order to retrieve all the relevant publications around the target of interest. These documents can easily be imported into OmniViz, and, by employing the analytical tools available, the important themes of the documents, and hence the nature of the target, can be revealed.

    The inclusion of disease and process information provides context to the gene-expression data, and allows the user to search for interesting targets by virtue of their functional role.

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