EXALT (EXpression signature AnaLysis Tool)

Category Genomics>Gene Expression Analysis/Profiling/Tools

Abstract EXALT (EXpression signature AnaLysis Tool) is a resource for examining 'gene expression signatures' in public domains.

A gene expression signature in a microarray data set is defined by EXALT as a list of 'significant genes' with their group comparison codes and corresponding statistical scores.

In essence, a signature represents a statistically validated ‘fingerprint’ associated with a biological observation made from a gene expression experiment.

EXALT has extracted signatures of differential genes within each experiment and built a large formatted collection of microarray results from NCBI GEO (see G6G Abstract Number 20013) and published cancer studies.

Thus, investigators can focus on discovery by searching, browsing, and querying on pre-computed gene expression signatures.

The EXALT system consists of four (4) components [two (2) program pipelines, a signature database (SigDB), and a search engine] and a web interface.

To compare a user-defined query with SigDB, gene expression signatures are first extracted from a pre-processed query data set using an array expression signature pipeline (AESP).

Each user-defined query signature is then compared with every subject signature in SigDB by computing similarity scores and confidence levels.

Thus, all signatures from the query dataset are compared with all signatures in SigDB. The EXALT comparisons are based on estimating the degree of 'signature similarity' expressed as a normalized total identity score (TIS) between 'expression signatures' derived from a query dataset and signatures in SigDB.

The significance of the similarity is determined by a simulation analysis.

Finally, reports of similarity are summarized at three (3) levels (gene, signature, and dataset) and sent to the user via a HyperText Markup Language (HTML) report pipeline (HRP).

Potential applications of EXALT --

There are many potential applications for global microarray data comparisons using EXALT. For example, investigators can gain significant increases in the power of detecting differentially expressed genes through in silico validation and comparisons with homologous microarray datasets.

EXALT can also enable large-scale searches for 'modules' of signatures with coordinated transcription across a wide range of conditions in multiple species.

Drug discovery is another area driving interest in comparing microarray datasets. Therapeutic effects and toxicity of new drugs could be investigated by correlating gene expression signatures associated with known drug or toxic responses.

Finally, enabling widespread use and comparisons of microarray data will enhance the value of public repositories such as GEO and stimulate other innovative approaches to exploiting these data.

System Requirements

The best performance of EXALT web site has been tested in IE6.0 or above.

Manufacturer

Manufacturer Web Site EXALT

Price Free

G6G Abstract Number 20227

G6G Manufacturer Number 102863