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Comparative Study
. 2007;8(7):R133.
doi: 10.1186/gb-2007-8-7-r133.

Strategy for encoding and comparison of gene expression signatures

Yajun Yi  1 , Chun Li, Clay Miller, Alfred L George Jr
Affiliations
Comparative Study

Strategy for encoding and comparison of gene expression signatures

Yajun Yi et al. Genome Biol. 2007.

Abstract

EXALT (EXpression signature AnaLysis Tool) is a computational system enabling comparisons of microarray data across experimental platforms and different laboratories http://seq.mc.vanderbilt.edu/exalt/. An essential feature of EXALT is a database holding thousands of gene expression signatures extracted from the Gene Expression Omnibus, and encoded in a searchable format. This novel approach to performing global comparisons of shared microarray data may have enormous value when coupled directly with a shared data repository.

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Figures

Figure 1
Figure 1
Schematic representation of EXALT system. A data flow diagram of computational steps is shown on the left, illustrating input of subject (Gene Expression Omnibus [GEO] dataset [GDS]) and query datasets, extraction of gene expression signatures, comparison with signature database, and generation of reports. Representative EXALT outputs are illustrated on the right, with three report levels including gene alignment, signature matches, and dataset matches. Reports are coded in HTML and include hypertext links (underlined blue text) to publicly accessible data sources or to other report levels. Some special terms were used in the gene alignment report. 'Total score' is the sum of positive identity score (PIS) and negative identity score (NIS). 'Concordance Identity Avg' is the average PIS per signature gene. 'Discordance Identity Avg' is the average NIS per signature gene. 'Concordant Similarity' is the number of concordant genes expressed as a percentage of the total number of genes in the signature. 'Discordant Similarity' is the number of discordant genes expressed as a percentage of the total number of genes in the signature. 'Alignment' refers to the list of query and matched subject triplets. AESP, array expression signature pipeline; EXALT, EXpression signature AnaLysis Tool; SigDB, signature database.
Figure 2
Figure 2
Significance trends among matching datasets. Six representative query datasets from the 124 self-matching results were compared using EXALT with all Gene Expression Omnibus (GEO) records. Corresponding adjusted mean P values for each dataset match are plotted on a log10 scale. The match number reflects the rank order of adjusted mean P values for each query dataset with one representing the best match. Self-matches exhibited the lowest adjusted mean P value for all query datasets and were ranked 1 in each search. EXALT, EXpression signature AnaLysis Tool; GDS, GEO dataset.
Figure 3
Figure 3
Cross-platform dataset matching revealed by EXALT. Heat-map illustrating the statistical significance among NCI-60 gene expression profiling experiments. The datasets include those reported by Staunton and coworkers [13] (dataset A), Butte and colleagues [12] (dataset B), Ross and coworkers [14] (dataset C), and GDS89. Datasets A and B were generated using Affymetrix arrays, whereas datasets C and GDS89 were generated using spotted cDNA arrays. Dataset comparisons exhibited adjusted mean P values below 0.01 (corresponding to values > 2.0 on the -log10 scale). The greatest significance levels were observed for self-matching and matches between studies using the same microarray platform. EXALT, EXpression signature AnaLysis Tool; GDS, Gene Expression Omnibus dataset.
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