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.