Acharya et al. BMC Genomics 2010, 11:467 http://www.biomedcentral.com/1471-2164/11/467 Page 5 of 10 Figure 1 Categorization of gene-sets in MGEx-Tdb based on the ‘number of genes per gene-set’. For example, there are 52 small gene-sets (each with less than 20 genes) and of these, 51 sets have been retrieved from literature. the rodent species. The majority of the gene-sets uploaded in the database have more than 500 genes each, but smaller gene-lists reported in manuscripts, have also been included in this database (Figure 1). Multiple gene-sets were indeed collected for certain conditions. For example, 124 gene-sets were collected for testicular cancer in humans from 7 reports, 35 gene- sets for normal human testis from 13 reports and 6 gene-sets for mouse spermatids from 5 reports. There are about 21 ESLCs, for each of which at least 2 differ- ent studies were compiled. Such comparable gene-sets were particularly useful in deriving a consensus of expression patterns and reliability-scores. However, there were many cases where we could get only one research article per condition such as adjudin and cad- mium chloride studies in rat, with 6 gene-sets each. During the comparative study, HPRD showed a better agreement with MCD (as shown in table 2) than other databases. However, it had the lowest coverage for human genes among the databases considered, with a score of 204. UniGene obtained 219, whereas MGEx- Tdb and BioGPS got the maximum possible 220 for coverage. It should be noted that HPRD is mainly a human protein database, with focus on multiple aspects of proteins. Unlike other databases considered, HPRD Table 2 Extent of agreement for gene expression pattern of 13 genes, between MCD and the databases Database Score (maximum = 26) HPRD MGEx-Tdb UniGene BioGPS 20 14 12 11 % agreement with reports on individual gene studies 77 54 46 42 provides the expression status that is established by manual curation of small-scale studies, at protein as well as mRNA levels. Hence, the higher agreement (see tables 2 and 3) with MCD as well as the lower coverage of HPRD is not surprising. MGEx-Tdb performed better, than other databases considered, in predicting the expression status of genes, when queried with various physiological conditions (see table 4, also see additional file 9 for methods). Even when queried with specific genes, MGEx-Tdb provided much more details (see table 3 and additional file 8). This new database also provided transcription informa- tion for more genes in the context of developmental stages, compared to the databases specialized for devel- opment-related gene expression patterns (see table 5, also see additional file 9 for methods). As expected, the tissue-specific compilation of mass- scale gene expression data resulted in agreement with MCD (individual gene studies, see table 2). MGEx-Tdb was as good as, or better than, UniGene and BioGPS, in terms of agreement with MCD. Since the results from HPRD agreed completely with MCD for 8 of the 13 query genes, it attained the highest % score for agree- ment with MCD as shown in table 2. This is despite the fact that HPRD showed only partial agreement with MCD for 3 genes, did not provide expression-related information for 1 gene and lacked any information for another. The newly created platform is also able to successfully separate the genes, which show consistent transcription status across the gene-sets/studies from those which do not. For example, using the output of MGEx-Tdb in case of testicular cancer, one can not only identify 8,410 transcribed and 8,207 dormant genes, but also categor- ize them further based on the reliability-score. Of the 8,410 genes, 674 had a reliability-score greater than 70, indicating that they have a higher probability of being expressed in human testicular cancer conditions. Simi- larly, 2,729 genes had a reliability-score between 10 and 70, while 1555 showed a score of 4 or less. In another example of 7,570 genes transcribed in 14 day old mice, 875 had a reliability-score of ≥6 and 2291 genes had a score of 2. Overall, MGEx-Tdb could offer the following advan- tages over the other databases analyzed: a) more useful query features, b) reliability of information provided, as indicated by high agreement with MCD, c) better output in terms of the number of genes, and d) the unique reliability indicator for each gene, under different ESLC. This new database did not agree with MCD to the same extent as HPRD, but showed better coverage and higher number of genes in the output for disease-related query. An overview of MGEx-Tdb usage is provided in the form of screen-shots in the additional file 10.