Acharya et al. BMC Genomics 2010, 11:467 http://www.biomedcentral.com/1471-2164/11/467 information was downloaded. The information included the NCBI gene id, official gene symbol, aliases, gene sequence, gene summary, chromosomal location, poten- tial promoter sequence [-1000 to +200 bp] and all transcript sequences (along with exon-intron details) corresponding to each gene. Using gene symbol and Swiss-Prot IDs downloaded from NCBI gene database, protein-related information encoded by that gene was downloaded from Swiss-Prot [19] (http://ca.expasy.org/ sprot). Similarly, transcription start sites were down- loaded from dbTSS [20] (ftp://ftp.hgc.jp/pub/hgc/db/ dbtss/). When the information was not available in dbTSS for a gene, the 5’ end of corresponding NCBI RefSeq sequences (transcripts) was used to represent the TSS position. Perl codes were written to ensure auto- matic incorporation of the downloaded data into the database. Comparison of MGEx-Tdb with other existing resources Initially several databases were considered for compari- son (details in additional file 4). But only UniGene, BioGPS and HPRD were selected and compared in detail as described below. Assessing the degree of agreement of gene expression status between the databases and the manually curated data (MCD) Literature search was performed to compile reports on expression status of 60 human genes, which were ran- domly chosen (to avoid bias, MGEx-Tdb was not used as source). Selected articles corresponding to these genes were read in detail and evidences were collected for certain ESLCs. The focus was on studies that addressed the expression of one or a few genes only. Mass scale studies such as genome-wide expression pro- filing studies, which were used to create MGEx-Tdb, were avoided. More than one independent experimental evidence for the same expression status, by at least two separate studies, were available for 13 of the 60 chosen genes (see additional file 5). The expression status was obtained from the newly developed database as well as from UniGene, BioGPS and HPRD, for each of the 13 genes. This information was compared with the unanimous expression pattern derived from MCD, and scores were then assigned to indicate the extent of agreement (see additional file 6 for scoring details). Each database was thus scored for concurrence with MCD for the 13 genes. This exercise was performed independently by two individuals and the results were concurrent (see additional file 7 for details). Coverage of the databases The number of genes for which the databases could provide expression status was noted. A total of 110 Page 4 of 10 human genes were used (i.e., 50 more randomly chosen genes added to the list of earlier selected 60 genes). Every database was given a score of one when a gene was present in the database, and an additional score of one if the expression information for that gene is also present in the database. Thus, the maximum total score a database could get was 220. Final in silico validation of the database (see additional file 8 for details) Ten different genes reported to be predominantly expressed in mammalian testicular cells were taken and compared for two aspects as described below. a) Relative amount of information per gene: Every database was scored for availability of information for each gene’s expression in testis, in specific cell type, condition and in different species (mouse, rat and human). b) Agreement of each gene’s information from data- base with that of the information available in the litera- ture: For this comparison, a procedure similar to the one used above (in the case of MCD vs. database com- parison) was employed. Results A database with a total of 62,185 genes has been cre- ated. The genes were derived from 769 gene-sets, which in turn were collected from online resources like ArrayExpress, GEO as well as, from publications (table 1). The new database provides 19 different ESLC for humans (25,158 genes), 74 for mice (22,919 genes) and 26 for rats (14,108 genes). While cancer-related mass scale gene expression pro- filing have almost been exclusive to humans, studies on hormone treatment and gene knock-outs were more common in mice. Chemical treatment studies have been very frequent in rats. In addition, the newly created plat- form has the potential to indicate the expression pattern of a gene in about 36 different tissues under normal conditions. The gene-sets in the new database are predominantly transcript-lists from microarray studies. Mass scale stu- dies were rare for testicular cell types in humans unlike Table 1 The contribution of the number of gene-sets from each resource across species Resources ArrayExpress GEO PubMed Total Human 36 (15537) 131 (6337) 43 (225) 210 (7366) No. of gene-sets* Mouse 9 (11438) 302 (6359) 138 (3791) 449 (7196) Rat 45 (10452) 24 (8594) 41 (1116) 110 (6721) *The value in parenthesis represents average gene count across the gene-sets.