BACKGROUND: We generated the gene expression profile of the total testis from the adult C57BL/6J male mice using serial analysis of gene expression (SAGE). Two high-quality SAGE libraries containing a total of 76 854 tags were constructed. An extensive bioinformatic analysis and comparison of SAGE transcriptomes of the total testis, testicular somatic cells and other mouse tissues was performed and the theory of male-biased gene accumulation on the X chromosome was tested. RESULTS: We sorted out 829 genes predominantly expressed from the germinal part and 944 genes from the somatic part of the testis. The genes preferentially and specifically expressed in total testis and testicular somatic cells were identified by comparing the testis SAGE transcriptomes to the available transcriptomes of seven non-testis tissues. We uncovered chromosomal clusters of adjacent genes with preferential expression in total testis and testicular somatic cells by a genome-wide search and found that the clusters encompassed a significantly higher number of genes than expected by chance. We observed a significant 3.2-fold enrichment of the proportion of X-linked genes specific for testicular somatic cells, while the proportions of X-linked genes specific for total testis and for other tissues were comparable. In contrast to the tissue-specific genes, an under-representation of X-linked genes in the total testis transcriptome but not in the transcriptomes of testicular somatic cells and other tissues was detected. CONCLUSION: Our results provide new evidence in favor of the theory of male-biased genes accumulation on the X chromosome in testicular somatic cells and indicate the opposite action of the meiotic X-inactivation in testicular germ cells.

• MeSH
• chromozom X MeSH
• databáze genetické MeSH
• genetická transkripce * MeSH
• genetická vazba MeSH
• genomika metody   MeSH
• genová knihovna MeSH
• interpretace statistických dat MeSH
• multigenová rodina MeSH
• myši inbrední C57BL MeSH
• myši MeSH
• pořadí genů MeSH
• regulace genové exprese * MeSH
• RNA metabolismus   MeSH
• sekvenční analýza DNA MeSH
• shluková analýza MeSH
• stanovení celkové genové exprese MeSH
• statistické modely MeSH
• testis metabolismus   MeSH
• výpočetní biologie metody   MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• RNA MeSH

The Mouse SAGE Site is a web-based database of all available public libraries generated by the Serial Analysis of Gene Expression (SAGE) from various mouse tissues and cell lines. The database contains mouse SAGE libraries organized in a uniform way and provides web-based tools for browsing, comparing and searching SAGE data with reliable tag-to-gene identification. A modified approach based on the SAGEmap database is used for reliable tag identification. The Mouse SAGE Site is maintained on an ongoing basis at the Institute of Molecular Genetics, Academy of Sciences of the Czech Republic and is accessible at the internet address http://mouse.biomed.cas.cz/sage/.

• MeSH
• databáze genetické * MeSH
• genová knihovna * MeSH
• internet MeSH
• myši genetika   MeSH
• stanovení celkové genové exprese * MeSH
• ukládání a vyhledávání informací MeSH
• výpočetní biologie MeSH
• zvířata MeSH
• Check Tag
• myši genetika   MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH

BACKGROUND: Large sets of well-characterized promoter sequences are required to facilitate the understanding of promoter architecture. The major sequence databases are a prospective source of upstream regulatory regions, but suffer from inaccurate annotation. The software tool PRESTA (PRomoter EST Association) presented in this study is designed for efficient recovery of characterized and partially verified promoters from GenBank and EMBL libraries. RESULTS: The PRESTA algorithm examines the putative GenBank/EMBL promoters and automatically removes most of the poorly annotated entries. The remaining records are connected to expressed sequence tags (ESTs) through a high-stringency BLAST search. The frequency and source of recovered ESTs provide an estimate of the activity and expression pattern of the promoter, and the ESTs' 5' ends assist in transcription start-site verification. The PRESTA database provides easy access to non-redundant upstream regulatory regions recently extracted by the PRESTA algorithm. The current size of this resource is 552 human and 241 mouse promoters. Surprisingly, no overlap between the PRESTA database and the Eukaryotic Promoter Database (EPD) was detected by sequence comparison. CONCLUSIONS: The PRESTA algorithm demonstrates the principle of promoter verification by mapping EST 5' ends. The publicly available PRESTA database collects hundreds of characterized and partially verified promoter sequences and is complementary to other promoter databases.

• MeSH
• algoritmy MeSH
• databáze nukleových kyselin MeSH
• exprese genu genetika   MeSH
• exprimované sekvenční adresy MeSH
• konformace nukleové kyseliny MeSH
• lidé MeSH
• myši MeSH
• on-line systémy MeSH
• promotorové oblasti (genetika) genetika   MeSH
• software * MeSH
• stanovení celkové genové exprese metody   MeSH
• ukládání a vyhledávání informací metody   MeSH
• výpočetní biologie metody   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH