GermOnlineWiki:Main Page
From GermOnlineWiki
GermOnline
GermOnline 4.0 provides high-throughput expression data relevant for germline development and fertility across species (Gattiker et al., manuscript in preparation). The samples shown are comprehensively annotated using the Multiomics Information Management and Annotation System (MIMAS 3.0, [1]). The expression and ChIP-Chip data are presented in the context of genome annotation information from Ensembl version 50 [2, 3, 4, 5]. Currently, results from a variety of experiments relevant for the mitotic and meiotic cell cycle, gametogenesis and fertility in human, rodents, fly and yeast are shown. It is our goal to include novel relevant all-exon and tiling array data and the output of ultra-high throughput sequencing expression experiments (RNA-Seq) as they become available.
We are currently migrating the content of GermOnline Wiki to Wikipedia as part of our ongoing effort in the field of community based biocuration.
You can search GermOnline by using various terms including, e.g. mouse gene symbol (Spo11), or MGI (MGI:1349669 ), and Ensembl (ENSMUSG00000005883) identifiers. The advanced search option enables you to retrieve lists of genes based on published genome biological data using an implementation of the BioMart system. To search the database using genome coordinates go to mapview (www.germonline.org/Homo_sapiens/mapview, change species name for other organisms). Try for example the mapview for Homo sapiens.
Please note that GermOnline is not a public array data repository like the NCBI's GEO and the EBI's ArrayExpress. However, direct links for downloading raw data from the repositories are provided for each study referenced in the report page.
References
- Gattiker A, Hermida L, Liechti R, Xenarios I, Collin O, Rougemont J, and Primig M. MIMAS 3.0 is a Multiomics Information Management and Annotation System. BMC Bioinformatics 2009 May 18; 10 151. doi:10.1186/1471-2105-10-151 pmid:19450266.
- Gattiker A, Niederhauser-Wiederkehr C, Moore J, Hermida L, and Primig M. The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction. Nucleic Acids Res 2007 Jan; 35(Database issue) D457-62. doi:10.1093/nar/gkl957 pmid:17145711.
- Wiederkehr C, Basavaraj R, Sarrauste de Menthière C, Hermida L, Koch R, Schlecht U, Amon A, Brachat S, Breitenbach M, Briza P, Caburet S, Cherry M, Davis R, Deutschbauer A, Dickinson HG, Dumitrescu T, Fellous M, Goldman A, Grootegoed JA, Hawley R, Ishii R, Jégou B, Kaufman RJ, Klein F, Lamb N, Maro B, Nasmyth K, Nicolas A, Orr-Weaver T, Philippsen P, Pineau C, Rabitsch KP, Reinke V, Roest H, Saunders W, Schröder M, Schedl T, Siep M, Villeneuve A, Wolgemuth DJ, Yamamoto M, Zickler D, Esposito RE, and Primig M. GermOnline, a cross-species community knowledgebase on germ cell differentiation. Nucleic Acids Res 2004 Jan 1; 32(Database issue) D560-7. doi:10.1093/nar/gkh055 pmid:14681481.
- Wiederkehr C, Basavaraj R, Sarrauste de Menthière C, Koch R, Schlecht U, Hermida L, Masdoua B, Ishii R, Cassen V, Yamamoto M, Lane C, Cherry M, Lamb N, and Primig M. Database model and specification of GermOnline Release 2.0, a cross-species community annotation knowledgebase on germ cell differentiation. Bioinformatics 2004 Mar 22; 20(5) 808-11. doi:10.1093/bioinformatics/bth030 pmid:14751982.
- Primig M, Wiederkehr C, Basavaraj R, Sarrauste de Menthière C, Hermida L, Koch R, Schlecht U, Dickinson HG, Fellous M, Grootegoed JA, Hawley RS, Jégou B, Maro B, Nicolas A, Orr-Weaver T, Schedl T, Villeneuve A, Wolgemuth DJ, Yamamoto M, Zickler D, Lamb N, and Esposito RE. GermOnline, a new cross-species community annotation database on germ-line development and gametogenesis. Nat Genet 2003 Dec; 35(4) 291-2. doi:10.1038/ng1203-291 pmid:14647278.
