The GermOnline 4.0 gateway is a cross-species microarray expression database focusing on germline development, meiosis and gametogenesis as well as the mitotic cell cycle 1. The database contains a unique combination of information:
1) High-throughput expression data obtained with whole-genome high-density oligonucleotide microarrays (GeneChips). 2) Sample annotation (mouse over the sample name and click on it) using the Multiomics Information Management and Annotation System (MIMAS 3.0 2). 3) In vivo protein-DNA binding data and protein-protein interaction data (available for selected species). 4) Genome annotation information from Ensembl version 50. 5) Orthologs are identified using data from Ensembl and OMA and linked to each other via a section in the report pages.
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.
Our database provides a free service for the community. It has become increasingly difficult to obtain sustainable funding for database projects but being able to publish an update paper in a well-cited journal does help. However, editors will (among other criteria) verify the citation rate of previously published papers. So, if you use GermOnline and you find it helpful, please cite Lardenois and Gattiker et al. Database 2010.
The current release of GermOnline provides users with a graphical display of individually selected studies of the mitotic cell cycle in normal or malign human cells as well as meiosis and gametogenesis in S. cerevisiae, A. thaliana, D. melanogaster, R. norvegicus, M. muculus and H. sapiens. A useful feature within the report pages enables you to access corresponding data via ortholog links. You can browse the available expression data sets by selecting a gene of interest and calling up the report page. For example, you can search by terms including the gene symbol (Mouse Spo11), a database identification number (MGI:1349669) or the Ensembl (ENSMUSG00000005883) identifier. Once you have reached the report page you need to scroll down to the microarray data section where you will see a display of referenced studies (the title and pubmed references are given). You can either select all datasets for simultaneous display or open and collapse individual displays. For more detailed information, please download the User guide
The advanced search option enables you to retrieve lists of genes based on published genome biological data using an implementation of the BioMart system. You first need to select the species (currently, data from S. cerevisiae and M. musculus are available), access the Query Form, select a database and the species and define your query in the filter form.
You are invited to contact firstname.lastname@example.org in case you intend to contribute raw CEL data files. Please note that the database displays only expression data obtained with high-density oligonucleotide microarrays (GeneChips).
S. cerevisiae: Genome Annotation | Gene Orthology | 3’UTR GeneChips | Protein-protein interaction | Tiling arrays | DNA-protein interaction. S. pombe: Genome Annotation | Gene Orthology | Protein-protein interaction. A. thaliana: Genome Annotation | Gene Orthology | 3’UTR GeneChips | Protein-protein interaction. C. elegans: Genome Annotation | Gene Orthology Protein-protein interaction. D. melanogaster: Genome Annotation | Gene Orthology | 3’UTR GeneChips | Protein-protein interaction. D. rerio: Genome Annotation | Gene Orthology |Protein-protein interaction. R. norvegicus: Genome Annotation | Gene Orthology | 3’UTR GeneChips | Protein-protein interaction. M. musculus: Genome Annotation | Gene Orthology | 3’UTR GeneChips | Protein-protein interaction. M. mulatta: Genome Annotation | Gene Orthology. P. troglodytes: Genome Annotation | Gene Orthology. H. sapiens: Genome Annotation | Gene Orthology | 3’UTR GeneChips | Protein-protein interaction.
1. Lardenois A et al. GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle. Database (Oxford) 2010; 2010 baq030. doi:10.1093/database/baq030 pmid:21149299. PubMed HubMed [Lardenois2010] 2. Gattiker A et al. 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. PubMed HubMed [Gattiker2009]