Last update: May 13, 2015

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Yeast Genome 2.0 GeneChip profiling data for wild type versus ume6 mutant strains are published in Molecular Genetics and Genomics.

The paper on mRNA expression in wild type and ume6 strains in growth media and sporulation medium is published by Lardenois, Becker et al. Mol Genet Genomics 2015.

Human testicular expression data published in Human Reproduction.

The biggest human data set we have ever analyzed was just published in Human Reproduction by Chalmel et al. Hum Reprod 2012. Enjoy.

The GermOnline Wiki is history.

We have now removed the Wiki entries from the GermOnline report pages. They were not updated any more and commercials and other nonsense was uploaded into the database. We'd like to thank all database developers and scientists who have participated in our community annotation experiment for their time and effort.

Profiling study of Sox9-deficient Sertoli cells published in BR&E!

Testicular expression data with mouse GeneChips are now available from Lardenois et al. BR&E 2010. This study reports evidence for adult sex reversal in testes bearing Sox9-deficient Sertoli cells and the induction of genes involved in inflammation whose human orthologs are up-regulated in patients whose testes lack germ cells (Spiess et al. Hum Reprod 2007).

Great user feedback on GermOnline's SGV from Michael Lichten!

Just went to http://sgv.genouest.org/ for the first time, Michael. Consider this a fan letter–you have outdone yourselves!

Michael Lichten LBMB/CCR/NCI Building 37 Room 6124 37 Convent Dr. MSC 4260 Bethesda, MD 20892-4260 USA email: lichten@helix.nih.gov phone: +1 301-496-9760 fax: +1 301-402-3095

Study on ncRNA transcriptome and meiotic role for Rrp6 published in PNAS!

Data available via the Saccharomyces Genomics Viewer are now published in Lardenois et al. PNAS 2010. This study reports a novel type of ncRNA - meiotic unannotated transcripts (MUTs) and shows a role for the conserved exoribonuclease Rrp6 in the transition from mitosis to meiosis.

GermOnline update paper published in Database!

We elaborate on the current state of GermOnline and its new Saccharomyces Genomics Viewer in a paper that just appeared in the new online journal Database which is published by Oxford University Press. The SGV enables users to access complex multi-sample data sets from different studies obtained with tiling arrays that contain overlapping probes which cover the entire yeast genome. GermOnline is a free service for the community but someone has to pay for its maintenance and its development. To get funding, we need to publish update papers and editors like to see high citation rates - so please, if you find GermOnline useful for your research cite Lardenois and Gattiker et al. Database 2010.

ChIP-Chip data display improved!

The graphical display of in vivo transcription factor binding activities was improved. Have a look at the interaction of budding yeast Abf1 and other factors with the upstream region of CDC3. Scroll down to the “Genome-wide DNA binding assay” section and click on the plus in front of the referenced studie's title.

Protein network data updated!

Using information from different databases such as BioGRID, IntAct, MINT and MIPS we have now the following numbers of physical and genetic interactions per species:

 19166 Arabidopsis_thaliana
 25628 Caenorhabditis_elegans
 142 Danio_rerio
 54108 Drosophila_melanogaster
 99130 Homo_sapiens
 16380 Mus_musculus
 5212 Rattus_norvegicus
 535582 Saccharomyces_cerevisiae
 31432 Schizosaccharomyces_pombe

ChIP-Chip data on selected transcription factors relevant for meiosis and spore formation in budding yeast available!

We have incorporated data from a large-scale study on the in vivo DNA binding pattern of a large number of transcription factors by Harbison et al. published in Nature. Factors were selected based on their relevance for normal progression through meiosis and gametogenesis.

ChIP-Chip data on Ndt80 and Sum1 available!

A new study reports findings about how middle meiotic genes are regulated by the repressor Sum1 and the activator Ndt80 in budding yeast. The ChIP-Chip data by Klutstein et al. published in BMC Genomics are available for viewing.

Fly report pages contain a direct link to FlyTED!

The “Quick link” section in the fly report page includes a direct link to the FlyTED database which contains images of RNA in situ hybridization experiments covering 819 genes. The project is described in Zhao et al. in Nucleic Acids Research.

Some more changes in the welcome page:-D

You may have noticed some new items in the welcome page. A new browse database link leads you to a page that shows all query options including browsing the database via individual species. For new users we have a userguide in pdf format. The Help link provides guidance on entry points and various types of ensembl data display. Check out the Demo link for brief tutorial videos.

Report pages now contain direct link to Genevestigator!

The “Quick link” section in the report page now contains a direct link to the fabulous Genevestigator database. Check out the latest paper by Hruz et al. in Advances in Bioinformatics.

Data on mitotic arrest by Spo13 over-expression published!

Genome-wide profiling data of the Spo13-mediated mitotic cell cycle arrest are now published in Genetics.

GermOnline is now on a dedicated server :-)

The database has been moved onto a newly installed server which is part of Biogenouest's bioinformatics platform. Thank you to O. Collin (IRISA) for excellent system administration.

Current release based on better MIMAS!

GermOnline 4.0 features a simpler search interface, genome annotation based on Ensembl version 50, and the improved array data annotation system MIMAS 3.0.

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news.txt · Last modified: 2015/05/13 10:46 by michaelprimig
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