Dönitz, Jürgen

[["dc.bibliographiccitation.journal","Nucleic acids research"],["dc.contributor.author","Dönitz, Jürgen"],["dc.contributor.author","Gerischer, Lizzy"],["dc.contributor.author","Hahnke, Stefan"],["dc.contributor.author","Pfeiffer, Stefan"],["dc.contributor.author","Bucher, Gregor"],["dc.date.accessioned","2019-07-09T11:44:35Z"],["dc.date.available","2019-07-09T11:44:35Z"],["dc.date.issued","2017-10-24"],["dc.description.abstract","The iBeetle-Base provides access to sequence and phenotype information for genes of the beetle Tribolium castaneum. It has been updated including more and updated data and new functions. RNAi phenotypes are now available for >50% of the genes, which represents an expansion of 60% compared to the previous version. Gene sequence information has been updated based on the new official gene set OGS3 and covers all genes. Interoperability with FlyBase has been enhanced: First, gene information pages of homologous genes are interlinked between both databases. Second, some steps of a new query pipeline allow transforming gene lists from either species into lists with related gene IDs, names or GO terms. This facilitates the comparative analysis of gene functions between fly and beetle. The backend of the pipeline is implemented as endpoints of a RESTful interface, such that it can be reused by other projects or tools. A novel online interface allows the community to propose GO terms for their gene of interest expanding the range of animals where GO terms are defined. iBeetle-Base is available at http://ibeetle-base.uni-goettingen.de/."],["dc.identifier.doi","10.1093/nar/gkx984"],["dc.identifier.pmid","29069517"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/14825"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/59041"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.issn","1362-4962"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.subject.ddc","610"],["dc.title","Expanded and updated data and a query pipeline for iBeetle-Base."],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","D343"],["dc.bibliographiccitation.issue","D1"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","D347"],["dc.bibliographiccitation.volume","46"],["dc.contributor.author","Wingender, Edgar"],["dc.contributor.author","Schoeps, Torsten"],["dc.contributor.author","Haubrock, Martin"],["dc.contributor.author","Krull, Mathias"],["dc.contributor.author","Dönitz, Jürgen"],["dc.date.accessioned","2019-07-09T11:45:00Z"],["dc.date.available","2019-07-09T11:45:00Z"],["dc.date.issued","2018"],["dc.description.abstract","TFClass is a resource that classifies eukaryotic transcription factors (TFs) according to their DNA-binding domains (DBDs), available online at http://tfclass.bioinf.med.uni-goettingen.de. The classification scheme of TFClass was originally derived for human TFs and is expanded here to the whole taxonomic class of mammalia. Combining information from different resources, checking manually the retrieved mammalian TFs sequences and applying extensive phylogenetic analyses, >39 000 TFs from up to 41 mammalian species were assigned to the Superclasses, Classes, Families and Subfamilies of TFClass. As a result, TFClass now provides the corresponding sequence collection in FASTA format, sequence logos and phylogenetic trees at different classification levels, predicted TF binding sites for human, mouse, dog and cow genomes as well as links to several external databases. In particular, all those TFs that are also documented in the TRANSFAC® database (FACTOR table) have been linked and can be freely accessed. TRANSFAC® FACTOR can also be queried through an own search interface."],["dc.identifier.doi","10.1093/nar/gkx987"],["dc.identifier.pmid","29087517"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/14998"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/59137"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.issn","1362-4962"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.subject.ddc","610"],["dc.title","TFClass: expanding the classification of human transcription factors to their mammalian orthologs"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]