Wingender, Edgar

[["dc.bibliographiccitation.journal","European Journal of Cell Biology"],["dc.bibliographiccitation.volume","83"],["dc.contributor.author","Liebich, I."],["dc.contributor.author","Wingender, Edgar"],["dc.date.accessioned","2018-11-07T10:50:36Z"],["dc.date.available","2018-11-07T10:50:36Z"],["dc.date.issued","2004"],["dc.format.extent","61"],["dc.identifier.isi","000220823900130"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/48694"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Urban & Fischer Verlag"],["dc.publisher.place","Jena"],["dc.relation.conference","Annual Meeting of the Deutschen-Gesellschaft-fur-Zellbiologie"],["dc.relation.eventlocation","Berlin, Germany"],["dc.relation.issn","0171-9335"],["dc.title","S/MARt DB: The database on chromatin organizing elements"],["dc.type","conference_abstract"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","332"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","334"],["dc.bibliographiccitation.volume","30"],["dc.contributor.author","Kel-Margoulis, Olga V."],["dc.contributor.author","Kel, Alexander E."],["dc.contributor.author","Reuter, Ingmar"],["dc.contributor.author","Deineko, Igor V."],["dc.contributor.author","Wingender, Edgar"],["dc.date.accessioned","2019-07-10T08:12:51Z"],["dc.date.available","2019-07-10T08:12:51Z"],["dc.date.issued","2002"],["dc.description.abstract","Originating from COMPEL, the TRANSCompel® database emphasizes the key role of specific interactions between transcription factors binding to their target sites providing specific features of gene regulation in a particular cellular content. Composite regulatory elements contain two closely situated binding sites for distinct transcription factors and represent minimal functional units providing combinatorial transcriptional regulation. Both specific factor–DNA and factor–factor interactions contribute to the function of composite elements (CEs). Information about the structure of known CEs and specific gene regulation achieved through such CEs appears to be extremely useful for promoter prediction, for gene function prediction and for applied gene engineering as well. Each database entry corresponds to an individual CE within a particular gene and contains information about two binding sites, two corresponding transcription factors and experiments confirming cooperative action between transcription factors. The COMPEL database, equipped with the search and browse tools, is available at http://www.gene-regulation.com/pub/databases.html#transcompel. Moreover, we have developed the program CATCHTM for searching potential CEs in DNA sequences. It is freely available as CompelPatternSearch at http://compel.bionet.nsc.ru/FunSite/CompelPatternSearch.html"],["dc.identifier.fs","12179"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?goescholar/4106"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/61059"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.issn","1362-4962"],["dc.relation.orgunit","Universitätsmedizin Göttingen"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.subject.ddc","610"],["dc.title","TRANSCompel: a database on composite regulatory elements in eukaryotic genes."],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3433"],["dc.bibliographiccitation.issue","15"],["dc.bibliographiccitation.journal","NUCLEIC ACIDS RESEARCH"],["dc.bibliographiccitation.lastpage","3442"],["dc.bibliographiccitation.volume","30"],["dc.contributor.author","Liebich, I."],["dc.contributor.author","Bode, J."],["dc.contributor.author","Reuter, I."],["dc.contributor.author","Wingender, E."],["dc.date.accessioned","2019-07-10T08:12:49Z"],["dc.date.available","2019-07-10T08:12:49Z"],["dc.date.issued","2002"],["dc.description.abstract","Based on the contents of the database S/MARt DB, the most comprehensive data collection of scaffold/matrix-attached regions (S/MARs) publicly available thus far, we initiated a systematic evaluation of the stored data. By analyzing the 245 S/MAR sequences presently described in this database, we found that the S/MARs contained in this collection are generally AT-rich, with certain significant exceptions. Comparative analyses showed that most of the AT-rich motifs which were found to be enriched in S/MARs are also enriched in randomized S/MAR sequences of the same AT content. Some sequence patterns previously suggested to be characteristic for S/MARs were also investigated, among them potential binding sites for homeodomain transcription factors. Even though hexanucleotides containing the core motif of homeodomain factors were frequently observed in S/MARs, only a few potential binding sites for these factors were found enriched when compared with regulatory regions or exon sequences. All our analyses indicated that, on average, the observed frequency of motifs in S/MAR elements is largely influenced by the AT content. Our results can serve as a guideline for further improvements in the definition of S/MARs, which are now believed to constitute the functional coordinate system for genomic regulatory regions."],["dc.identifier.fs","12175"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?goescholar/4015"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/61045"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.issn","1362-4962"],["dc.relation.orgunit","Universitätsmedizin Göttingen"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.subject.ddc","610"],["dc.title","Evaluation of sequence motifs found in scaffold/matrix-attached regions (S/MARs)."],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1190"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","Bioinformatics"],["dc.bibliographiccitation.lastpage","1197"],["dc.bibliographiccitation.volume","22"],["dc.contributor.author","Kel, Alexander E."],["dc.contributor.author","Konovalova, T."],["dc.contributor.author","Waleev, T."],["dc.contributor.author","Cheremushkin, E."],["dc.contributor.author","Kel-Margoulis, Olga V."],["dc.contributor.author","Wingender, Edgar"],["dc.date.accessioned","2018-11-07T09:48:57Z"],["dc.date.available","2018-11-07T09:48:57Z"],["dc.date.issued","2006"],["dc.description.abstract","Motivation: Functionally related genes involved in the same molecular-genetic, biochemical or physiological process are often regulated coordinately. Such regulation is provided by precisely organized binding of a multiplicity of special proteins [transcription factors (TFs)] to their target sites (cis-elements) in regulatory regions of genes. Cis-element combinations provide a structural basis for the generation of unique patterns of gene expression. Results: Here we present a new approach for defining promoter models based on the composition of TF binding sites and their pairs. We utilize a multicomponent fitness function for selection of the promoter model that fits best to the observed gene expression profile. We demonstrate examples of successful application of the fitness function with the help of a genetic algorithm for the analysis of functionally related or co-expressed genes as well as testing on simulated and permutated data."],["dc.identifier.doi","10.1093/bioinformatics/btl041"],["dc.identifier.isi","000237319300007"],["dc.identifier.pmid","16473870"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/35413"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Oxford Univ Press"],["dc.relation.issn","1367-4803"],["dc.title","Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","European Journal of Cell Biology"],["dc.bibliographiccitation.volume","84"],["dc.contributor.author","Choi, C."],["dc.contributor.author","Kel-Margoulis, Olga V."],["dc.contributor.author","Kel, Alexander E."],["dc.contributor.author","Krull, M."],["dc.contributor.author","Pistor, S."],["dc.contributor.author","Voss, Nico"],["dc.contributor.author","Wingender, Edgar"],["dc.date.accessioned","2018-11-07T11:19:06Z"],["dc.date.available","2018-11-07T11:19:06Z"],["dc.date.issued","2005"],["dc.format.extent","23"],["dc.identifier.isi","000228527700027"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/55192"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Urban & Fischer Verlag"],["dc.publisher.place","Jena"],["dc.relation.conference","Annual Meeting of the Deutsche-Gesellschaft-fur-Zellbiologie"],["dc.relation.eventlocation","Heidelberg, GERMANY"],["dc.relation.issn","0171-9335"],["dc.title","The TRANSPATH((R)) database: Identifying candidate pathways regulating the ubiquitin ligase parkin, a marker of Parkinson disease"],["dc.type","conference_abstract"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","D540"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","D545"],["dc.bibliographiccitation.volume","34"],["dc.contributor.author","Potapov, Anatolij P."],["dc.contributor.author","Liebich, Ines"],["dc.contributor.author","Doenitz, Juergen"],["dc.contributor.author","Schwarzer, Knut"],["dc.contributor.author","Sasse, Nicole"],["dc.contributor.author","Schoeps, Torsten"],["dc.contributor.author","Crass, Torsten"],["dc.contributor.author","Wingender, Edgar"],["dc.date.accessioned","2018-11-07T10:39:42Z"],["dc.date.available","2018-11-07T10:39:42Z"],["dc.date.issued","2006"],["dc.description.abstract","EndoNet is a new database that provides information about the components of endocrine networks and their relations. It focuses on the endocrine cell-to-cell communication and enables the analysis of intercellular regulatory pathways in humans. In the EndoNet data model, two classes of components span a bipartite directed graph. One class represents the hormones ( in the broadest sense) secreted by defined donor cells. The other class consists of the acceptor or target cells expressing the corresponding hormone receptors. The identity and anatomical environment of cell types, tissues and organs is defined through references to the CYTOMER (R) ontology. With the EndoNet user interface, it is possible to query the database for hormones, receptors or tissues and to combine several items from different search rounds in one complex result set, from which a network can be reconstructed and visualized. For each entity, a detailed characteristics page is available. Some well-established endocrine pathways are offered as showcases in the form of predefined result sets. These sets can be used as a starting point for a more complex query or for obtaining a quick overview. The EndoNet database is accessible at http://endonet.bioinf.med.uni-goettingen.de/."],["dc.identifier.doi","10.1093/nar/gkj121"],["dc.identifier.isi","000239307700117"],["dc.identifier.pmid","16381928"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/46112"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Oxford Univ Press"],["dc.relation.issn","1362-4962"],["dc.relation.issn","0305-1048"],["dc.title","EndoNet: an information resource about endocrine networks"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Naunyn-Schmiedeberg s Archives of Pharmacology"],["dc.bibliographiccitation.volume","389"],["dc.contributor.author","Schlick, S."],["dc.contributor.author","Tiburcy, Malte"],["dc.contributor.author","Zeidler, S."],["dc.contributor.author","Lutz, S."],["dc.contributor.author","Wingender, Edgar"],["dc.contributor.author","Zimmermann, Wolfram-Hubertus"],["dc.date.accessioned","2018-11-07T10:19:01Z"],["dc.date.available","2018-11-07T10:19:01Z"],["dc.date.issued","2016"],["dc.format.extent","S12"],["dc.identifier.isi","000398368200040"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/41573"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Springer"],["dc.publisher.place","New york"],["dc.relation.conference","82nd Annual Meeting of the German-Society-for-Exerimental-and-Clinical-Pharmacology-and-Toxicology (DGPT) / 18th Annual Meeting of the Network-Clinical-Pharmacology-Germany (VKliPha)"],["dc.relation.eventlocation","Berlin, GERMANY"],["dc.relation.issn","1432-1912"],["dc.relation.issn","0028-1298"],["dc.title","Hyaluronic acid deposition determines engineered heart muscle characteristics and can be pharmacologically targeted to enhance function"],["dc.type","conference_abstract"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","97"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","100"],["dc.bibliographiccitation.volume","31"],["dc.contributor.author","Krull, Mathias"],["dc.contributor.author","Voss, Nico"],["dc.contributor.author","Choi, Claudia"],["dc.contributor.author","Pistor, Susanne"],["dc.contributor.author","Potapov, Anatolij"],["dc.contributor.author","Wingender, Edgar"],["dc.date.accessioned","2019-07-10T08:12:52Z"],["dc.date.available","2019-07-10T08:12:52Z"],["dc.date.issued","2003"],["dc.description.abstract","TRANSPATH® is a database system about gene regulatory networks that combines encyclopedic information on signal transduction with tools for visualization and analysis. The integration with TRANSFAC®, a database about transcription factors and their DNA binding sites, provides the possibility to obtain complete signaling pathways from ligand to target genes and their products, which may themselves be involved in regulatory action. As of July 2002, the TRANSPATH Professional release 3.2 contains about 9800 molecules, >1800 genes and >11 400 reactions collected from ~5000 references. With the ArrayAnalyzerTM, an integrated tool has been developed for evaluation of microarray data. It uses the TRANSPATH data set to identify key regulators in pathways connected with up- or down-regulated genes of the respective array. The key molecules and their surrounding networks can be viewed with the PathwayBuilderTM, a tool that offers four different modes of visualization. More information on TRANSPATH is available at http://www.biobase.de/pages/products/databases.html."],["dc.identifier.fs","12173"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?goescholar/4112"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/61065"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.issn","1362-4962"],["dc.relation.orgunit","Universitätsmedizin Göttingen"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.subject.ddc","610"],["dc.title","TRANSPATH (R): an integrated database on signal transduction and a tool for array analysis"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","I509"],["dc.bibliographiccitation.issue","18"],["dc.bibliographiccitation.journal","Bioinformatics"],["dc.bibliographiccitation.lastpage","I514"],["dc.bibliographiccitation.volume","28"],["dc.contributor.author","Li, Jie"],["dc.contributor.author","Hua, X. U."],["dc.contributor.author","Haubrock, Martin"],["dc.contributor.author","Wang, J."],["dc.contributor.author","Wingender, Edgar"],["dc.date.accessioned","2018-11-07T09:05:52Z"],["dc.date.available","2018-11-07T09:05:52Z"],["dc.date.issued","2012"],["dc.description.abstract","The great variety of human cell types in morphology and function is due to the diverse gene expression profiles that are governed by the distinctive regulatory networks in different cell types. It is still a challenging task to explain how the regulatory networks achieve the diversity of different cell types. Here, we report on our studies of the design principles of the tissue regulatory system by constructing the regulatory networks of eight human tissues, which subsume the regulatory interactions between transcription factors (TFs), microRNAs (miRNAs) and non-TF target genes. The results show that there are in-/out-hubs of high in-/out-degrees in tissue networks. Some hubs (strong hubs) maintain the hub status in all the tissues where they are expressed, whereas others (weak hubs), in spite of their ubiquitous expression, are hubs only in some tissues. The network motifs are mostly feed-forward loops. Some of them having no miRNAs are the common motifs shared by all tissues, whereas the others containing miRNAs are the tissue-specific ones owned by one or several tissues, indicating that the transcriptional regulation is more conserved across tissues than the post-transcriptional regulation. In particular, a common bow-tie framework was found that underlies the motif instances and shows diverse patterns in different tissues. Such bow-tie framework reflects the utilization efficiency of the regulatory system as well as its high variability in different tissues, and could serve as the model to further understand the structural adaptation of the regulatory system to the specific requirements of different cell functions."],["dc.identifier.doi","10.1093/bioinformatics/bts387"],["dc.identifier.isi","000308532300030"],["dc.identifier.pmid","22962474"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/25421"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Oxford Univ Press"],["dc.publisher.place","Oxford"],["dc.relation.conference","11th European Conference on Computational Biology (ECCB) / Conference of the Intelligent Systems in Molecular Biology (ISMB)"],["dc.relation.eventlocation","Basel, SWITZERLAND"],["dc.relation.issn","1367-4803"],["dc.title","The architecture of the gene regulatory networks of different tissues"],["dc.type","conference_paper"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","481"],["dc.bibliographiccitation.issue","5-6"],["dc.bibliographiccitation.journal","SAR and QSAR in Environmental Research"],["dc.bibliographiccitation.lastpage","494"],["dc.bibliographiccitation.volume","19"],["dc.contributor.author","Kel, Alexander E."],["dc.contributor.author","Voss, Nico"],["dc.contributor.author","Valeev, T."],["dc.contributor.author","Stegmaier, Philip"],["dc.contributor.author","Kel-Margoulis, Olga V."],["dc.contributor.author","Wingender, Edgar"],["dc.date.accessioned","2018-11-07T11:20:44Z"],["dc.date.available","2018-11-07T11:20:44Z"],["dc.date.issued","2008"],["dc.description.abstract","Different signal transduction pathways leading to the activation of transcription factors (TFs) converge at key molecules that master the regulation of many cellular processes. Such crossroads of signalling networks often appear as Achilles Heels causing a disease when not functioning properly. Novel computational tools are needed for analysis of the gene expression data in the context of signal transduction and gene regulatory pathways and for identification of the key nodes in the networks. An integrated computational system, ExPlain (TM) (www.biobase.de) was developed for causal interpretation of gene expression data and identification of key signalling molecules. The system utilizes data from two databases (TRANSFAC (R) and TRANSPATH (R)) and integrates two programs: (1) Composite Module Analyst (CMA) analyses 5'-upstream regions of co-expressed genes and applies a genetic algorithm to reveal composite modules (CMs) consisting of co-occurring single TF binding sites and composite elements; (2) ArrayAnalyzer (TM) is a fast network search engine that analyses signal transduction networks controlling the activities of the corresponding TFs and seeks key molecules responsible for the observed concerted gene activation. ExPlain (TM) system was applied to microarray data on inflammatory bowel diseases (IBD). The results obtained suggest a number of highly interesting biological hypotheses about molecular mechanisms of pathological genetic disregulation."],["dc.identifier.doi","10.1080/10629360802083806"],["dc.identifier.isi","000259995500004"],["dc.identifier.pmid","18853298"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/55611"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Taylor & Francis Ltd"],["dc.relation.issn","1062-936X"],["dc.title","ExPlain (TM): finding upstream drug targets in disease gene regulatory networks"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]