Wingender, Edgar

[["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","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","1"],["dc.bibliographiccitation.issue","227"],["dc.bibliographiccitation.journal","BMC bioinformatics"],["dc.bibliographiccitation.lastpage","15"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Potapov, Anatolij P."],["dc.contributor.author","Goemann, Björn"],["dc.contributor.author","Wingender, Edgar"],["dc.date.accessioned","2019-07-10T08:12:56Z"],["dc.date.available","2019-07-10T08:12:56Z"],["dc.date.issued","2008"],["dc.description.abstract","Background: Currently, there is a gap between purely theoretical studies of the topology of large bioregulatory networks and the practical traditions and interests of experimentalists. While the theoretical approaches emphasize the global characterization of regulatory systems, the practical approaches focus on the role of distinct molecules and genes in regulation. To bridge the gap between these opposite approaches, one needs to combine 'general' with 'particular' properties and translate abstract topological features of large systems into testable functional characteristics of individual components. Here, we propose a new topological parameter the pairwise disconnectivity index of a network's element that is capable of such bridging. Results: The pairwise disconnectivity index quantifies how crucial an individual element is for sustaining the communication ability between connected pairs of vertices in a network that is displayed as a directed graph. Such an element might be a vertex (i.e., molecules, genes), an edge (i.e., reactions, interactions), as well as a group of vertices and/or edges. The index can be viewed as a measure of topological redundancy of regulatory paths which connect different parts of a given network and as a measure of sensitivity (robustness) of this network to the presence (absence) of each individual element. Accordingly, we introduce the notion of a path-degree of a vertex in terms of its corresponding incoming, outgoing and mediated paths, respectively. The pairwise disconnectivity index has been applied to the analysis of several regulatory networks from various organisms. The importance of an individual vertex or edge for the coherence of the network is determined by the particular position of the given element in the whole network.Conclusion: Our approach enables to evaluate the effect of removing each element (i.e., vertex, edge, or their combinations) from a network. The greatest potential value of this approach is its ability to systematically analyze the role of every element, as well as groups of elements, in a regulatory network."],["dc.identifier.fs","208708"],["dc.identifier.ppn","575637900"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/4333"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/61079"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.orgunit","Universitätsmedizin Göttingen"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.subject.ddc","610"],["dc.title","The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks"],["dc.title.alternative","Methodology article"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","520"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC Research Notes"],["dc.bibliographiccitation.volume","4"],["dc.contributor.author","Ante, Michael"],["dc.contributor.author","Wingender, Edgar"],["dc.contributor.author","Fuchs, Mathias"],["dc.date.accessioned","2019-07-09T11:53:24Z"],["dc.date.available","2019-07-09T11:53:24Z"],["dc.date.issued","2011"],["dc.description.abstract","Background Reconstruction of protein-protein interaction or metabolic networks based on expression data often involves in silico predictions, while on the other hand, there are unspecific networks of in vivo interactions derived from knowledge bases. We analyze networks designed to come as close as possible to data measured in vivo, both with respect to the set of nodes which were taken to be expressed in experiment as well as with respect to the interactions between them which were taken from manually curated databases Results A signaling network derived from the TRANSPATH database and a metabolic network derived from KEGG LIGAND are each filtered onto expression data from breast cancer (SAGE) considering different levels of restrictiveness in edge and vertex selection. We perform several validation steps, in particular we define pathway over-representation tests based on refined null models to recover functional modules. The prominent role of the spindle checkpoint-related pathways in breast cancer is exhibited. High-ranking key nodes cluster in functional groups retrieved from literature. Results are consistent between several functional and topological analyses and between signaling and metabolic aspects. Conclusions This construction involved as a crucial step the passage to a mammalian protein identifier format as well as to a reaction-based semantics of metabolism. This yielded good connectivity but also led to the need to perform benchmark tests to exclude loss of essential information. Such validation, albeit tedious due to limitations of existing methods, turned out to be informative, and in particular provided biological insights as well as information on the degrees of coherence of the networks despite fragmentation of experimental data. Key node analysis exploited the networks for potentially interesting proteins in view of drug target prediction."],["dc.identifier.doi","10.1186/1756-0500-4-520"],["dc.identifier.fs","583431"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/7428"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/60417"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.rights","CC BY 2.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/2.0"],["dc.subject.ddc","610"],["dc.title","Integration of gene expression data with prior knowledge for network analysis and validation"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","935"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","Nature Biotechnology"],["dc.bibliographiccitation.lastpage","942"],["dc.bibliographiccitation.volume","28"],["dc.contributor.author","Demir, Emek"],["dc.contributor.author","Cary, Michael P."],["dc.contributor.author","Paley, Suzanne"],["dc.contributor.author","Fukuda, Ken"],["dc.contributor.author","Lemer, Christian"],["dc.contributor.author","Vastrik, Imre"],["dc.contributor.author","Wu, Guanming"],["dc.contributor.author","D'Eustachio, Peter"],["dc.contributor.author","Schaefer, Carl"],["dc.contributor.author","Luciano, Joanne"],["dc.contributor.author","Schacherer, Frank"],["dc.contributor.author","Martinez-Flores, Irma"],["dc.contributor.author","Hu, Zhenjun"],["dc.contributor.author","Jimenez-Jacinto, Veronica"],["dc.contributor.author","Joshi-Tope, Geeta"],["dc.contributor.author","Kandasamy, Kumaran"],["dc.contributor.author","Lopez-Fuentes, Alejandra C."],["dc.contributor.author","Mi, Huaiyu"],["dc.contributor.author","Pichler, Elgar"],["dc.contributor.author","Rodchenkov, Igor"],["dc.contributor.author","Splendiani, Andrea"],["dc.contributor.author","Tkachev, Sasha"],["dc.contributor.author","Zucker, Jeremy"],["dc.contributor.author","Gopinath, Gopal"],["dc.contributor.author","Rajasimha, Harsha"],["dc.contributor.author","Ramakrishnan, Ranjani"],["dc.contributor.author","Shah, Imran"],["dc.contributor.author","Syed, Mustafa"],["dc.contributor.author","Anwar, Nadia"],["dc.contributor.author","Babur, Özgün"],["dc.contributor.author","Blinov, Michael"],["dc.contributor.author","Brauner, Erik"],["dc.contributor.author","Corwin, Dan"],["dc.contributor.author","Donaldson, Sylva"],["dc.contributor.author","Gibbons, Frank"],["dc.contributor.author","Goldberg, Robert"],["dc.contributor.author","Hornbeck, Peter"],["dc.contributor.author","Luna, Augustin"],["dc.contributor.author","Murray-Rust, Peter"],["dc.contributor.author","Neumann, Eric"],["dc.contributor.author","Reubenacker, Oliver"],["dc.contributor.author","Samwald, Matthias"],["dc.contributor.author","van Iersel, Martijn"],["dc.contributor.author","Wimalaratne, Sarala"],["dc.contributor.author","Allen, Keith"],["dc.contributor.author","Braun, Burk"],["dc.contributor.author","Whirl-Carrillo, Michelle"],["dc.contributor.author","Cheung, Kei-Hoi"],["dc.contributor.author","Dahlquist, Kam"],["dc.contributor.author","Finney, Andrew"],["dc.contributor.author","Gillespie, Marc"],["dc.contributor.author","Glass, Elizabeth"],["dc.contributor.author","Gong, Li"],["dc.contributor.author","Haw, Robin"],["dc.contributor.author","Honig, Michael"],["dc.contributor.author","Hubaut, Olivier"],["dc.contributor.author","Kane, David"],["dc.contributor.author","Krupa, Shiva"],["dc.contributor.author","Kutmon, Martina"],["dc.contributor.author","Leonard, Julie"],["dc.contributor.author","Marks, Debbie"],["dc.contributor.author","Merberg, David"],["dc.contributor.author","Petri, Victoria"],["dc.contributor.author","Pico, Alex"],["dc.contributor.author","Ravenscroft, Dean"],["dc.contributor.author","Ren, Liya"],["dc.contributor.author","Shah, Nigam"],["dc.contributor.author","Sunshine, Margot"],["dc.contributor.author","Tang, Rebecca"],["dc.contributor.author","Whaley, Ryan"],["dc.contributor.author","Letovksy, Stan"],["dc.contributor.author","Buetow, Kenneth H."],["dc.contributor.author","Rzhetsky, Andrey"],["dc.contributor.author","Schachter, Vincent"],["dc.contributor.author","Sobral, Bruno S."],["dc.contributor.author","Dogrusoz, Ugur"],["dc.contributor.author","McWeeney, Shannon"],["dc.contributor.author","Aladjem, Mirit"],["dc.contributor.author","Birney, Ewan"],["dc.contributor.author","Collado-Vides, Julio"],["dc.contributor.author","Goto, Susumu"],["dc.contributor.author","Hucka, Michael"],["dc.contributor.author","Novère, Nicolas Le"],["dc.contributor.author","Maltsev, Natalia"],["dc.contributor.author","Pandey, Akhilesh"],["dc.contributor.author","Thomas, Paul"],["dc.contributor.author","Wingender, Edgar"],["dc.contributor.author","Karp, Peter D."],["dc.contributor.author","Sander, Chris"],["dc.contributor.author","Bader, Gary D."],["dc.date.accessioned","2019-07-09T11:52:52Z"],["dc.date.available","2019-07-09T11:52:52Z"],["dc.date.issued","2010"],["dc.description.abstract","Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery."],["dc.identifier.doi","10.1038/nbt.1666"],["dc.identifier.fs","574085"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/6096"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/60297"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.subject.ddc","610"],["dc.title","The BioPAX community standard for pathway data sharing"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["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"]]

[["dc.bibliographiccitation.firstpage","374"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","378"],["dc.bibliographiccitation.volume","31"],["dc.contributor.author","Matys, V."],["dc.contributor.author","Haubrock, M."],["dc.contributor.author","Wingender, E."],["dc.date.accessioned","2022-06-08T07:59:10Z"],["dc.date.available","2022-06-08T07:59:10Z"],["dc.date.issued","2003"],["dc.description.abstract","The TRANSFAC® database on eukaryotic transcriptional regulation, comprising data on transcription factors, their target genes and regulatory binding sites, has been extended and further developed, both in number of entries and in the scope and structure of the collected data. Structured fields for expression patterns have been introduced for transcription factors from human and mouse, using the CYTOMER® database on anatomical structures and developmental stages. The functionality of MatchTM, a tool for matrix-based search of transcription factor binding sites, has been enhanced. For instance, the program now comes along with a number of tissue-(or state-)specific profiles and new profiles can be created and modified with MatchTM Profiler. The GENE table was extended and gained in importance, containing amongst others links to LocusLink, RefSeq and OMIM now. Further, (direct) links between factor and target gene on one hand and between gene and encoded factor on the other hand were introduced. The TRANSFAC® public release is available at http://www.gene-regulation.com. For yeast an additional release including the latest data was made available separately as TRANSFAC® Saccharomyces Module (TSM) at http://transfac.gbf.de. For CYTOMER® free download versions are available at http://www.biobase.de:8080/index.html."],["dc.identifier.doi","10.1093/nar/gkg108"],["dc.identifier.fs","12171"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?goescholar/4111"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/110656"],["dc.notes.intern","DOI-Import GROB-575"],["dc.relation.eissn","1362-4962"],["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","TRANSFAC(R): transcriptional regulation, from patterns to profiles"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","372"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","NUCLEIC ACIDS RESEARCH"],["dc.bibliographiccitation.lastpage","374"],["dc.bibliographiccitation.volume","30"],["dc.contributor.author","Liebich, Ines"],["dc.contributor.author","Bode, Jürgen"],["dc.contributor.author","Frisch, Matthias"],["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","S/MARt DB, the S/MAR transaction database, is a relational database covering scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins that are involved in the chromosomal attachment to the nuclear scaffold. The data are mainly extracted from original publications, but a World Wide Web interface for direct submissions is also available. S/MARt DB is closely linked to the TRANSFAC database on transcription factors and their binding sites. It is freely accessible through the World Wide Web (http://transfac.gbf.de/SMARtDB/) for non-profit research."],["dc.identifier.fs","12178"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?goescholar/4105"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/61058"],["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","S/MARt DB: a database on scaffold/matrix attached regions."],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","266"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","269"],["dc.bibliographiccitation.volume","31"],["dc.contributor.author","Munch, Richard"],["dc.contributor.author","Hiller, Karsten"],["dc.contributor.author","Barg, Heiko"],["dc.contributor.author","Heldt, Dana"],["dc.contributor.author","Linz, Simone"],["dc.contributor.author","Wingender, Edgar"],["dc.contributor.author","Jahn, Dieter"],["dc.date.accessioned","2019-07-10T08:12:52Z"],["dc.date.available","2019-07-10T08:12:52Z"],["dc.date.issued","2003"],["dc.description.abstract","The database PRODORIC aims to systematically organize information on prokaryotic gene expression, and to integrate this information into regulatory networks. The present version focuses on pathogenic bacteria such as Pseudomonas aeruginosa. PRODORIC links data on environmental stimuli with trans-acting transcription factors, cis-acting promoter elements and regulon definition. Interactive graphical representations of operon, gene and promoter structures including regulator-binding sites, transcriptional and translational start sites, supplemented with information on regulatory proteins are available at varying levels of detail. The data collection provided is based on exhaustive analyses of scientific literature and computational sequence prediction. Included within PRODORIC are tools to define and predict regulator binding sites. It is accessible at http://prodoric.tu-bs.de."],["dc.identifier.fs","12172"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?goescholar/4109"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/61062"],["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","PRODORIC: prokaryotic database of gene regulation."],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]