KOPS - The Institutional Repository of the University of Konstanz

ISMARA : automated modeling of genomic signals as a democracy of regulatory motifs

ISMARA : automated modeling of genomic signals as a democracy of regulatory motifs

Cite This

Files in this item

Checksum: MD5:ec232fc4d055e6da619ca81f8e9c10fb

BALWIERZ, Piotr J., Mikhail PACHKOV, Phil ARNOLD, Andreas J. GRUBER, Mihaela ZAVOLAN, Erik VAN NIMWEGEN, 2014. ISMARA : automated modeling of genomic signals as a democracy of regulatory motifs. In: Genome research. Cold Spring Harbor Laboratory Press. 24(5), pp. 869-884. ISSN 1054-9803. eISSN 1549-5469. Available under: doi: 10.1101/gr.169508.113

@article{Balwierz2014-05ISMAR-51013, title={ISMARA : automated modeling of genomic signals as a democracy of regulatory motifs}, year={2014}, doi={10.1101/gr.169508.113}, number={5}, volume={24}, issn={1054-9803}, journal={Genome research}, pages={869--884}, author={Balwierz, Piotr J. and Pachkov, Mikhail and Arnold, Phil and Gruber, Andreas J. and Zavolan, Mihaela and van Nimwegen, Erik} }

<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:void="http://rdfs.org/ns/void#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > <rdf:Description rdf:about="https://kops.uni-konstanz.de/rdf/resource/123456789/51013"> <dc:contributor>Pachkov, Mikhail</dc:contributor> <dc:creator>van Nimwegen, Erik</dc:creator> <dc:contributor>van Nimwegen, Erik</dc:contributor> <foaf:homepage rdf:resource="http://localhost:8080/jspui"/> <dc:contributor>Balwierz, Piotr J.</dc:contributor> <dcterms:issued>2014-05</dcterms:issued> <dc:contributor>Arnold, Phil</dc:contributor> <dc:contributor>Zavolan, Mihaela</dc:contributor> <dc:rights>terms-of-use</dc:rights> <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/51013/3/Balwierz_2-1211bs4q2j2qe8.pdf"/> <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/rdf/resource/123456789/28"/> <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/51013"/> <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2020-09-24T09:09:00Z</dc:date> <dc:creator>Pachkov, Mikhail</dc:creator> <dcterms:abstract xml:lang="eng">Accurate reconstruction of the regulatory networks that control gene expression is one of the key current challenges in molecular biology. Although gene expression and chromatin state dynamics are ultimately encoded by constellations of binding sites recognized by regulators such as transcriptions factors (TFs) and microRNAs (miRNAs), our understanding of this regulatory code and its context-dependent read-out remains very limited. Given that there are thousands of potential regulators in mammals, it is not practical to use direct experimentation to identify which of these play a key role for a particular system of interest. We developed a methodology that models gene expression or chromatin modifications in terms of genome-wide predictions of regulatory sites and completely automated it into a web-based tool called ISMARA (Integrated System for Motif Activity Response Analysis). Given only gene expression or chromatin state data across a set of samples as input, ISMARA identifies the key TFs and miRNAs driving expression/chromatin changes and makes detailed predictions regarding their regulatory roles. These include predicted activities of the regulators across the samples, their genome-wide targets, enriched gene categories among the targets, and direct interactions between the regulators. Applying ISMARA to data sets from well-studied systems, we show that it consistently identifies known key regulators ab initio. We also present a number of novel predictions including regulatory interactions in innate immunity, a master regulator of mucociliary differentiation, TFs consistently disregulated in cancer, and TFs that mediate specific chromatin modifications.</dcterms:abstract> <dc:creator>Zavolan, Mihaela</dc:creator> <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/rdf/resource/123456789/28"/> <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2020-09-24T09:09:00Z</dcterms:available> <dc:language>eng</dc:language> <dc:creator>Gruber, Andreas J.</dc:creator> <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/51013/3/Balwierz_2-1211bs4q2j2qe8.pdf"/> <dc:contributor>Gruber, Andreas J.</dc:contributor> <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/> <dcterms:rights rdf:resource="https://rightsstatements.org/page/InC/1.0/"/> <dc:creator>Arnold, Phil</dc:creator> <dc:creator>Balwierz, Piotr J.</dc:creator> <dcterms:title>ISMARA : automated modeling of genomic signals as a democracy of regulatory motifs</dcterms:title> </rdf:Description> </rdf:RDF>

Downloads since Sep 24, 2020 (Information about access statistics)

Balwierz_2-1211bs4q2j2qe8.pdf 22

This item appears in the following Collection(s)

Search KOPS


Browse

My Account