DAnCER: disease-annotated chromatin epigenetics resource.
Identifieur interne : 001696 ( Main/Exploration ); précédent : 001695; suivant : 001697DAnCER: disease-annotated chromatin epigenetics resource.
Auteurs : Andrei L. Turinsky [Canada] ; Brian Turner ; Rosanne C. Borja ; James A. Gleeson ; Michael Heath ; Shuye Pu ; Thomas Switzer ; Dong Dong ; Yunchen Gong ; Tuan On ; Xuejian Xiong ; Andrew Emili ; Jack Greenblatt ; John Parkinson ; Zhaolei Zhang ; Shoshana J. WodakSource :
- Nucleic acids research [ 1362-4962 ] ; 2011.
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : Chromatin.
- genetics : Caenorhabditis elegans, Disease, Drosophila melanogaster, Saccharomyces cerevisiae.
- Animals, Databases, Genetic, Epigenomics, Humans, Mice, Molecular Sequence Annotation, Protein Conformation, Protein Interaction Mapping.
Abstract
Chromatin modification (CM) is a set of epigenetic processes that govern many aspects of DNA replication, transcription and repair. CM is carried out by groups of physically interacting proteins, and their disruption has been linked to a number of complex human diseases. CM remains largely unexplored, however, especially in higher eukaryotes such as human. Here we present the DAnCER resource, which integrates information on genes with CM function from five model organisms, including human. Currently integrated are gene functional annotations, Pfam domain architecture, protein interaction networks and associated human diseases. Additional supporting evidence includes orthology relationships across organisms, membership in protein complexes, and information on protein 3D structure. These data are available for 962 experimentally confirmed and manually curated CM genes and for over 5000 genes with predicted CM function on the basis of orthology and domain composition. DAnCER allows visual explorations of the integrated data and flexible query capabilities using a variety of data filters. In particular, disease information and functional annotations are mapped onto the protein interaction networks, enabling the user to formulate new hypotheses on the function and disease associations of a given gene based on those of its interaction partners. DAnCER is freely available at http://wodaklab.org/dancer/.
DOI: 10.1093/nar/gkq857
PubMed: 20876685
Affiliations:
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Turinsky</name><affiliation wicri:level="4"><nlm:affiliation>Hospital for Sick Children, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Hospital for Sick Children, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation></author><author><name sortKey="Turner, Brian" sort="Turner, Brian" uniqKey="Turner B" first="Brian" last="Turner">Brian Turner</name></author><author><name sortKey="Borja, Rosanne C" sort="Borja, Rosanne C" uniqKey="Borja R" first="Rosanne C" last="Borja">Rosanne C. Borja</name></author><author><name sortKey="Gleeson, James A" sort="Gleeson, James A" uniqKey="Gleeson J" first="James A" last="Gleeson">James A. 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Turinsky</name><affiliation wicri:level="4"><nlm:affiliation>Hospital for Sick Children, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Hospital for Sick Children, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation></author><author><name sortKey="Turner, Brian" sort="Turner, Brian" uniqKey="Turner B" first="Brian" last="Turner">Brian Turner</name></author><author><name sortKey="Borja, Rosanne C" sort="Borja, Rosanne C" uniqKey="Borja R" first="Rosanne C" last="Borja">Rosanne C. Borja</name></author><author><name sortKey="Gleeson, James A" sort="Gleeson, James A" uniqKey="Gleeson J" first="James A" last="Gleeson">James A. Gleeson</name></author><author><name sortKey="Heath, Michael" sort="Heath, Michael" uniqKey="Heath M" first="Michael" last="Heath">Michael Heath</name></author><author><name sortKey="Pu, Shuye" sort="Pu, Shuye" uniqKey="Pu S" first="Shuye" last="Pu">Shuye Pu</name></author><author><name sortKey="Switzer, Thomas" sort="Switzer, Thomas" uniqKey="Switzer T" first="Thomas" last="Switzer">Thomas Switzer</name></author><author><name sortKey="Dong, Dong" sort="Dong, Dong" uniqKey="Dong D" first="Dong" last="Dong">Dong Dong</name></author><author><name sortKey="Gong, Yunchen" sort="Gong, Yunchen" uniqKey="Gong Y" first="Yunchen" last="Gong">Yunchen Gong</name></author><author><name sortKey="On, Tuan" sort="On, Tuan" uniqKey="On T" first="Tuan" last="On">Tuan On</name></author><author><name sortKey="Xiong, Xuejian" sort="Xiong, Xuejian" uniqKey="Xiong X" first="Xuejian" last="Xiong">Xuejian Xiong</name></author><author><name sortKey="Emili, Andrew" sort="Emili, Andrew" uniqKey="Emili A" first="Andrew" last="Emili">Andrew Emili</name></author><author><name sortKey="Greenblatt, Jack" sort="Greenblatt, Jack" uniqKey="Greenblatt J" first="Jack" last="Greenblatt">Jack Greenblatt</name></author><author><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name></author><author><name sortKey="Zhang, Zhaolei" sort="Zhang, Zhaolei" uniqKey="Zhang Z" first="Zhaolei" last="Zhang">Zhaolei Zhang</name></author><author><name sortKey="Wodak, Shoshana J" sort="Wodak, Shoshana J" uniqKey="Wodak S" first="Shoshana J" last="Wodak">Shoshana J. Wodak</name></author></analytic><series><title level="j">Nucleic acids research</title><idno type="eISSN">1362-4962</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Caenorhabditis elegans (genetics)</term><term>Chromatin (metabolism)</term><term>Databases, Genetic</term><term>Disease (genetics)</term><term>Drosophila melanogaster (genetics)</term><term>Epigenomics</term><term>Humans</term><term>Mice</term><term>Molecular Sequence Annotation</term><term>Protein Conformation</term><term>Protein Interaction Mapping</term><term>Saccharomyces cerevisiae (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Chromatin</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Caenorhabditis elegans</term><term>Disease</term><term>Drosophila melanogaster</term><term>Saccharomyces cerevisiae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Databases, Genetic</term><term>Epigenomics</term><term>Humans</term><term>Mice</term><term>Molecular Sequence Annotation</term><term>Protein Conformation</term><term>Protein Interaction Mapping</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Chromatin modification (CM) is a set of epigenetic processes that govern many aspects of DNA replication, transcription and repair. CM is carried out by groups of physically interacting proteins, and their disruption has been linked to a number of complex human diseases. CM remains largely unexplored, however, especially in higher eukaryotes such as human. Here we present the DAnCER resource, which integrates information on genes with CM function from five model organisms, including human. Currently integrated are gene functional annotations, Pfam domain architecture, protein interaction networks and associated human diseases. Additional supporting evidence includes orthology relationships across organisms, membership in protein complexes, and information on protein 3D structure. These data are available for 962 experimentally confirmed and manually curated CM genes and for over 5000 genes with predicted CM function on the basis of orthology and domain composition. DAnCER allows visual explorations of the integrated data and flexible query capabilities using a variety of data filters. In particular, disease information and functional annotations are mapped onto the protein interaction networks, enabling the user to formulate new hypotheses on the function and disease associations of a given gene based on those of its interaction partners. DAnCER is freely available at http://wodaklab.org/dancer/.</div></front></TEI><affiliations><list><country><li>Canada</li></country><region><li>Ontario</li></region><settlement><li>Toronto</li></settlement><orgName><li>Université de Toronto</li></orgName></list><tree><noCountry><name sortKey="Borja, Rosanne C" sort="Borja, Rosanne C" uniqKey="Borja R" first="Rosanne C" last="Borja">Rosanne C. Borja</name><name sortKey="Dong, Dong" sort="Dong, Dong" uniqKey="Dong D" first="Dong" last="Dong">Dong Dong</name><name sortKey="Emili, Andrew" sort="Emili, Andrew" uniqKey="Emili A" first="Andrew" last="Emili">Andrew Emili</name><name sortKey="Gleeson, James A" sort="Gleeson, James A" uniqKey="Gleeson J" first="James A" last="Gleeson">James A. Gleeson</name><name sortKey="Gong, Yunchen" sort="Gong, Yunchen" uniqKey="Gong Y" first="Yunchen" last="Gong">Yunchen Gong</name><name sortKey="Greenblatt, Jack" sort="Greenblatt, Jack" uniqKey="Greenblatt J" first="Jack" last="Greenblatt">Jack Greenblatt</name><name sortKey="Heath, Michael" sort="Heath, Michael" uniqKey="Heath M" first="Michael" last="Heath">Michael Heath</name><name sortKey="On, Tuan" sort="On, Tuan" uniqKey="On T" first="Tuan" last="On">Tuan On</name><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name><name sortKey="Pu, Shuye" sort="Pu, Shuye" uniqKey="Pu S" first="Shuye" last="Pu">Shuye Pu</name><name sortKey="Switzer, Thomas" sort="Switzer, Thomas" uniqKey="Switzer T" first="Thomas" last="Switzer">Thomas Switzer</name><name sortKey="Turner, Brian" sort="Turner, Brian" uniqKey="Turner B" first="Brian" last="Turner">Brian Turner</name><name sortKey="Wodak, Shoshana J" sort="Wodak, Shoshana J" uniqKey="Wodak S" first="Shoshana J" last="Wodak">Shoshana J. Wodak</name><name sortKey="Xiong, Xuejian" sort="Xiong, Xuejian" uniqKey="Xiong X" first="Xuejian" last="Xiong">Xuejian Xiong</name><name sortKey="Zhang, Zhaolei" sort="Zhang, Zhaolei" uniqKey="Zhang Z" first="Zhaolei" last="Zhang">Zhaolei Zhang</name></noCountry><country name="Canada"><region name="Ontario"><name sortKey="Turinsky, Andrei L" sort="Turinsky, Andrei L" uniqKey="Turinsky A" first="Andrei L" last="Turinsky">Andrei L. Turinsky</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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