SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data
Identifieur interne : 000821 ( Main/Exploration ); précédent : 000820; suivant : 000822SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data
Auteurs : Maya Polishchuk [Israël, Russie] ; Inbal Paz [Israël] ; Zohar Yakhini [Israël] ; Yael Mandel-Gutfreund [Israël]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : RNA.
- chemical , metabolism : RNA-Binding Proteins.
- Binding Sites, Internet, Nucleic Acid Conformation, Nucleotide Motifs, Position-Specific Scoring Matrices, Sequence Analysis, RNA, Software.
Abstract
Gene expression regulation is highly dependent on binding of RNA-binding proteins (RBPs) to their RNA targets. Growing evidence supports the notion that both RNA primary sequence and its local secondary structure play a role in specific Protein-RNA recognition and binding. Despite the great advance in high-throughput experimental methods for identifying sequence targets of RBPs, predicting the specific sequence and structure binding preferences of RBPs remains a major challenge. We present a novel webserver, SMARTIV, designed for discovering and visualizing combined RNA sequence and structure motifs from high-throughput RNA-binding data, generated from
Url:
DOI: 10.1093/nar/gky453
PubMed: 29800452
PubMed Central: 6030986
Affiliations:
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46150, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>School of Computer Science, Herzliya Interdisciplinary Center, Herzliya 46150</wicri:regionArea><wicri:noRegion>Herzliya 46150</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF4">Department of Computer Science, Technion-Israel Institute of Technology, Haifa 32000, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Computer Science, Technion-Israel Institute of Technology, Haifa 32000</wicri:regionArea><wicri:noRegion>Haifa 32000</wicri:noRegion></affiliation></author><author><name sortKey="Mandel Gutfreund, Yael" sort="Mandel Gutfreund, Yael" uniqKey="Mandel Gutfreund Y" first="Yael" last="Mandel-Gutfreund">Yael Mandel-Gutfreund</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Biology, Technion-Israel Institute of Technology, Haifa 32000</wicri:regionArea><wicri:noRegion> Haifa 32000</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF4">Department of Computer Science, Technion-Israel Institute of Technology, Haifa 32000, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Computer Science, Technion-Israel Institute of Technology, Haifa 32000</wicri:regionArea><wicri:noRegion>Haifa 32000</wicri:noRegion></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2018">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Binding Sites</term><term>Internet</term><term>Nucleic Acid Conformation</term><term>Nucleotide Motifs</term><term>Position-Specific Scoring Matrices</term><term>RNA (chemistry)</term><term>RNA-Binding Proteins (metabolism)</term><term>Sequence Analysis, RNA</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN ()</term><term>Analyse de séquence d'ARN</term><term>Conformation d'acide nucléique</term><term>Internet</term><term>Logiciel</term><term>Matrices de scores</term><term>Motifs nucléotidiques</term><term>Protéines de liaison à l'ARN (métabolisme)</term><term>Sites de fixation</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>RNA-Binding Proteins</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Protéines de liaison à l'ARN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term><term>Internet</term><term>Nucleic Acid Conformation</term><term>Nucleotide Motifs</term><term>Position-Specific Scoring Matrices</term><term>Sequence Analysis, RNA</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN</term><term>Analyse de séquence d'ARN</term><term>Conformation d'acide nucléique</term><term>Internet</term><term>Logiciel</term><term>Matrices de scores</term><term>Motifs nucléotidiques</term><term>Sites de fixation</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><p>Gene expression regulation is highly dependent on binding of RNA-binding proteins (RBPs) to their RNA targets. Growing evidence supports the notion that both RNA primary sequence and its local secondary structure play a role in specific Protein-RNA recognition and binding. Despite the great advance in high-throughput experimental methods for identifying sequence targets of RBPs, predicting the specific sequence and structure binding preferences of RBPs remains a major challenge. We present a novel webserver, SMARTIV, designed for discovering and visualizing combined RNA sequence and structure motifs from high-throughput RNA-binding data, generated from <italic>in-vivo</italic> experiments. The uniqueness of SMARTIV is that it predicts motifs from enriched <italic>k</italic>-mers that combine information from ranked RNA sequences and their predicted secondary structure, obtained using various folding methods. Consequently, SMARTIV generates Position Weight Matrices (PWMs) in a combined sequence and structure alphabet with assigned <italic>P</italic>-values. SMARTIV concisely represents the sequence and structure motif content as a single graphical logo, which is informative and easy for visual perception. SMARTIV was examined extensively on a variety of high-throughput binding experiments for RBPs from different families, generated from different technologies, showing consistent and accurate results. Finally, SMARTIV is a user-friendly webserver, highly efficient in run-time and freely accessible via <ext-link ext-link-type="uri" xlink:href="http://smartiv.technion.ac.il/">http://smartiv.technion.ac.il/</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Li, X C" uniqKey="Li X">X.C. Li</name></author><author><name sortKey="Kazan, H" uniqKey="Kazan H">H. Kazan</name></author><author><name sortKey="Lipshitz, H D" uniqKey="Lipshitz H">H.D. Lipshitz</name></author><author><name sortKey="Morris, Q D" uniqKey="Morris Q">Q.D. 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Burnett</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Israël</li><li>Russie</li></country><region><li>District fédéral central</li></region><settlement><li>Moscou</li></settlement></list><tree><country name="Israël"><noRegion><name sortKey="Polishchuk, Maya" sort="Polishchuk, Maya" uniqKey="Polishchuk M" first="Maya" last="Polishchuk">Maya Polishchuk</name></noRegion><name sortKey="Mandel Gutfreund, Yael" sort="Mandel Gutfreund, Yael" uniqKey="Mandel Gutfreund Y" first="Yael" last="Mandel-Gutfreund">Yael Mandel-Gutfreund</name><name sortKey="Mandel Gutfreund, Yael" sort="Mandel Gutfreund, Yael" uniqKey="Mandel Gutfreund Y" first="Yael" last="Mandel-Gutfreund">Yael Mandel-Gutfreund</name><name sortKey="Paz, Inbal" sort="Paz, Inbal" uniqKey="Paz I" first="Inbal" last="Paz">Inbal Paz</name><name sortKey="Yakhini, Zohar" sort="Yakhini, Zohar" uniqKey="Yakhini Z" first="Zohar" last="Yakhini">Zohar Yakhini</name><name sortKey="Yakhini, Zohar" sort="Yakhini, Zohar" uniqKey="Yakhini Z" first="Zohar" last="Yakhini">Zohar Yakhini</name></country><country name="Russie"><region name="District fédéral central"><name sortKey="Polishchuk, Maya" sort="Polishchuk, Maya" uniqKey="Polishchuk M" first="Maya" last="Polishchuk">Maya Polishchuk</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:6030986
|texte= SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data
}}
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HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:29800452" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
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