Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas
Identifieur interne : 000396 ( Ncbi/Merge ); précédent : 000395; suivant : 000397Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas
Auteurs : Christophe Liseron-Monfils [Canada] ; Tim Lewis [Canada] ; Daniel Ashlock [Canada] ; Paul D. Mcnicholas [Canada] ; François Fauteux [Canada] ; Martina Strömvik [Canada] ; Manish N. Raizada [Canada]Source :
- BMC Plant Biology [ 1471-2229 ] ; 2013.
Abstract
The discovery of genetic networks and
A benchmark data set was used to evaluate the accuracy of three motif discovery programs: BioProspector, Weeder and MEME. Analysis showed that each motif discovery tool had limited accuracy and appeared to retrieve a distinct set of motifs. Therefore, using the benchmark, statistical filters were optimized to reduce the false discovery ratio, and then remaining motifs from all programs were combined to improve motif prediction. These principles were integrated into a user-friendly pipeline for motif discovery in maize called Promzea, available at
An online tool customized for promoter motif discovery in plants has been generated called Promzea. Promzea was validated
Url:
DOI: 10.1186/1471-2229-13-42
PubMed: 23497159
PubMed Central: 3658923
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas</title>
<author><name sortKey="Liseron Monfils, Christophe" sort="Liseron Monfils, Christophe" uniqKey="Liseron Monfils C" first="Christophe" last="Liseron-Monfils">Christophe Liseron-Monfils</name>
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<author><name sortKey="Raizada, Manish N" sort="Raizada, Manish N" uniqKey="Raizada M" first="Manish N" last="Raizada">Manish N. Raizada</name>
<affiliation wicri:level="1"><nlm:aff id="I1">Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada</nlm:aff>
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<series><title level="j">BMC Plant Biology</title>
<idno type="eISSN">1471-2229</idno>
<imprint><date when="2013">2013</date>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>The discovery of genetic networks and <italic>cis</italic>
-acting DNA motifs underlying their regulation is a major objective of transcriptome studies. The recent release of the maize genome (<italic>Zea mays</italic>
L.) has facilitated <italic>in silico</italic>
searches for regulatory motifs. Several algorithms exist to predict <italic>cis</italic>
-acting elements, but none have been adapted for maize.</p>
</sec>
<sec><title>Results</title>
<p>A benchmark data set was used to evaluate the accuracy of three motif discovery programs: BioProspector, Weeder and MEME. Analysis showed that each motif discovery tool had limited accuracy and appeared to retrieve a distinct set of motifs. Therefore, using the benchmark, statistical filters were optimized to reduce the false discovery ratio, and then remaining motifs from all programs were combined to improve motif prediction. These principles were integrated into a user-friendly pipeline for motif discovery in maize called Promzea, available at <ext-link ext-link-type="uri" xlink:href="http://www.promzea.org">http://www.promzea.org</ext-link>
and on the Discovery Environment of the iPlant Collaborative website. Promzea was subsequently expanded to include rice and Arabidopsis. Within Promzea, a user enters cDNA sequences or gene IDs; corresponding upstream sequences are retrieved from the maize genome. Predicted motifs are filtered, combined and ranked. Promzea searches the chosen plant genome for genes containing each candidate motif, providing the user with the gene list and corresponding gene annotations. Promzea was validated <italic>in silico</italic>
using a benchmark data set: the Promzea pipeline showed a 22% increase in nucleotide sensitivity compared to the best standalone program tool, Weeder, with equivalent nucleotide specificity. Promzea was also validated by its ability to retrieve the experimentally defined binding sites of transcription factors that regulate the maize anthocyanin and phlobaphene biosynthetic pathways. Promzea predicted additional promoter motifs, and genome-wide motif searches by Promzea identified 127 non-anthocyanin/phlobaphene genes that each contained all five predicted promoter motifs in their promoters, perhaps uncovering a broader co-regulated gene network. Promzea was also tested against tissue-specific microarray data from maize.</p>
</sec>
<sec><title>Conclusions</title>
<p>An online tool customized for promoter motif discovery in plants has been generated called Promzea. Promzea was validated <italic>in silico</italic>
by its ability to retrieve benchmark motifs and experimentally defined motifs and was tested using tissue-specific microarray data. Promzea predicted broader networks of gene regulation associated with the historic anthocyanin and phlobaphene biosynthetic pathways. Promzea is a new bioinformatics tool for understanding transcriptional gene regulation in maize and has been expanded to include rice and Arabidopsis.</p>
</sec>
</div>
</front>
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</TEI>
<pmc article-type="product-review" xml:lang="en"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Plant Biol</journal-id>
<journal-id journal-id-type="iso-abbrev">BMC Plant Biol</journal-id>
<journal-title-group><journal-title>BMC Plant Biology</journal-title>
</journal-title-group>
<issn pub-type="epub">1471-2229</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">23497159</article-id>
<article-id pub-id-type="pmc">3658923</article-id>
<article-id pub-id-type="publisher-id">1471-2229-13-42</article-id>
<article-id pub-id-type="doi">10.1186/1471-2229-13-42</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Software</subject>
</subj-group>
</article-categories>
<title-group><article-title>Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" id="A1"><name><surname>Liseron-Monfils</surname>
<given-names>Christophe</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>cliseron@uoguelph.ca</email>
</contrib>
<contrib contrib-type="author" id="A2"><name><surname>Lewis</surname>
<given-names>Tim</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>Timothy.D.F.L@gmail.com</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>Ashlock</surname>
<given-names>Daniel</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>dashlock@uoguelph.ca</email>
</contrib>
<contrib contrib-type="author" id="A4"><name><surname>McNicholas</surname>
<given-names>Paul D</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>pmcnicho@uoguelph.ca</email>
</contrib>
<contrib contrib-type="author" id="A5"><name><surname>Fauteux</surname>
<given-names>François</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<email>francois.fauteux2@mail.mcgill.ca</email>
</contrib>
<contrib contrib-type="author" id="A6"><name><surname>Strömvik</surname>
<given-names>Martina</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<email>martina.stromvik@mcgill.ca</email>
</contrib>
<contrib contrib-type="author" corresp="yes" id="A7"><name><surname>Raizada</surname>
<given-names>Manish N</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>raizada@uoguelph.ca</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada</aff>
<aff id="I2"><label>2</label>
Department of Mathematics and Statistics, University of Guelph, Guelph, ON N1G 2W1, Canada</aff>
<aff id="I3"><label>3</label>
Department of Plant Sciences, McGill University, Ste. Anne de Bellevue, QC H9X 3V9, Canada</aff>
<pub-date pub-type="collection"><year>2013</year>
</pub-date>
<pub-date pub-type="epub"><day>15</day>
<month>3</month>
<year>2013</year>
</pub-date>
<volume>13</volume>
<fpage>42</fpage>
<lpage>42</lpage>
<history><date date-type="received"><day>1</day>
<month>4</month>
<year>2012</year>
</date>
<date date-type="accepted"><day>8</day>
<month>3</month>
<year>2013</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2013 Liseron-Monfils et al.; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2013</copyright-year>
<copyright-holder>Liseron-Monfils et al.; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://www.biomedcentral.com/1471-2229/13/42"></self-uri>
<abstract><sec><title>Background</title>
<p>The discovery of genetic networks and <italic>cis</italic>
-acting DNA motifs underlying their regulation is a major objective of transcriptome studies. The recent release of the maize genome (<italic>Zea mays</italic>
L.) has facilitated <italic>in silico</italic>
searches for regulatory motifs. Several algorithms exist to predict <italic>cis</italic>
-acting elements, but none have been adapted for maize.</p>
</sec>
<sec><title>Results</title>
<p>A benchmark data set was used to evaluate the accuracy of three motif discovery programs: BioProspector, Weeder and MEME. Analysis showed that each motif discovery tool had limited accuracy and appeared to retrieve a distinct set of motifs. Therefore, using the benchmark, statistical filters were optimized to reduce the false discovery ratio, and then remaining motifs from all programs were combined to improve motif prediction. These principles were integrated into a user-friendly pipeline for motif discovery in maize called Promzea, available at <ext-link ext-link-type="uri" xlink:href="http://www.promzea.org">http://www.promzea.org</ext-link>
and on the Discovery Environment of the iPlant Collaborative website. Promzea was subsequently expanded to include rice and Arabidopsis. Within Promzea, a user enters cDNA sequences or gene IDs; corresponding upstream sequences are retrieved from the maize genome. Predicted motifs are filtered, combined and ranked. Promzea searches the chosen plant genome for genes containing each candidate motif, providing the user with the gene list and corresponding gene annotations. Promzea was validated <italic>in silico</italic>
using a benchmark data set: the Promzea pipeline showed a 22% increase in nucleotide sensitivity compared to the best standalone program tool, Weeder, with equivalent nucleotide specificity. Promzea was also validated by its ability to retrieve the experimentally defined binding sites of transcription factors that regulate the maize anthocyanin and phlobaphene biosynthetic pathways. Promzea predicted additional promoter motifs, and genome-wide motif searches by Promzea identified 127 non-anthocyanin/phlobaphene genes that each contained all five predicted promoter motifs in their promoters, perhaps uncovering a broader co-regulated gene network. Promzea was also tested against tissue-specific microarray data from maize.</p>
</sec>
<sec><title>Conclusions</title>
<p>An online tool customized for promoter motif discovery in plants has been generated called Promzea. Promzea was validated <italic>in silico</italic>
by its ability to retrieve benchmark motifs and experimentally defined motifs and was tested using tissue-specific microarray data. Promzea predicted broader networks of gene regulation associated with the historic anthocyanin and phlobaphene biosynthetic pathways. Promzea is a new bioinformatics tool for understanding transcriptional gene regulation in maize and has been expanded to include rice and Arabidopsis.</p>
</sec>
</abstract>
<kwd-group><kwd>Promoter</kwd>
<kwd><italic>cis</italic>
-acting</kwd>
<kwd>Motif</kwd>
<kwd>Maize</kwd>
<kwd>Anthocyanin</kwd>
<kwd>Phlobaphene</kwd>
<kwd>Bioprospector</kwd>
<kwd>MEME</kwd>
<kwd>Weeder</kwd>
<kwd>C1</kwd>
<kwd>P</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Canada</li>
</country>
<region><li>Québec</li>
</region>
<settlement><li>Montréal</li>
</settlement>
<orgName><li>Université McGill</li>
</orgName>
</list>
<tree><country name="Canada"><noRegion><name sortKey="Liseron Monfils, Christophe" sort="Liseron Monfils, Christophe" uniqKey="Liseron Monfils C" first="Christophe" last="Liseron-Monfils">Christophe Liseron-Monfils</name>
</noRegion>
<name sortKey="Ashlock, Daniel" sort="Ashlock, Daniel" uniqKey="Ashlock D" first="Daniel" last="Ashlock">Daniel Ashlock</name>
<name sortKey="Fauteux, Francois" sort="Fauteux, Francois" uniqKey="Fauteux F" first="François" last="Fauteux">François Fauteux</name>
<name sortKey="Lewis, Tim" sort="Lewis, Tim" uniqKey="Lewis T" first="Tim" last="Lewis">Tim Lewis</name>
<name sortKey="Mcnicholas, Paul D" sort="Mcnicholas, Paul D" uniqKey="Mcnicholas P" first="Paul D" last="Mcnicholas">Paul D. Mcnicholas</name>
<name sortKey="Raizada, Manish N" sort="Raizada, Manish N" uniqKey="Raizada M" first="Manish N" last="Raizada">Manish N. Raizada</name>
<name sortKey="Stromvik, Martina" sort="Stromvik, Martina" uniqKey="Stromvik M" first="Martina" last="Strömvik">Martina Strömvik</name>
</country>
</tree>
</affiliations>
</record>
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