MersV1, Main, Exploration, bibRecord, 000397

SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing.

Identifieur interne : 000397 ( Main/Exploration ); précédent : 000396; suivant : 000398

SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing.

Auteurs : Dennis C. Wylie [États-Unis] ; Hans A. Hofmann [États-Unis] ; Boris V. Zemelman [États-Unis]

Source :

Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2019.

RBID : pubmed:30903136

Abstract

We set out to develop an algorithm that can mine differential gene expression data to identify candidate cell type-specific DNA regulatory sequences. Differential expression is usually quantified as a continuous score-fold-change, test-statistic, P-value-comparing biological classes. Unlike existing approaches, our de novo strategy, termed SArKS, applies non-parametric kernel smoothing to uncover promoter motif sites that correlate with elevated differential expression scores. SArKS detects motif k-mers by smoothing sequence scores over sequence similarity. A second round of smoothing over spatial proximity reveals multi-motif domains (MMDs). Discovered motif sites can then be merged or extended based on adjacency within MMDs. False positive rates are estimated and controlled by permutation testing.

DOI: 10.1093/bioinformatics/btz198
PubMed: 30903136

Affiliations:

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing.</title>
<author><name sortKey="Wylie, Dennis C" sort="Wylie, Dennis C" uniqKey="Wylie D" first="Dennis C" last="Wylie">Dennis C. Wylie</name>
<affiliation wicri:level="4"><nlm:affiliation>Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX</wicri:regionArea>
<placeName><region type="state">Texas</region>
<settlement type="city">Austin (Texas)</settlement>
</placeName>
<orgName type="university">Université du Texas à Austin</orgName>
</affiliation>
</author>
<author><name sortKey="Hofmann, Hans A" sort="Hofmann, Hans A" uniqKey="Hofmann H" first="Hans A" last="Hofmann">Hans A. Hofmann</name>
<affiliation wicri:level="4"><nlm:affiliation>Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX</wicri:regionArea>
<placeName><region type="state">Texas</region>
<settlement type="city">Austin (Texas)</settlement>
</placeName>
<orgName type="university">Université du Texas à Austin</orgName>
</affiliation>
</author>
<author><name sortKey="Zemelman, Boris V" sort="Zemelman, Boris V" uniqKey="Zemelman B" first="Boris V" last="Zemelman">Boris V. Zemelman</name>
<affiliation wicri:level="4"><nlm:affiliation>Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX</wicri:regionArea>
<placeName><region type="state">Texas</region>
<settlement type="city">Austin (Texas)</settlement>
</placeName>
<orgName type="university">Université du Texas à Austin</orgName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2019">2019</date>
<idno type="RBID">pubmed:30903136</idno>
<idno type="pmid">30903136</idno>
<idno type="doi">10.1093/bioinformatics/btz198</idno>
<idno type="wicri:Area/PubMed/Corpus">000599</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000599</idno>
<idno type="wicri:Area/PubMed/Curation">000599</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000599</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000395</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000395</idno>
<idno type="wicri:Area/Ncbi/Merge">002157</idno>
<idno type="wicri:Area/Ncbi/Curation">002157</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">002157</idno>
<idno type="wicri:Area/Main/Merge">000400</idno>
<idno type="wicri:Area/Main/Curation">000397</idno>
<idno type="wicri:Area/Main/Exploration">000397</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing.</title>
<author><name sortKey="Wylie, Dennis C" sort="Wylie, Dennis C" uniqKey="Wylie D" first="Dennis C" last="Wylie">Dennis C. Wylie</name>
<affiliation wicri:level="4"><nlm:affiliation>Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX</wicri:regionArea>
<placeName><region type="state">Texas</region>
<settlement type="city">Austin (Texas)</settlement>
</placeName>
<orgName type="university">Université du Texas à Austin</orgName>
</affiliation>
</author>
<author><name sortKey="Hofmann, Hans A" sort="Hofmann, Hans A" uniqKey="Hofmann H" first="Hans A" last="Hofmann">Hans A. Hofmann</name>
<affiliation wicri:level="4"><nlm:affiliation>Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX</wicri:regionArea>
<placeName><region type="state">Texas</region>
<settlement type="city">Austin (Texas)</settlement>
</placeName>
<orgName type="university">Université du Texas à Austin</orgName>
</affiliation>
</author>
<author><name sortKey="Zemelman, Boris V" sort="Zemelman, Boris V" uniqKey="Zemelman B" first="Boris V" last="Zemelman">Boris V. Zemelman</name>
<affiliation wicri:level="4"><nlm:affiliation>Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX</wicri:regionArea>
<placeName><region type="state">Texas</region>
<settlement type="city">Austin (Texas)</settlement>
</placeName>
<orgName type="university">Université du Texas à Austin</orgName>
</affiliation>
</author>
</analytic>
<series><title level="j">Bioinformatics (Oxford, England)</title>
<idno type="eISSN">1367-4811</idno>
<imprint><date when="2019" type="published">2019</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">We set out to develop an algorithm that can mine differential gene expression data to identify candidate cell type-specific DNA regulatory sequences. Differential expression is usually quantified as a continuous score-fold-change, test-statistic, P-value-comparing biological classes. Unlike existing approaches, our de novo strategy, termed SArKS, applies non-parametric kernel smoothing to uncover promoter motif sites that correlate with elevated differential expression scores. SArKS detects motif k-mers by smoothing sequence scores over sequence similarity. A second round of smoothing over spatial proximity reveals multi-motif domains (MMDs). Discovered motif sites can then be merged or extended based on adjacency within MMDs. False positive rates are estimated and controlled by permutation testing.</div>
</front>
</TEI>
<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Texas</li>
</region>
<settlement><li>Austin (Texas)</li>
</settlement>
<orgName><li>Université du Texas à Austin</li>
</orgName>
</list>
<tree><country name="États-Unis"><region name="Texas"><name sortKey="Wylie, Dennis C" sort="Wylie, Dennis C" uniqKey="Wylie D" first="Dennis C" last="Wylie">Dennis C. Wylie</name>
</region>
<name sortKey="Hofmann, Hans A" sort="Hofmann, Hans A" uniqKey="Hofmann H" first="Hans A" last="Hofmann">Hans A. Hofmann</name>
<name sortKey="Zemelman, Boris V" sort="Zemelman, Boris V" uniqKey="Zemelman B" first="Boris V" last="Zemelman">Boris V. Zemelman</name>
</country>
</tree>
</affiliations>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000397 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000397 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Sante
   |area=    MersV1
   |flux=    Main
   |étape=   Exploration
   |type=    RBID
   |clé=     pubmed:30903136
   |texte=   SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing.
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i   -Sk "pubmed:30903136" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd   \
       | NlmPubMed2Wicri -a MersV1

This area was generated with Dilib version V0.6.33.
Data generation: Mon Apr 20 23:26:43 2020. Site generation: Sat Mar 27 09:06:09 2021

Serveur d'exploration MERS

SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing.

SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing.

Source :

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

	Serveur d'exploration MERS
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.