Phase Transitions in Gene Knockdown Networks of Transitive RNAi
Identifieur interne : 002E06 ( Main/Exploration ); précédent : 002E05; suivant : 002E07Phase Transitions in Gene Knockdown Networks of Transitive RNAi
Auteurs : Shibin Qiu [États-Unis] ; Terran Lane [États-Unis]Source :
- Lecture Notes in Computer Science [ 0302-9743 ]
Abstract
Abstract: Since gene silencing by RNA interference (RNAi) has been observed when inexact matches exist in siRNA-mRNA binding, the number of mismatched nucleotides allowed by nature becomes an important quantity in characterizing RNAi specificity. We use scale-free graphs to model the knockdown interactions among different genes and estimate the allowable flexibility by examining transitive RNAi, which amplifies siRNA and cyclically silences targets. Simulation results in S. pombe indicate that continually increasing the number of mismatches risks transcriptome-wide knockdown and eventually turns RNAi from defensive to self-destructive. At the phase transition, the number of mismatches indicates a critical value beyond which tRNAi would cause an organism instable. This critical value suggests an upper limit of no more than 6 nt mismatches in the binding.
Url:
DOI: 10.1007/11758525_119
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Istex, to step Corpus: 000889
- to stream Istex, to step Curation: 000889
- to stream Istex, to step Checkpoint: 000981
- to stream Main, to step Merge: 002E36
- to stream Main, to step Curation: 002E06
Le document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Phase Transitions in Gene Knockdown Networks of Transitive RNAi</title>
<author><name sortKey="Qiu, Shibin" sort="Qiu, Shibin" uniqKey="Qiu S" first="Shibin" last="Qiu">Shibin Qiu</name>
</author>
<author><name sortKey="Lane, Terran" sort="Lane, Terran" uniqKey="Lane T" first="Terran" last="Lane">Terran Lane</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">ISTEX</idno>
<idno type="RBID">ISTEX:F3ABD0F4A9FFD9ED349428C0FF5E0D88F2D12679</idno>
<date when="2006" year="2006">2006</date>
<idno type="doi">10.1007/11758525_119</idno>
<idno type="url">https://api.istex.fr/ark:/67375/HCB-C7RQ59DT-J/fulltext.pdf</idno>
<idno type="wicri:Area/Istex/Corpus">000889</idno>
<idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">000889</idno>
<idno type="wicri:Area/Istex/Curation">000889</idno>
<idno type="wicri:Area/Istex/Checkpoint">000981</idno>
<idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Checkpoint">000981</idno>
<idno type="wicri:doubleKey">0302-9743:2006:Qiu S:phase:transitions:in</idno>
<idno type="wicri:Area/Main/Merge">002E36</idno>
<idno type="wicri:Area/Main/Curation">002E06</idno>
<idno type="wicri:Area/Main/Exploration">002E06</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Phase Transitions in Gene Knockdown Networks of Transitive RNAi</title>
<author><name sortKey="Qiu, Shibin" sort="Qiu, Shibin" uniqKey="Qiu S" first="Shibin" last="Qiu">Shibin Qiu</name>
<affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Nouveau-Mexique</region>
</placeName>
<wicri:cityArea>Dept. of Computer Science, University of New Mexico, 87131, Albuquerque</wicri:cityArea>
</affiliation>
<affiliation wicri:level="1"><country wicri:rule="url">États-Unis</country>
</affiliation>
</author>
<author><name sortKey="Lane, Terran" sort="Lane, Terran" uniqKey="Lane T" first="Terran" last="Lane">Terran Lane</name>
<affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Nouveau-Mexique</region>
</placeName>
<wicri:cityArea>Dept. of Computer Science, University of New Mexico, 87131, Albuquerque</wicri:cityArea>
</affiliation>
<affiliation wicri:level="1"><country wicri:rule="url">États-Unis</country>
</affiliation>
</author>
</analytic>
<monogr></monogr>
<series><title level="s" type="main" xml:lang="en">Lecture Notes in Computer Science</title>
<idno type="ISSN">0302-9743</idno>
<idno type="eISSN">1611-3349</idno>
<idno type="ISSN">0302-9743</idno>
</series>
</biblStruct>
</sourceDesc>
<seriesStmt><idno type="ISSN">0302-9743</idno>
</seriesStmt>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Abstract: Since gene silencing by RNA interference (RNAi) has been observed when inexact matches exist in siRNA-mRNA binding, the number of mismatched nucleotides allowed by nature becomes an important quantity in characterizing RNAi specificity. We use scale-free graphs to model the knockdown interactions among different genes and estimate the allowable flexibility by examining transitive RNAi, which amplifies siRNA and cyclically silences targets. Simulation results in S. pombe indicate that continually increasing the number of mismatches risks transcriptome-wide knockdown and eventually turns RNAi from defensive to self-destructive. At the phase transition, the number of mismatches indicates a critical value beyond which tRNAi would cause an organism instable. This critical value suggests an upper limit of no more than 6 nt mismatches in the binding.</div>
</front>
</TEI>
<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Nouveau-Mexique</li>
</region>
</list>
<tree><country name="États-Unis"><region name="Nouveau-Mexique"><name sortKey="Qiu, Shibin" sort="Qiu, Shibin" uniqKey="Qiu S" first="Shibin" last="Qiu">Shibin Qiu</name>
</region>
<name sortKey="Lane, Terran" sort="Lane, Terran" uniqKey="Lane T" first="Terran" last="Lane">Terran Lane</name>
<name sortKey="Lane, Terran" sort="Lane, Terran" uniqKey="Lane T" first="Terran" last="Lane">Terran Lane</name>
<name sortKey="Qiu, Shibin" sort="Qiu, Shibin" uniqKey="Qiu S" first="Shibin" last="Qiu">Shibin Qiu</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 002E06 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 002E06 | 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= ISTEX:F3ABD0F4A9FFD9ED349428C0FF5E0D88F2D12679 |texte= Phase Transitions in Gene Knockdown Networks of Transitive RNAi }}
This area was generated with Dilib version V0.6.33. |