Augmented Annotation of the Schizosaccharomyces pombe Genome Reveals Additional Genes Required for Growth and Viability
Identifieur interne : 000564 ( Main/Merge ); précédent : 000563; suivant : 000565Augmented Annotation of the Schizosaccharomyces pombe Genome Reveals Additional Genes Required for Growth and Viability
Auteurs : Danny A. Bitton ; Valerie Wood [Royaume-Uni] ; Paul J. Scutt ; Agnes Grallert ; Tim Yates ; Duncan L. Smith [Royaume-Uni] ; Iain M. Hagan ; Crispin J. MillerSource :
- Genetics [ 0016-6731 ] ; 2011.
Abstract
Genome annotation is a synthesis of computational prediction and experimental evidence. Small genes are notoriously difficult to detect because the patterns used to identify them are often indistinguishable from chance occurrences, leading to an arbitrary cutoff threshold for the length of a protein-coding gene identified solely by
Url:
DOI: 10.1534/genetics.110.123497
PubMed: 21270388
PubMed Central: 3070528
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000597
- to stream Pmc, to step Curation: 000597
- to stream Pmc, to step Checkpoint: 000346
- to stream Ncbi, to step Merge: 000446
- to stream Ncbi, to step Curation: 000446
- to stream Ncbi, to step Checkpoint: 000446
Links to Exploration step
PMC:3070528Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Augmented Annotation of the <italic>Schizosaccharomyces pombe</italic>
Genome Reveals Additional Genes Required for Growth and Viability</title>
<author><name sortKey="Bitton, Danny A" sort="Bitton, Danny A" uniqKey="Bitton D" first="Danny A." last="Bitton">Danny A. Bitton</name>
<affiliation><nlm:aff id="d32e100">Cancer Research UK Applied Computational Biology and Bioinformatics Group,</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Wood, Valerie" sort="Wood, Valerie" uniqKey="Wood V" first="Valerie" last="Wood">Valerie Wood</name>
<affiliation wicri:level="1"><nlm:aff id="d32e100">Cancer Research UK, London Research Institute, London WC2A 3PX, United Kingdom</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Cancer Research UK, London Research Institute, London WC2A 3PX</wicri:regionArea>
<wicri:noRegion>London WC2A 3PX</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Scutt, Paul J" sort="Scutt, Paul J" uniqKey="Scutt P" first="Paul J." last="Scutt">Paul J. Scutt</name>
<affiliation><nlm:aff id="d32e100">Cancer Research UK Applied Computational Biology and Bioinformatics Group,</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Grallert, Agnes" sort="Grallert, Agnes" uniqKey="Grallert A" first="Agnes" last="Grallert">Agnes Grallert</name>
<affiliation><nlm:aff id="d32e100">Cancer Research UK Cell Division Group,</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Yates, Tim" sort="Yates, Tim" uniqKey="Yates T" first="Tim" last="Yates">Tim Yates</name>
<affiliation><nlm:aff id="d32e100">Cancer Research UK Applied Computational Biology and Bioinformatics Group,</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Smith, Duncan L" sort="Smith, Duncan L" uniqKey="Smith D" first="Duncan L." last="Smith">Duncan L. Smith</name>
<affiliation wicri:level="4"><nlm:aff wicri:cut=" and" id="d32e100">Biological Mass Spectrometry Facility, Cancer Research UK, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Manchester M20 4BX, United Kingdom</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Biological Mass Spectrometry Facility, Cancer Research UK, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Manchester M20 4BX</wicri:regionArea>
<orgName type="university">Université de Manchester</orgName>
<placeName><settlement type="city">Manchester</settlement>
<region type="nation">Angleterre</region>
<region nuts="2" type="region">Grand Manchester</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Hagan, Iain M" sort="Hagan, Iain M" uniqKey="Hagan I" first="Iain M." last="Hagan">Iain M. Hagan</name>
<affiliation><nlm:aff id="d32e100">Cancer Research UK Cell Division Group,</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Miller, Crispin J" sort="Miller, Crispin J" uniqKey="Miller C" first="Crispin J." last="Miller">Crispin J. Miller</name>
<affiliation><nlm:aff id="d32e100">Cancer Research UK Applied Computational Biology and Bioinformatics Group,</nlm:aff>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">21270388</idno>
<idno type="pmc">3070528</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070528</idno>
<idno type="RBID">PMC:3070528</idno>
<idno type="doi">10.1534/genetics.110.123497</idno>
<date when="2011">2011</date>
<idno type="wicri:Area/Pmc/Corpus">000597</idno>
<idno type="wicri:Area/Pmc/Curation">000597</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000346</idno>
<idno type="wicri:Area/Ncbi/Merge">000446</idno>
<idno type="wicri:Area/Ncbi/Curation">000446</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">000446</idno>
<idno type="wicri:doubleKey">0016-6731:2011:Bitton D:augmented:annotation:of</idno>
<idno type="wicri:Area/Main/Merge">000564</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Augmented Annotation of the <italic>Schizosaccharomyces pombe</italic>
Genome Reveals Additional Genes Required for Growth and Viability</title>
<author><name sortKey="Bitton, Danny A" sort="Bitton, Danny A" uniqKey="Bitton D" first="Danny A." last="Bitton">Danny A. Bitton</name>
<affiliation><nlm:aff id="d32e100">Cancer Research UK Applied Computational Biology and Bioinformatics Group,</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Wood, Valerie" sort="Wood, Valerie" uniqKey="Wood V" first="Valerie" last="Wood">Valerie Wood</name>
<affiliation wicri:level="1"><nlm:aff id="d32e100">Cancer Research UK, London Research Institute, London WC2A 3PX, United Kingdom</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Cancer Research UK, London Research Institute, London WC2A 3PX</wicri:regionArea>
<wicri:noRegion>London WC2A 3PX</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Scutt, Paul J" sort="Scutt, Paul J" uniqKey="Scutt P" first="Paul J." last="Scutt">Paul J. Scutt</name>
<affiliation><nlm:aff id="d32e100">Cancer Research UK Applied Computational Biology and Bioinformatics Group,</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Grallert, Agnes" sort="Grallert, Agnes" uniqKey="Grallert A" first="Agnes" last="Grallert">Agnes Grallert</name>
<affiliation><nlm:aff id="d32e100">Cancer Research UK Cell Division Group,</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Yates, Tim" sort="Yates, Tim" uniqKey="Yates T" first="Tim" last="Yates">Tim Yates</name>
<affiliation><nlm:aff id="d32e100">Cancer Research UK Applied Computational Biology and Bioinformatics Group,</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Smith, Duncan L" sort="Smith, Duncan L" uniqKey="Smith D" first="Duncan L." last="Smith">Duncan L. Smith</name>
<affiliation wicri:level="4"><nlm:aff wicri:cut=" and" id="d32e100">Biological Mass Spectrometry Facility, Cancer Research UK, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Manchester M20 4BX, United Kingdom</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Biological Mass Spectrometry Facility, Cancer Research UK, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Manchester M20 4BX</wicri:regionArea>
<orgName type="university">Université de Manchester</orgName>
<placeName><settlement type="city">Manchester</settlement>
<region type="nation">Angleterre</region>
<region nuts="2" type="region">Grand Manchester</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Hagan, Iain M" sort="Hagan, Iain M" uniqKey="Hagan I" first="Iain M." last="Hagan">Iain M. Hagan</name>
<affiliation><nlm:aff id="d32e100">Cancer Research UK Cell Division Group,</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Miller, Crispin J" sort="Miller, Crispin J" uniqKey="Miller C" first="Crispin J." last="Miller">Crispin J. Miller</name>
<affiliation><nlm:aff id="d32e100">Cancer Research UK Applied Computational Biology and Bioinformatics Group,</nlm:aff>
</affiliation>
</author>
</analytic>
<series><title level="j">Genetics</title>
<idno type="ISSN">0016-6731</idno>
<idno type="e-ISSN">1943-2631</idno>
<imprint><date when="2011">2011</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>Genome annotation is a synthesis of computational prediction and experimental evidence. Small genes are notoriously difficult to detect because the patterns used to identify them are often indistinguishable from chance occurrences, leading to an arbitrary cutoff threshold for the length of a protein-coding gene identified solely by <italic>in silico</italic>
analysis. We report a systematic reappraisal of the <italic>Schizosaccharomyces pombe</italic>
genome that ignores thresholds. A complete six-frame translation was compared to a proteome data set, the Pfam domain database, and the genomes of six other fungi. Thirty-nine novel loci were identified. RT-PCR and RNA-Seq confirmed transcription at 38 loci; 33 novel gene structures were delineated by 5′ and 3′ RACE. Expression levels of 14 transcripts fluctuated during meiosis. Translational evidence for 10 genes, evolutionary conservation data supporting 35 predictions, and distinct phenotypes upon ORF deletion (one essential, four slow-growth, two delayed-division phenotypes) suggest that all 39 predictions encode functional proteins. The popularity of <italic>S. pombe</italic>
as a model organism suggests that this augmented annotation will be of interest in diverse areas of molecular and cellular biology, while the generality of the approach suggests widespread applicability to other genomes.</p>
</div>
</front>
</TEI>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Musique/explor/MozartV1/Data/Main/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000564 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Merge/biblio.hfd -nk 000564 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Wicri/Musique |area= MozartV1 |flux= Main |étape= Merge |type= RBID |clé= PMC:3070528 |texte= Augmented Annotation of the Schizosaccharomyces pombe Genome Reveals Additional Genes Required for Growth and Viability }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Merge/RBID.i -Sk "pubmed:21270388" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Merge/biblio.hfd \ | NlmPubMed2Wicri -a MozartV1
This area was generated with Dilib version V0.6.20. |