TCW: Transcriptome Computational Workbench
Identifieur interne : 000283 ( Main/Exploration ); précédent : 000282; suivant : 000284TCW: Transcriptome Computational Workbench
Auteurs : Carol Soderlund [États-Unis] ; William Nelson [États-Unis] ; Mark Willer [États-Unis] ; David R. Gang [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2013.
Abstract
The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility.
The Transcriptome Computational Workbench (TCW) provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms). The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina) or assembling long sequences (e.g. Sanger, 454, transcripts), annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results.
It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the transcriptome. TCW is freely available from
Url:
DOI: 10.1371/journal.pone.0069401
PubMed: 23874959
PubMed Central: 3714256
Affiliations:
Links toward previous steps (curation, corpus...)
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- to stream Pmc, to step Checkpoint: 000261
- to stream Ncbi, to step Merge: 000426
- to stream Ncbi, to step Curation: 000426
- to stream Ncbi, to step Checkpoint: 000426
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Le document en format XML
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Gang</name><affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>Washington State University, Pullman, Washington, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Washington State University, Pullman, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility.</p></sec><sec><title>Methodology</title><p>The Transcriptome Computational Workbench (TCW) provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms). The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina) or assembling long sequences (e.g. Sanger, 454, transcripts), annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results.</p></sec><sec><title>Conclusion</title><p>It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the transcriptome. TCW is freely available from <ext-link ext-link-type="uri" xlink:href="http://www.agcol.arizona.edu/software/tcw">www.agcol.arizona.edu/software/tcw</ext-link>.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="The Go, Consortium" uniqKey="The Go C">Consortium The GO</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Garber, M" uniqKey="Garber M">M Garber</name></author><author><name sortKey="Grabherr, Mg" uniqKey="Grabherr M">MG Grabherr</name></author><author><name sortKey="Guttman, M" uniqKey="Guttman M">M Guttman</name></author><author><name sortKey="Trapnell, C" uniqKey="Trapnell C">C Trapnell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Conesa, A" uniqKey="Conesa A">A Conesa</name></author><author><name sortKey="Gotz, S" uniqKey="Gotz S">S Gotz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hunter, S" 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uniqKey="Gao J">J Gao</name></author><author><name sortKey="Fei, Z" uniqKey="Fei Z">Z Fei</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Darling, Ac" uniqKey="Darling A">AC Darling</name></author><author><name sortKey="Mau, B" uniqKey="Mau B">B Mau</name></author><author><name sortKey="Blattner, Fr" uniqKey="Blattner F">FR Blattner</name></author><author><name sortKey="Perna, Nt" uniqKey="Perna N">NT Perna</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Soderlund, C" uniqKey="Soderlund C">C Soderlund</name></author><author><name sortKey="Bomhoff, M" uniqKey="Bomhoff M">M Bomhoff</name></author><author><name sortKey="Nelson, Wm" uniqKey="Nelson W">WM Nelson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Theocharidis, A" uniqKey="Theocharidis A">A Theocharidis</name></author><author><name sortKey="Van Dongen, S" uniqKey="Van Dongen S">S van Dongen</name></author><author><name sortKey="Enright, Aj" uniqKey="Enright A">AJ Enright</name></author><author><name sortKey="Freeman, Tc" uniqKey="Freeman T">TC Freeman</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Arizona</li><li>Washington (État)</li></region></list><tree><country name="États-Unis"><region name="Arizona"><name sortKey="Soderlund, Carol" sort="Soderlund, Carol" uniqKey="Soderlund C" first="Carol" last="Soderlund">Carol Soderlund</name></region><name sortKey="Gang, David R" sort="Gang, David R" uniqKey="Gang D" first="David R." last="Gang">David R. Gang</name><name sortKey="Nelson, William" sort="Nelson, William" uniqKey="Nelson W" first="William" last="Nelson">William Nelson</name><name sortKey="Willer, Mark" sort="Willer, Mark" uniqKey="Willer M" first="Mark" last="Willer">Mark Willer</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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