UPSC-BASE--Populus transcriptomics online.
Identifieur interne : 003C93 ( Main/Exploration ); précédent : 003C92; suivant : 003C94UPSC-BASE--Populus transcriptomics online.
Auteurs : Andreas Sjödin [Suède] ; Max Bylesjö ; Oskar Skogström ; Daniel Eriksson ; Peter Nilsson ; Patrik Rydén ; Stefan Jansson ; Jan KarlssonSource :
- The Plant journal : for cell and molecular biology [ 0960-7412 ] ; 2006.
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Abstract
The increasing accessibility and use of microarrays in transcriptomics has accentuated the need for purpose-designed storage and analysis tools. Here we present UPSC-BASE, a database for analysis and storage of Populus DNA microarray data. A microarray analysis pipeline has also been established to allow consistent and efficient analysis (from small to large scale) of samples in various experimental designs. A range of optimized experimental protocols is provided for each step in generating the data. Within UPSC-BASE, researchers can perform standard and advanced microarray analysis procedures in a user-friendly environment. Background corrections, normalizations, quality-control tools, visualizations, hypothesis tests and export tools are provided without requirements for expert-level knowledge. Although the database has been developed primarily for handling Populus DNA microarrays, most of the tools are generic and can be used for other types of microarray. UPSC-BASE is also a repository of Populus microarray information, providing data from 21 experiments on a total of 407 microarray hybridizations in the public domain of the database. There are also an additional 10 experiments containing 347 hybridizations, where the automatically analysed data are searchable.
DOI: 10.1111/j.1365-313X.2006.02920.x
PubMed: 17092314
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uniqKey="Eriksson D" first="Daniel" last="Eriksson">Daniel Eriksson</name></author><author><name sortKey="Nilsson, Peter" sort="Nilsson, Peter" uniqKey="Nilsson P" first="Peter" last="Nilsson">Peter Nilsson</name></author><author><name sortKey="Ryden, Patrik" sort="Ryden, Patrik" uniqKey="Ryden P" first="Patrik" last="Rydén">Patrik Rydén</name></author><author><name sortKey="Jansson, Stefan" sort="Jansson, Stefan" uniqKey="Jansson S" first="Stefan" last="Jansson">Stefan Jansson</name></author><author><name sortKey="Karlsson, Jan" sort="Karlsson, Jan" uniqKey="Karlsson J" first="Jan" last="Karlsson">Jan Karlsson</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2006">2006</date><idno type="RBID">pubmed:17092314</idno><idno type="pmid">17092314</idno><idno type="doi">10.1111/j.1365-313X.2006.02920.x</idno><idno type="wicri:Area/Main/Corpus">003C85</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" 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Regulation, Plant</term><term>Internet</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Bases de données génétiques</term><term>Internet</term><term>Régulation de l'expression des gènes végétaux</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The increasing accessibility and use of microarrays in transcriptomics has accentuated the need for purpose-designed storage and analysis tools. Here we present UPSC-BASE, a database for analysis and storage of Populus DNA microarray data. A microarray analysis pipeline has also been established to allow consistent and efficient analysis (from small to large scale) of samples in various experimental designs. A range of optimized experimental protocols is provided for each step in generating the data. Within UPSC-BASE, researchers can perform standard and advanced microarray analysis procedures in a user-friendly environment. Background corrections, normalizations, quality-control tools, visualizations, hypothesis tests and export tools are provided without requirements for expert-level knowledge. Although the database has been developed primarily for handling Populus DNA microarrays, most of the tools are generic and can be used for other types of microarray. UPSC-BASE is also a repository of Populus microarray information, providing data from 21 experiments on a total of 407 microarray hybridizations in the public domain of the database. There are also an additional 10 experiments containing 347 hybridizations, where the automatically analysed data are searchable.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">17092314</PMID><DateCompleted><Year>2007</Year><Month>03</Month><Day>16</Day></DateCompleted><DateRevised><Year>2006</Year><Month>11</Month><Day>22</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0960-7412</ISSN><JournalIssue CitedMedium="Print"><Volume>48</Volume><Issue>5</Issue><PubDate><Year>2006</Year><Month>Dec</Month></PubDate></JournalIssue><Title>The Plant journal : for cell and molecular biology</Title><ISOAbbreviation>Plant J</ISOAbbreviation></Journal><ArticleTitle>UPSC-BASE--Populus transcriptomics online.</ArticleTitle><Pagination><MedlinePgn>806-17</MedlinePgn></Pagination><Abstract><AbstractText>The increasing accessibility and use of microarrays in transcriptomics has accentuated the need for purpose-designed storage and analysis tools. 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