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UPSC-BASE - Populus transcriptomics online
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2006 (English)In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 48, no 5, 806-817 p.Article in journal (Refereed) Published
Abstract [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.

Place, publisher, year, edition, pages
2006. Vol. 48, no 5, 806-817 p.
Keyword [en]
microarray, database, genomics, expression profiling, transcriptome, bioconductor, expressed sequence tags, cdna microarray data, plant functional genomics, gene-expression, arabidopsis, poplar, normalization, database, wood, design
URN: urn:nbn:se:kth:diva-16129DOI: 10.1111/j.1365-313X.2006.02920.xISI: 000242042900013ScopusID: 2-s2.0-33750033745OAI: diva2:334171
QC 20100525Available from: 2010-08-05 Created: 2010-08-05Bibliographically approved

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