Sjodin A, Bylesjo M, Skogstrom O, Eriksson D, Nilsson P, Ryden P, Jansson S, Karlsson J
UPSC-BASE - Populus transcriptomics online
Plant Journal: 2006 48:806-817
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.
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