title: UPSC-BASE--Populus transcriptomics online.
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.
authors.affiliation: Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden.
authors.forename: Andreas
authors.initials: A
authors.lastname: Sjödin
authors.forename: Max
authors.initials: M
authors.lastname: Bylesjö
authors.forename: Oskar
authors.initials: O
authors.lastname: Skogström
authors.forename: Daniel
authors.initials: D
authors.lastname: Eriksson
authors.forename: Peter
authors.initials: P
authors.lastname: Nilsson
authors.forename: Patrik
authors.initials: P
authors.lastname: Rydén
authors.forename: Stefan
authors.initials: S
authors.lastname: Jansson
authors.forename: Jan
authors.initials: J
authors.lastname: Karlsson
mesh_terms: D030541:Databases, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D020407:Internet; D032107:Populus / Q000235:genetics*