Dataset Information

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

ABSTRACT: Gene Expression Atlas (http://www.ebi.ac.uk/gxa) is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive and the European Nucleotide Archive. A simple interface allows the user to query for differential gene expression either by gene names or attributes or by biological conditions, e.g. diseases, organism parts or cell types. Since our previous report we made 20 monthly releases and, as of Release 11.08 (August 2011), the database supports 19 species, which contains expression data measured for 19,014 biological conditions in 136,551 assays from 5598 independent studies.

SUBMITTER: Kapushesky M

PROVIDER: S-EPMC3245177 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature

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Publications

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

Kapushesky Misha M Adamusiak Tomasz T Burdett Tony T Culhane Aedin A Farne Anna A Filippov Alexey A Holloway Ele E Klebanov Andrey A Kryvych Nataliya N Kurbatova Natalja N Kurnosov Pavel P Malone James J Melnichuk Olga O Petryszak Robert R Pultsin Nikolay N Rustici Gabriella G Tikhonov Andrew A Travillian Ravensara S RS Williams Eleanor E Zorin Andrey A Parkinson Helen H Brazma Alvis A

Nucleic acids research 20111107 Database issue

Gene Expression Atlas (http://www.ebi.ac.uk/gxa) is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive and the European Nucleotide Archive. A simple interface allows the user to query for differential g ...[more]

PMID: 22064864

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Project description:BACKGROUND:Exome and genome sequencing is becoming the method of choice for rare disease diagnostics. One of the key challenges remaining is distinguishing the disease causing variants from the benign background variation. After analysis and annotation of the sequencing data there are typically thousands of candidate variants requiring further investigation. One of the most effective and least biased ways to reduce this number is to assess the rarity of a variant in any population. Currently, there are a number of reliable sources of information for major population frequencies when considering single nucleotide variants (SNVs) and small insertion and deletions (INDELs), with gnomAD as the most prominent public resource available. However, local variation or frequencies in sub-populations may be underrepresented in these public resources. In contrast, for structural variation (SV), the background frequency in the general population is more or less unknown mostly due to challenges in calling SVs in a consistent way. Keeping track of local variation is one way to overcome these problems and significantly reduce the number of potential disease causing variants retained for manual inspection, both for SNVs and SVs. RESULTS:Here, we present loqusdb, a tool to solve the challenge of keeping track of any type of variant observations from genome sequencing data. Loqusdb was designed to handle a large flow of samples and unlike other solutions, samples can be added continuously to the database without rebuilding it, facilitating improvements and additions. We assessed the added value of a local observations database using 98 samples annotated with information from a background of 888 unrelated individuals. CONCLUSIONS:We show both how powerful SV analysis can be when filtering for population frequencies and how the number of apparently rare SNVs/INDELs can be reduced by adding local population information even after annotating the data with other large frequency databases, such as gnomAD. In conclusion, we show that a local frequency database is an attractive, and a necessary addition to the publicly available databases that facilitate the analysis of exome and genome data in a clinical setting.

Dataset Information

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

Publications

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

Similar Datasets

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