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Version 1.8

Gemma 1.8 is a major new release that includes changes to the software and data, including: We are now much more selective in our choice of experiments to include in coexpression analysis. This means that fewer data sets are available for coexpression, but they are generally of higher quality. The way we store coexpression data […]

Version 1.8

Gemma 1.8 is a major new release that includes changes to the software and data, including:

  • We are now much more selective in our choice of experiments to include in coexpression analysis. This means that fewer data sets are available for coexpression, but they are generally of higher quality.
  • The way we store coexpression data has been revised to improve performance and allow more flexible queries.
  • We have re-curated many experimental designs to make them more interpretable and consistent across studies.
  • Most Affymetrix data sets are now reanalyzed from CEL files. We have also introduced many more RNA-seq data sets, which are analyzed from raw reads.
  • We have added new quality controls and many data sets are now batch-corrected. Data sets that lack batch information are among those excluded from some analyses.
  • Neurocarta is now Phenocarta, and has been expanded in gene-disease coverage.
  • There have been numerous bug fixes and improvements to the site.

Much more is planned including more data and features. Please email gemma@chibi.ubc.ca with bug reports, feature requests, or other feedback.

Overview

Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. Users can search, access and visualize coexpression and differential expression results. Some of Gemma's key features:

  • Gemma re-annotates expression platforms as the sequence level to allow more consistent cross-platform comparisons.
  • Gemma supports a variety of expression technologies, including Affymetrix, Illumina and other oligonucleotide arrays, one channel and ratiometric cDNA arrays. Support for RNA-seq data is incomplete but in the works.
  • Gemma provides manual and automated annotations of data sets to enhance usability of the data.
  • Gemma can provide external sites with processed data, web services, software and other means of including Gemma tools and data in other systems.
  • Gemma allows users to securely upload their own data, to be shared either "privately" with users of their choice. Gemma also allows users to create and save gene or data set groups for use in queries.

Go to Gemma tool.

Zoubarev, A., et al., Gemma: A resource for the re-use, sharing and meta-analysis of expression profiling data. Bioinformatics, 2012. (link)