FGED

World-view of human expression data

Fri, 1 Oct 2010 00:00:00 GMT

Analysis of a large microarray data set compiled from many laboratories reveals the overall structure of gene expression space into six "continents". Lukk et al. Nature Biotech. 2010

Shared microarray data leads to discovery

Mon, 27 Sep 2010 00:00:00 GMT

Useable public microarray datasets enabled the discovery of the first serum/plasma proteins for diagnosing acute rejection across types of transplanted organs...read more.

MGED is now FGED

Wed, 14 Jul 2010 00:00:00 GMT

The MGED Society has decided to change its name to the Functional Genomics Data Society to reflect its current mission which embraces functional genomics and not just microarrays or gene expression.

Published E-Letter in Science.

Mon, 15 Feb 2010 00:00:00 GMT

MGED urges scientific journals to adopt and support MINSEQE to preserve MIAME-enabled achievements in this new age of advancing UHTS. More details in E-Letter.

Published Dataset Availability.

Wed, 25 Nov 2009 00:00:00 GMT

The MGED Society mission includes facilitating deposition of functional genomics datasets (e.g. microarray studies) in public archives. In addition to addressing what and how data gets deposited, we are very much concerned with seeing that authors adhere to journal requirements for data deposition. A new service is available for facilitating data deposition. We will document the results to assist others seeking the same dataset and to aid reviewers of related publications and grants.

GEO and ArrayExpress agree to exchange UHTS sequencing data.

Thu, 05 Nov 2009 00:00:00 GMT

ArrayExpress and GEO have entered into a metadata exchange agreement, meaning that ultra high throughput sequencing (UHTS) experiments will appear in both databases regardless of where they were submitted. This complements the exchange of underlying raw data between the short read archives, SRA and ERA. Raw sequencing data submitted to ArrayExpress or GEO will be sent to ERA or SRA respectively. You do not need to submit to the sequence repositories separately.

Annotare - MAGE-TAB annotation tool

Thu, 05 Nov 2009 00:00:00 GMT

Annotare is an annotation tool for high throughput gene expression experiments in MAGE-TAB format. Biologists can describe their investigations with the investigators' contact details, experimental design, protocols that were employed and references to publications, details of biological samples, arrays, and experimental data produced in the investigation. Annotare is open source and free to download. See the tutorial.

Repeatability of published microarray studies

Thu, 05 Feb 2009 00:00:00 GMT

A Nature Genetics article details the reproducibility of published gene expression studies. It concludes that journals should do more to enforce public data availability and better descriptions for data processing and analysis.

Second-Generation Sequencing Article mentions the involvement of MINSEQE

Thu, 08 Jan 2009 00:00:00 GMT

A Bioinform article details the progress of high-throughput sequencing in 2008 and mentions the importance of standards such as the MGED co-ordinated MINSEQE draft to compare results.

Deposition rates of expression microarray datasets can be improved

Tue, 25 Nov 2008 00:00:00 GMT

A retrospective study shows the deposition rate of some selective published microarray datasets was less than half, although it's asserted that these depositions are more routine. It goes on to suggest how deposition rates can be improved.

Minimum Information about a high-throughput Nucleotide SeQuencing Experiment - MINSEQE (Draft Proposal)

Thu, 10 Apr 2008 00:00:00 GMT

As an output of discussions at the recent MGED-organized UHTS standardization workshop (in Berkeley, March 17-18, 2008), a new Minimum Information checklist is being developed called MINSEQE. We welcome your feedback on this proposal.

Benefits of sharing microarray data include higher citations!

Fri, 07 Dec 2007 00:00:00 GMT

A research article on "Sharing Detailed Research Data Is Associated with Increased Citation Rate".

MIAME 2.0

Wed, 06 Jun 2007 00:00:00 GMT

Updated MIAME homepage and MIAME 2.0 proposal.