Atlas article is a featured publication in NAR: Featured Articles highlight the best papers published in NAR. These articles are chosen by the Executive Editors on the recommendation of Editorial Board Members and Referees. They represent the top 5% of papers in terms of originality, significance and scientific excellence. Read all about it.
4th Oct 2009
Student Project Placement: An exciting student project placement is available to develop an interface for the Human Gene Expression Map...more details.
16/06/2009
Gene Expression Atlas - Release 1.1.0: New features include an ontology driven interface using EFO, newly added datasets, expression profile similarity searching and top 10 variable genes per experiment...try them now.
04/06/2009
Bioinformatician with ArrayExpress:A new job position working as a bioinformatician with ArrayExpress has opened up...more details.
05/05/2009
ArrayExpress Atlas - 1000 experiments:The latest release of ArrayExpress Atlas has grown to reach the milestone of 1000 experiments.
26/02/2009
ArrayExpress Atlas Student Masters Project:An MSc Masters project placement is available within the Microarray Group. It will involve developing an advanced ontology querying interface to ArrayExpress Atlas. For further details, please check this page.
14/11/2008
ArrayExpress Bioconductor Package:Use the ArrayExpress Bioconductor Package to access ArrayExpress data and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet. This package was developed with Emerald funding.
27/08/2008
Sorting by Experiment Technology Type:Quickly identify ChIP-Chip or RNAi experiments using the new drop down filter.
27/08/2008
Links to variably expressed genes in the Atlas from the browse interface:E.g. query E-GEOD-4262 and identify genes where expression varies with the experimental factors.
27/06/2008
ArrayExpress Interface:A new ArrayExpress user interface has been released with improved response times including support for web browsers Safari and Opera. Try it now from here.
29/05/2008
ArrayExpress Ontology - EFO: The ArrayExpress Team have developed an application ontology of sample and factor annotations - the EFO. The ontology is used to map user submitted annotations during curation, to improve query performance and to integrate ArrayExpress data with publicly available ontologies, including the Disease Ontology, CHEBI, and the Cell Type Ontology. The ontology is publicly available from the EBI's Ontology Lookup Service - OLS and is released every two months. The EFO can be used by any database storing sample properties or experimental variables and we invite comment and term submission from any interested user .
29/05/2008
UHT sequencing transcriptomics data in ArrayExpress: ArrayExpress now stores high ultra throughput sequencing data and is compliant with the MINSEQE standard. Submissions are accepted and downloadable in MAGE-TAB format.
29/05/2008
High resolution analysis of the S. pombe transcriptome: Wilhelm et al. (Nature, 2008)
, have analysed the S.pombe transcriptome at single nucleotide resolution using Illumina sequencing technology and tiling arrays. ArrayExpress has made available
this data.
28/05/2008
ArrayExpress Atlas Beta:Explore in which conditions a gene is expressed or which genes are differentially expressed in a particular condition, tissue, cell type, etc. Try it now from here.
10/03/2008
New MSc Project Proposals:Two MSc projects are available in our group. For further details, please see this page.
11/12/2007
ArrayExpress database doubles in size to 100,000 hybridisations:ArrayExpress has doubled in size reaching the 100,000 hybridisation milestone...more.
18/05/2007
MGED 10 Travel bursaries for EU students:Three bursaries funded by EMERALD for PhD students from the EU member countries are available for travel purposes to the MGED 10 meeting. More details available from MGED 10 Student Travel Bursaries web page.
24/03/2007
Featured Data Set:A meta analysis of gene expression data from 6000 human publicly available diseased, normal samples and cell lines obtained from GEO and ArrayExpress. Cel files were generated on Affymetrix HG-U133A chips, normalized with GCRMA and have meta data annotation generated by a text mining and manual curation approach. Cel files, a MAGE-TAB format experiment description with sample annotation, and normalized data are available for download. FTP
23/03/2007
MAGE-TAB support:ArrayExpress now supports MAGE-TAB submissions and a conversion script is available for the previous spreadsheet format. A beta release of our software for generating and parsing MAGE-TAB is available from the Tab2MAGE SourceForge site.
26/02/2007
MAGE-TAB:A simple spreadsheet-based, MIAME-supportive format for microarray data - MAGE-TABv1.0. [tar.gz - 12,075kb]
New Job Positions in Group: The EBI Functional Genomics Group has three open job positions...more details.
11/07/2005
Student Position in Bioinformatics / Computer Science.: The EBI Functional Genomics Team offers a student project of 6 months duration for a Student in Bioinformatics/ Computer Science...more.
01/06/2005
Bulk ArrayExpress Data through FTP: If you wish to have bulk access to ArrayExpress data files, including original Affymetrix formatted .CEL files, please go to the FTP site from here.
06/01/2005
EMBO Practical Course Registration Open Now: Registration is now open for the EMBO Practical Course to be held on the Genome Campus here from 3th April to 9th April, 2005. Deadline for registration is 31/01/2005. Please register from here.
27/10/2004
New Job Positions - CLOSED NOW: Two new positions for a Bioinformatics Specialist and a Software Engineer are needed in the group. For more information, please check here. Closed Now.
27/09/2004
New Student Project Proposal - CLOSED NOW: Please find a functional genomics ontology development student project proposal from this web page. Closed Now.
24/02/2004
Student Project Proposals - CLOSED NOW: Please find 3 student project proposals from this web page. Closed Now.
16/02/2004
New Database Programmer Job Position: A new position is open for an ArrayExpress Database Programmer. For more information, please check here.
23/12/2003
MAGE Post Jamboree Web Page Ready: Please find MAGE Post Jamboree Web Page from here.
10/12/2003
New Nutrigenomics Project Scientific Officer Job Position: A new position is open for a Nutrigenomics Project Scientific Officer. For more information, please check here.
05/11/2003
New Curator Job Position: A new position is open for an ArrayExpress Database Curator. For more information, please check here.
03/11/2003
EP:NG version 1.0a now available: The new release (1.0a) of Expression Profiler (code name: Next Generation) is now available for alpha testing: EP:NG.
New SOFG Website: The new
Standards and Ontologies for Functional Genomics (SOFG)
website can be found at http://www.sofg.org.
01/08/2003
New Toxicogenomics Webpages:
New toxicogenomics webpages are found here.
Also, a new toxicological specific MIAMExpress will be
available for submissions from here.
"Free Access Costs Money" Article:
Scientists support microarray data sharing but microarray
repositories with a free access policy may find it difficult
to provide such complicated information without more funding...more.
17/12/2002
New SOFG Post Conference
Webpage: Find the SOFG presentations, abstract book
and post conference review information from the SOFG
Post Conference webpage.
17/12/2002
EMBO Course 2003
Now Open For Registration: Register for the "EMBO
practical course on Analysis and Informatics of Microarray
Data" from here.
New and Updated Microarray
Research Webpages.: The microarray research pages
have been revamped...more.
04/12/2002
SOFG Presentations
Are Now Available: Presentations from the Standards
and Ontologies for Functional Genomics (SOFG) Conference
are now available from here.
01/12/2002
MIAMExpress Release
1.0 Is Now Accepting Submissions To ArrayExpress:
MIAMExpress 1.0 is available for ArrayExpress submissions
from here.
07/10/2002
Nature and The Lancet
endorse Standard for Microarray experiments: Prominent
journal have endorsed MIAME's proposed standards for microarray
experiments...more
06/08/2002
E-SNGR-2 to E-SNGR-7,
data files for Mata et al., Nature Genetics (published
online): These datasets are now available in ArrayExpress.
For more details, please check here.
28/06/2002
E-RUBN-1, datafiles
for Spellman and Rubin, Journal of Biology, 2002:
This data set is now available from here.
It will be available in ArrayExpress as soon as possible.
20/06/2002
E-RUBN-1, datafiles
for Spellman and Rubin, Journal of Biology, 2002:
This data set is temporarily unavailable due to technical
reasons. For more details, please check here.
24/05/2002
SOFG Conference:
The Standards and Ontologies for Functional Genomics (SOFG)
Conference will be held from 17th to 20th November, 2002.
For more details, please check here.
14/05/2002
New Job Position
- Software Developer: A software developer is required
in the microarray group. For more details, please check
here.
11/02/2002
ArrayExpress / MIAMExpress
Online: The EBI is currently working with Affymetrix
to upload GeneChip design descriptions to ArrayExpress.
30/01/2002
Affymetrix Collaboration:
ArrayExpress
now accepts submissions via MIAMExpress.
The ArrayExpress database can also be queried from here.
17/01/2002
New Web Site Design:
New layout and design for the Functional Genomics website
at EBI. Thank you to Jean-Jack Riethoven for helping me.
Please send any comments to
.
