NetAffx Feature Update NetAffx 4.2 available. Several major NetAffx features have been updated, and some outdated features have been retired in order to improve your interactive GeneChip array data analysis. More features will be coming in a few months. The full announcement is available here.

• Updated Quick Queries -faster, better sorted responses.
• Expanded Export and Batch Upload: now you can save the first 10,000 probe set records.
• Streamlined navigation.
• Updated NetAffx help
  • Glossaries for the details pages define all the annotation data offered (see help icons on probe set detail pages).
  • Updated and revised NetAffx FAQ
• In addition, some outdated NetAffx Features are also being retired. For details, see the NetAffx 4.2 Feature Announcement.
  • Probe Set Display for IVT probe sets.
  • The Array Finder Application.
  • The GO Browser.
• New downloads and annotations for Exon and WT Gene arrays are also being posted. The data patch includes the removal of a few erroneous gene symbol assignments and retirement of some weak transcript and cross-hyb assignments.

NetAffx Annotation Update 23 Live today. Annotations updated for all Expression and Exon Arrays. Full source data information is available here.

• Nearest/Overlapping Gene Mappings are now available for all Mapping Arrays.
• Rhesus Array human mappings are now fully replaced with Rhesus genes where available.
• To eliminate some poor quality probe set annotations, ENSEMBL EST Gene records are discontinued.

NetAffx Feature updates and retirements in late July. At the end of July NetAffx will be sprucing up it's search, navigation and documentation to make the direct NetAffx experience more manageable and efficient. At the same time some outdated features, the Array Finder, SVG Probe Display and GO Browser will be retired. Be sure to come by and take a look.

Annotation File Patch - KEGG Annotations Discountinued. KEGG Pathway Annotations will no longer be available through NetAffx. Archive Annotation Files have also been revised to reflect this policy. MAGE XML files may be temporarily offline while they are amended.
A patch of the 'Total Probes' column in control Exon and Gene Annotation CSV files is also included.

Genome-Wide SNP 6.0 Array Support Live on NetAffx. View SNP and CN (Copy Number) content live on NetAffx, or download the annotation files in bulk on the product support page.

Targeted Genotyping Bovine 25k Array Support Live on NetAffx. Available in the Genotyping Section.

WT Gene Human 1.0 Array Support Live on NetAffx. See the New Exon/Gene Array Support Section documenting the latest in Expression quantitation; the Human Gene 1.0 ST array.

Annotation Update - Release 22 live today. Annotations updated for all Expression and Exon Arrays. Full source data information is available here.

• Support for the new Xenopus tropicalis Array.
• Update to Drosophila Flybase 5.1 support.
• Update to JGI Poplar v1.1 support.
• UCSC Probe level tracks available for applicable 3? IVT arrays.
• Protein similarity data has been supplemented with Unigene similarity data to document EST only probe sets.
• Annotations for Protein Families have been discontinued.
• Changes to the Annotation CSV file formats
  • Headers for IVT annotation files contain descriptions of content.
  • Columns for protein families are discontinued.
  • GO term IDs now include leading zeroes in conformity with GO Consortium standards.

GenomeWideSNP 5.0 Live on NetAffx. With today's release of the GenomeWideSNP 5.0 Array, all array content is searchable in the Genotyping section of NetAffx.

NetAffx Annotation files for the current release are now available via stable URLs. These links will be located within "current" subdirectories for each array technology, where applicable. For example, the annotation files for the HG-U133_Plus_2 array are downloadable from these links:
http://www.affymetrix.com/Auth/analysis/downloads/current_ivt/HG-U133_Plus_2.annot.csv.zip
http://www.affymetrix.com/Auth/analysis/downloads/current_ivt/HG-U133_Plus_2.annot.xml.zip
http://www.affymetrix.com/Auth/analysis/downloads/current_ivt/HG-U133_Plus_2.ortholog.csv.zip
Note that the file contained within a zip archive will be version stamped for the release (example: HG-U133_Plus_2.na21.annot.csv).

Exon array annotations will be available from a current_exon subdirectory, for instance RaEx-1_0-v2 files here:
http://www.affymetrix.com/Auth/analysis/downloads/current_exon/RaEx-1_0-st-v1.rn4.transcript.csv.zip
http://www.affymetrix.com/Auth/analysis/downloads/current_exon/RaEx-1_0-st-v1.rn4.probeset.csv.zip

And Genotyping annotation files are organized under their own current_genotyping directory, like the Mapping250K_Nsp and Mapping250K_Sty arrays here:
http://www.affymetrix.com/Auth/analysis/downloads/current_genotyping/Mapping250K_Nsp.annot.csv.zip
http://www.affymetrix.com/Auth/analysis/downloads/current_genotyping/Mapping250K_Sty.annot.csv.zip

Annotation Update - Release 21 live today. Expression and Exon Array annotations are updated for all organisms.

New Genome versions are supported for Rat, Rhesus, Chicken Zebrafish and Drosophila annotations. Documentation describing the source data incorporated in Release 21, is available here.

Downloaded Annotation file names now incorporate a release number, which include an na## extension (e.g. na21 for NetAffx Release 21) in their suffixes.

ToxFX Array Support Live on NetAffx. The Iconix ToxFX Rat toxicology screening array can be searched in NetAffx. Look in the Expression Query page search 'Rat ToxFX'.

Cotton Array Support Live on NetAffx. The New Cotton IVT Expression Array is now searchable on NetAffx.

Annotation Update - Release 20 (R20) and new documentation for NetAffx. Expression and Exon Array annotations are updated for all organisms. This release features a new revision of Anopheles assignments and the new NCBIv36 Human Mouse and Rat genome builds.

New: Documentation for Release 20 is available, describing the source data collected to create this annotation update.

New: Whitepapers describing the NetAffx Annotation Pipeline and getting the most from NetAffx Details Pages are now available on the NetAffx Support page.