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NetAffx™ Analysis Center Announcement Archive

April 30, 2014

Release of NetAffx NA34 for WT Expression Arrays

The software pipeline for creating annotations for the NetAffx Gene and Exon products has been re-evaluated in order to reduce many false positive results. As with the rest of the update, this release incorporates new genome builds for mouse (mm10), rat (rn5), chicken (galgal4), and cow (bosTau6).

Click here for full documentation on sources used in NA34.

April 28, 2014

Update for MOUSEDIVm520650 genotyping array

Minor annotation update for MOUSEDIVm520650 array, released as na34.1

January 22, 2014

Release of NetAffx NA34 for IVT Expression and Genotyping Arrays

In addition to the usual updates for biological annotations for transcripts, gene symbols, OMIM, Gene Ontology and over a score of other data sources, NetAffx update NA34 includes new genome builds for mouse (mm10), rat (rn5), chicken (galgal4), and cow (bosTau6) and dbSNP build 137.

The annotation process for WT Gene, WT Exon and HTA arrays has undergone a major overhaul to improve the quality of annotations for these arrays. This has caused a delay in the NA34 support for the Whole Transcript Expression arrays. These updates will be released shortly.

Click here for full documentation on sources used in NA34.

May 23, 2013

Update for GenomeWide SNP 6.0, GenomeWide SNP 5.0, and Axiom Bovine arrays

GenomeWide SNP 6.0 na33 annotation update released. Minor performance updates for GenomeWide SNP 5.0 and Axiom Bovine arrays.

May 2, 2013

Improved GO coverage for WTGene array transcript annotation csv files available

They are available through the NetAffx XML annotation feed, and the online catalog:

  • AraGene
  • BovGene
  • CanGene
  • ChiGene
  • PorGene
  • RheGene
  • ZebGene

April 3, 2013

Update to WTGene array annotation files available today

Annotation csv files for WT Gene files have been released and are available through the NetAffx XML annotation update feed, available on Expression Console.

  • AraGene
  • CanGene
  • CHOGene
  • EquGene
  • FelGene
  • HuGene
  • MoGene
  • PorGene
  • RaGene
  • RCnGene
  • RJpGene

The files had been withdrawn and issues of control probe set inventory, badly formed data, and excessive annotations in some cases have been fixed as well as adjustments for Bioconductor and Affymetrix Transcription Analysis Console software.

Just a note: Exon Arrays will not be supported by TAC . The files for MarGene, SoyGene, RheGene, and BovGene annotation files are still in process, but will be released soon.

March 14, 2013

NetAffx Update NA33 for Genotyping Arrays available

We apologize for the delay, we have been revamping the Genotyping Annotation pipeline. The na33 Genotyping Annotation update includes these new features:

  • Allele frequency data from 1000 Genomes for most Axiom products
  • Genomic coordinate and annotation update for mouse (UCSC mm10), chicken (UCSC galGal4), bovine (UCSC bosTau6)
  • Online Mendelian Inheritance in Man (R) (OMIM) update
  • dbSNP update to build 137
  • More uniform CSV format, such as ordering overloaded columns by the identifier and allele frequency populations displayed as a 3-letter acronym. (More details can be found in the CSV packaged README)

NetAffx annotation updates for Genotyping arrays are now available on the web search and through the NetAffx XML feed.
WGSA Mapping (10k, 100k, 500k) and Panel arrays have been retired and new updates will no longer be created, though archival annotations are still available.

Feb 20, 2013

Support for Human Transcriptome Array (HTA) and Transcriptome Analysis Console (TAC) available

In addition to the tiling probe sets found in WT Gene and Exon Arrays, Junction probe sets allow HTA array/ TAC software users to explore and quantitate alternative splice populations in their biological samples. To search through the content in the Gene/Exon Search tab above.

March 11, 2012

New Axiom Array search support available on NetAffx

Content for the Axiom Exome array is now searchable on NetAffx.

December 10, 2012

NA33 WT Exon 1.0 and Gene 1.x annotation files for Human, Mouse and Rat Updated

Serious genome coordinate errors were discovered in the latest annotation files for the below arrays. Updated versions have been placed in their respecitve catalog locations on the site and in the NetAffx XML Feed:

November 21, 2012

NetAffx Update NA33 for Expression Arrays available today

NetAffx annotation updates for IVT and Expression arrays are now available on the web search and through the NetAffx XML feed.

This update features coverage for the new v2 HuGene, MoGene, and RaGene arrays as well as 10 new model organism WT arrays (CHO, arabidopsis, bovine, feline, canine, chicken, horse, sheep, pig. marmoset) with more to be available in the coming months.

Annotation updates for WGSA (SNP6 SNP5 500k etc) and Axiom arrays is undergoing testing and will will be available around the new year.

Some features will be retired in this update. BLASTP and MAGE-XML format Annotation files will no longer be available for Expression. Also, the NetAffx DAS server is scheduled to be taken off line before the end of 2012.

In the future, we will be releasing NetAffx updates about every 6 months.

View the documentation on the NA33 update here.

March 8, 2012

Support for Zebrafish and Bovine Model Organism WT Gene Arrays

Search for the content of the Zebrafish and Bovine Model Organism Arrays is now available. CSV annotation files will also be showing up in the SDK and on the support web pages tomorrow. Support for more Model Organism Array Support coming up.

July 18, 2011

NetAffx Annotation Update 32 is available.

NetAffx Annotation Update 32 is available for download. Annotation Update NA32 features full online search support for the new Cytoscan HD, Axiom European and Asian Genotyping Arrays. Expression Array annotations have also been updated, incuding SusScr2 genome build support for the IVT PorcineArray. On another note, MIP Panel Arrays are retiring from the Affymetrix Product Catalog and so their content will no longer be searchable on NetAffx from this point forward.

For full documentation see the NetAffx32 documentation.

May 10, 2011

Create Axiom myDesign Targeted Genotyping (TG) Arrays online.

Now you can design your own Axiom Array with as few as 1,500 markers for candidate gene, replication, and fine mapping studies. Access the Axiom Genomic Database today.

Jan 22, 2011

Correction for Error in Genotyping Annotation Update 31 Available

A bug has been found in the Netaffx na31 Genotyping annotation files. In cases where the SNP strand changed in the transition from genome build NCBIv36 to GCRhv37, the annotations do not reflect the proper strand of record. This only affects a few hundred probe sets and does not affect Axiom Array Annotations. It will be corrected in the upcoming na32 release in a couple of months. A list of the 388 probe sets known to have this problem can be found here. Reference data for the proper dbSNP orientation for Affymetrix arrays can also be found at dbGap .

Sep 3, 2010

NetAffx Annotation Update 31 is available

Annotations are updated and available for all Affymetrix Catalog IVT, Gene, Exon and Mapping Arrays. Annotations for all catalog Human Mapping arrays are now updated to the new human genome build GRCh37 (ucsc hg19) and dbSNP build 131. For All catalog products the latest builds of NCBI databases (GenBank, Refseq, Unigene) have been captured. Ensembl data for human arrays are still based on build #55 (GRCh37). Updates to SGD (Jan 2010), Flybase (r5,25), JGI (Poplar v2 Jan 2010), miRBase (v15, May 2010) have also been captured in this release. For full documentation see the NetAffx31 documentation.

August 3, 2010

Annotation Update 31 delays

We apologise for delays in delivering NetAffx Annotation Update 31. The update is nearly complete now and will be out in August.

Apr 12, 2010

NetAffx Annotation Update 31 slated for June/July

The first NetAffx Update for 2010 has been moved up to midyear - June/July. We apologise for any inconvenience. NA31 will feature GRChv37 updates for all genotyping arrays including the Cytogenetics Array.

Jan 22, 2011

HuGene Annotation file update

Probe set CSV annotation files in NetAffx update 30 for the HuGene arrays (v1.0 and v1.1) contained a small number of extra probe sets that were either not present in or had different probe count with respect to the library files. A new version of the probe set CSV files ("na30.1") for these arrays corrects these issues. Other annotation contents in these and all other files are unaffected.

Dec 11, 2009

MoGene and RaGene Annotation file update

CSV annotation files in NetAffx update 30 for the MoGene and RaGene arrays (v1.0 and v1.1) contained a single control probe set that had been removed from the library files in June 2009. The new version of the CSV files ("na30.1") corrects this and removes the control probe set in question from the files. Annotations for all other probe sets and transcript clusters are unaffected.

Oct 15th, 2009

Axiom Genotyping Array and GTC 4.0 Support Axiom Genotpying array support is now online on NetAffx. Search through the Axiom content live on NetAffx.

GTC 4 support on Netaffx is also live today. GTC 4 updates and streamlines analysis for 500k, SNP5, SNP6 and Axiom arrays. Check it out here. Includes SQLite versions of the Annotation CSV files for the above Genotyping arrays, available on their respective product pages and the NetAffx SDK.

Sept 28th, 2009

Mouse Diversity Array Support Annotation Updates Mouse Diversity genotyping array support is now online on NetAffx.

Human Genome GRCh37 To Be Supported in Annotation Update NA30 With the next Annotation Update in mid November, human IVT and WT expression Array annotations will be updated to the latest genome build, GRCh37. Genotyping array annotations will remain in NCBIv36 to harmonize with current dbSNP builds.

NA29 Header correction The GenomeWideSNP 6 Annotation CSV file from na29 has been updated to correct a typo in the header where the genome build was recorded as NCBIv36 and should have been NCBIv36.1. No annotation content was changed.

July 24th, 2009

NetAffx Annotation Update 29 Available Annotations for all catalog arrays are updated and available for all Affymetrix Catalog IVT, Gene, Exon and Mapping Arrays.
One exception for the update is the Cytogenetics Array - the na29 update will be published in the near future.
New data sources used for this update include genome builds and transcript annotations from TAIR8 for Arabidopsis, and from JGI's Glyma1 release for soybean. Documentation of this update's contributing data sources can be found here.

Oct 15th, 2009

Axiom Genotyping Array and GTC 4.0 Support Axiom Genotpying array support is now online on NetAffx. Search through the Axiom content live on NetAffx.

GTC 4 support on Netaffx is also live today. GTC 4 updates and streamlines analysis for 500k, SNP5, SNP6 and Axiom arrays. Check it out here. Includes SQLite versions of the Annotation CSV files for the above Genotyping arrays, available on their respective product pages and the NetAffx SDK.

Sept 28th, 2009

Mouse Diversity Array Support Annotation Updates Mouse Diversity genotyping array support is now online on NetAffx.

Human Genome NCBIv38 Supported in Annotation Update NA30 With the next Annotation Update in mid November, human IVT and WT expression Array annotations will be updated to the latest genome build, NCBIv37. Genotyping array annotations will remain in NCBIv36 to harmonize with current dbSNP builds.

NA29 Header correction The GenomeWideSNP 6 Annotation CSV file from na29 has been updated to correct a typo in the header where the genome build was recorded as NCBIv36 and should have been NCBIv36.1. No annotation content was changed.

July 24th, 2009

NetAffx Annotation Update 29 Available Annotations for all catalog arrays are updated and available for all Affymetrix Catalog IVT, Gene, Exon and Mapping Arrays.
One exception for the update is the Cytogenetics Array - the na29 update will be published in the near future.
New data sources used for this update include genome builds and transcript annotations from TAIR8 for Arabidopsis, and from JGI's Glyma1 release for soybean. Documentation of this update's contributing data sources can be found here.

June 17th, 2009

MoGene and RaGene library file update

New Mouse and Rat r4 analysis files were updated to remove a single (non end-user) control probeset from pgf, ps and mps files. This probeset contained probes that had GC-counts of 1 and 2, for which there is no matching GC background control (antigenomic) bin. This caused the dabg option (only in APT, not EC) to fail the step that verifies the existence of a matching GC bin.

May 6th, 2009

Cytogenetics Array Support Live on NetAffx

Single Gene level, High Density Cytogenetics through the Cytogenetics Whole Genome 2.7M Array is live today on NetAffx. Search through all 2.7 million markers on line. Comprehensive whole genome coverage for detection of chromosomal duplications or deletions.

Or Browse the Cytogenetics Array content on UCSC with our custom CytoGenetics Array Track.

March 23rd, 2009

NetAffx Annotation Update 28 Available.
Annotations for all catalog arrays are updated and available for all Affymetrix Catalog IVT, Gene, Exon and Mapping Arrays.
This Annotation Update features online support of Exon Level Probe sets for Gene Arrays, including updated genome browser tracks for all WT Array products. Xenopus laevis 2 IVT Array content is also now searchable online.
Documentation of this Update's Contributing Source can be found here.

February 27th, 2009

HT Perfect Match Array Annotation Patch
Annotation CSV files correcting PM Probe set names in annotation CSV file support are now available for: HT HG U133 Plus PM, HT MG 340 Plus PM, and HT RN 230 Plus PM arrays.

January 23rd, 2009

Exon-Level Analysis Enabled on Human, Mouse and Rat whole-transcript GeneChip® Gene Arrays
Library files are now available to enable EXON-level analysis on GeneChip Gene Arrays, offering affordable whole-genome differential splicing analysis. The new "r4" library files enable the grouping of probes into exon specific probe sets as well as the gene-level probe sets that were previously available.
Files are available on the corresponding array support pages and via the NetAffx SDK.
Update, Feb 15 2009: The NetAffx CSV probe set annotation files for the Gene Arrays have been revised to synchronize better with r3 annotations; removed extra versions of probe sets that map multiple times in the same gene.
Update, Jun 17 2009: New Mouse and Rat r4 analysis files were updated to remove a single (non end-user) control probeset from pgf, ps and mps files. This probeset contained probes that had GC-counts of 1 and 2, for which there is no matching GC background control (antigenomic) bin. This caused the dabg option (only in APT, not EC) to fail the step that verifies the existence of a matching GC bin.

December 1st, 2008

NetAffx Annotation Update 27 Available.
Transcript and Functional annotations for all Affymetrix Catalog arrays updated for 3' IVT Expression, Exon/Gene and Genotyping Arrays. Full source data information is available here.

October 13th, 2008

Welcome to NetAffx 5
Along with a new design, look and style, some of the most requested major NetAffx features updates are included:

  • Better workflow navigation. Easier access to the entire range of NetAffx functions and utilities, reliable access to your usual ones.
  • Condensed Report mode on the result table.
  • LD Mapper Estimate the coverage of Affymetrix Genotyping Arrays over lists of rsIDs, genes or genomic regions.
  • Pop-up NetAffx help on each page. The Help Button will give you hints on your current page.
  • Glossaries define all the annotation data offered (see ivt expression, wt expression, genotyping).

New releases, product support, application Announcements

October 13th, 2008

Welcome to NetAffx 5
Along with a new design, look and style, some of the most requested major NetAffx features updates are included:

  • Better workflow navigation. Easier access to the entire range of NetAffx functions and utilities, reliable access to your usual ones.
  • Condensed Report mode on the result table.
  • LD Mapper Estimate the coverage of Affymetrix Genotyping Arrays over lists of rsIDs, genes or genomic regions.
  • Pop-up NetAffx help on each page. The Help Button will give you hints on your current page.
  • Glossaries define all the annotation data offered (see ivt expression, wt expression, genotyping).

July 21st, 2008

NetAffx Annotation Update 26 Available.
Transcript and Functional Annotations updated for Expression, Exon/Gene and Genotyping Arrays. Full source data information is available here.
Featuring:

  • Annotation coverage for Gene and Exon Arrays has been improved.
  • Includes updates to the Bovine Genome and RAP2 Rice annotations.

March 21st, 2008

NetAffx Annotation Update 25 Live today.
Transcript and Functional Annotations updated for all Expression, Exon/Gene and Mapping Arrays. na25 source documentation is available here.
Featuring:

  • New Genome Builds for Mouse (NCBIv37), Anopheles (anoGamP3), Zebrafish (danRer5) and C elegans (ce4).
  • Includes dbSNP version 128

November 13th, 2007

NetAffx Annotation Update 24 Release Notes.
Transcript and Functional Annotations updated for all Expression, Exon/Gene and Mapping Arrays. Full source data information is available here.
Also Featuring:

  • New Bovine genome version and the drosophila genome version has changed to BGDP version 5.
  • Revision to Exon and Gene array annotation pipeline gives cleaner annotation sets.

September 20th, 2007

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.

July 17th, 2007

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.

June 15th, 2007

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.

June 11th, 2007

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.

May 31st, 2007

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.

May 4, 2007

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

March 30, 2007

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.

March 19, 2007

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.

February 16, 2007

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.

Jan 5, 2007

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

November 28, 2006

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.

Genotyping Arrays are also updated, except for MIP panel annotations, which will be available in early January.

Downloaded Annotation file names now incorporate a release number, which include an

na## extension (e.g. na21 for NetAffx Release 21) in their suffixes.

October 30, 2006

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'.

October 17, 2006

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

July 17, 2006

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.

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