NetAffx™ Analysis Center
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.
