NetAffx™ Analysis Center
Get unprecedented access to array content.
The NetAffx™ Analysis Center enables researchers to correlate their GeneChip® array results with array design and annotation information.
- NetAffx Query Search transcript clusters and probe sets for a particular term or identifier
- Batch Query Retrieve annotations for a probe list
- Probe Match Find probe sets that identically match a nucleotide sequence(s)
- NetAffx Query - Search probe sets for a term or identifier
- Batch Query - Retrieve annotations for a probe list
- BLAST - Find probe sets that BLAST align to your sequence(s) through BLAST
- Probe Match - Find probes that identically match your sequence(s)
- UCSC Query - Query the UCSC Browser including a custom track for your array of interest.
- NetAffx Query - Search probe sets for a term or identifier
- Batch Query - Retrieve annotations for a probe list
- LD Mapper - Evaluate GenomeWideSNP arrays coverage for your list of rsIDs, genes, or genomic regions
- UCSC Query - Query the UCSC public genome by position
- SNP Finder - Search for SNPs between microsatellites
The Axiom™ Design Center enables you to quickly select and configure a custom Axiom™ myDesign™ Array for your genotyping studies. You can choose from the 11 million common and rare markers in the Axiom Genomic Database and/or submit your own sequence information.
- NetAffx Query - Search probe sets for a term or identifier
- Batch Query - Retrieve annotations for a probe list
Announcements
New releases, product support, applications
For an archival listing of NetAffx Announcements click here
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
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 in approximately one week.
Link for TAC: http://www.affymetrix.com/browse/level_seven_software_products_only.jsp?categoryIdClicked=&productId=prod760001#1_1
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.
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.
Resources and Help
Selected resources and documentation for getting the most out of the NetAffx™ Analysis Center
NetAffx Help Center
The complete index of documentation available for NetAffx users. Including:
Sources for NetAffx Annotation Updates See documentation for sources and versions of data that went into the annotation updates.
Glossaries of Annotation Terms (3'IVT Expression, WT Expression, Genotyping)
Whitepapers
- Using the NetAffx XML feed Use simple scripts to track changes in annotations or library files with the NetAffx XML Feed.
- NetAffx Annotation Whitepaper How does the NetAffx calculate the relationship between the probe set and the current transcript record. (3'IVT)
- Sleuthing with NetAffx Tips and examples on how to unravel difficultprobe sets and SNPs.