title: [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array
status: Public on Jul 18 2002
contact.city: Santa Clara
contact.last: Affymetrix
contact.email: geo@ncbi.nlm.nih.gov, support@affymetrix.com
contact.state: CA
contact.country: USA
contact.web_link: http://www.affymetrix.com/index.affx
contact.institute: Affymetrix, Inc.
contact.phone: 888-362-2447
organism: Arabidopsis thaliana
description: Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html
  
  June 03, 2009: annotation table updated with netaffx build 28
  June 07, 2012: annotation table updated with netaffx build 32
  July 01, 2016: annotation table updated with netaffx build 35
manufacture_protocol: see manufacturer's web site
  
  The current release has 22810 entries and was indexed 26-Jun-2003.
  Annotation data from TAIR, Gene Ontology Consortium and TIGR were mapped to the Arabidopsis ATH1 Array probe sets. The AGI (Arabidopsis Genome Initiative) ID (e.g. AT5G23000) corresponding to the gene represented on the array was used to map annotation data obtained from TAIR, Gene Ontology and TIGR databases. Similarly, gene title and gene symbol, as well as the EC annotations for the AGI ID were extracted from the TIGR database.  These annotation mappings were validated by a two-pronged approach. First, probe sets were randomly selected and manually curated to check for consistency between Gene Ontology terms, gene title and protein domain associations. Furthermore, associations within and between data sets from different public databases were also used to check for consistencies. For example, consider the association of gene ontology terms and InterPro IDs. Several Gene Onoltogy terms have InterPro ID(s) curated as supporting evidence for assigning the term to an AGI locus. This relationship was used to validate the consistency of the ontology terms from Gene Onotlogy and InterPro domain annotations from TAIR.  The GeneChip® Arabidopsis ATH1 Genome Array contains more than 22,500 probe sets representing approximately 24,000 genes. Sequences used in the design were selected and clustered in collaboration with TIGR and were derived from TIGR's ATH1-121501 Database. Oligoneuclotide probes are synthesized in situ to each corresponding sequence. Eleven pairs of oligoneuclotide probes are used to measure the level of transcription of each sequence represented on the GeneChip Arabidopsis ATH1 Genome Array. Most sequences represented on the previous generation GeneChip® Arabidopsis Genome Array are also represented on the ATH1 array. Due to the dynamic nature of public databases, probe sets for these sequences will not be identical and in some cases will be represented by a completely new probe set. As a result, data generated with different versions of the Arabidopsis array may not always produce concordant results. The probe arrays are for research use only and not intended for use in diagnosis of diseases.
  