What is on the Arabidopsis ATH1-121501 GeneChip?

 

The Arabidopsis ATH1, or ATH1-121501,  Genome Array contains 22,814 probe sets,  representing 22,768 Arabidopsis elements. There are 22,703 elements assigned to genomic loci by TAIR annotation team. There are 22,521 nuclear loci, 102 mitochondria loci and 80 chloroplast loci.  The array is based on information from the International Arabidopsis Sequencing Project that was completed in December, 2000 and annotated by TIGR. To represent as many gene sequences on the array wherever possible, non-unique probe sets were used to represent two or more highly similar genes. The total number of unique loci is 22,464 as being determined by TAIR.  Data from the TIGR database (ATH1-121501) is available in the NetAffx™ Analysis Center at www.affymetrix.com. Technical notes on GeneChip arrays and their operation can be found at the Affymetrix website. 

Search and Access Probe Sets on ATH1-121501:

There are  six ways to find probe sets on ATH1-121501 GeneChip.

•  Search by Gene Expression Profiles:  Finding probe sets showing desired expression profile in absolute value and in variation using multiple filters. It can be conducted on a single experiment basis, or on cross-experiment basis. This is the recommended methods for integration with data analysis.

• Browse by Probe Set List:  All microarray elements can be retrieved from the list of probe sets.

• Sequence Similarity-Based Search via BLAST

  Use can input his own sequence, and use BarleyBase BLAST page to find Arabidopsis or Barley1 exemplar sequences homologues.  The BLAST result page let user to view expression of found sequences.
   

• Keyword-Based Search.

         Construct complex search terms with keywords and Boolean operators to search against the exemplar sequence annotations.

• Browse and Retrieve Probe Sets According to Their Pathway or Gene Family Membership

         Starting from list of major pathways, retrieve all probe sets corresponding to a pathway, or retrieve just probe sets corresponding to a given gene in the pathway by clicking on a pathway graphic. Currently, about 2,500 ATH1-121501 GeneChip probe sets can be assigned to KEGG pathways.

       There are 5,477 genes assigned to 796 gene families in Arabidopsis. For ATH1-121501 GeneChip, 4175 probe sets are assigned to the gene families.

•  Select a Probe Set to align it with exemplar sequence, or retrieve expression from a list of Probe Sets.