Complete Arabidopsis Transcriptome MicroArray (CATMA)

Design of Gene Family Tags (GFTs)

Robin Liechti & Philippe Reymond

Department of Plant Molecular Biology - University of Lausanne - Switzerland

The comparison of the AGIs present in CATMA v3 and those in TAIR6_cdna (November 2005) produced a list of 3352 AGIs not represented by a Gene Specific Tag (GST).

From those, 1014 were small genes (less than 150 bp) or were mitochondrial or chloroplastic genes. To complete the Arabidopsis transcriptome coverage in CATMA v4 microarray, we designed probes for the remaining 2338 AGIs

Using, NCBI-Blast (Stephen F. Altschul et al, 1997), AGIs were grouped in 992 gene families for which a Family Specific Sequence was designed. Some families also include AGIs already represented by a GST, although the number of these genes has been minimized.

Using Primer3 (Steve Rozen and Helen J. Skaletsky, 2000), a Gene Family Tag was designed for each Family Specific Sequence.

A Gene Specific Tag could however be designed for 546 AGIs (singletons). The reason why the design of GSTs for these singletons by the SPADS software (Vincent Thareau et al, 2003) failed in the CATMA project remains unclear.

A graph showing the density of the number of genes present in a family is presented below


last update: 2007-02-14