Each microarray contains 11769 oligonucleotide probes, whose design was based on gene transcript sequences from the Lycopersicon Combined Built # 3 unigene database (http://www.SGN.cornell.edu).edu
Research based on gene transcript (eg, mRNA), an assembly of protein-coding exons, is fully described throughout the literature, taking the fate of spliced noncoding introns to be completely digested for granted (Nott et al 2003).
An Affymetrix GeneChip whole genome tiling array was designed, and analyzed at the gene and exon level analysis with a total of 524,909 sense strand probes (average of 16 probes per gene), based on gene model predicted transcripts for T. pseudonana, version 3.0 (http://genome.jgi-psf.org/Thaps3/Thaps3.home.html).html
Based on gene annotations and transcript abundance data we identified candidate genes.
In addition to the confirmation of almost 77% of RAP transcripts, the results also provide evidence for expression of transcripts not represented in the microarray including transcripts without FL-cDNA support, transcripts based on gene prediction programs, or those identified by homology to other plants (Fig. 3).
The cancer-specific transcripts were classified based on gene function by searching the RefSeq database and GO.
We compared our set of transcripts to the JGI Besttranscriptpt' models, which are mostly based on gene prediction.
All subsequent analyses in this study were based on genes rather than transcripts because a nonnegligible portion (approximately 13.5%) of the transcripts contained more than one gene (supplementary fig. S1 A, Supplementary Material online), which may confound the investigation of gene expression and evolution.
In the present study all analyses will be based on genes instead of transcripts, thereby avoiding the bias introduced by different genes having different numbers of transcripts.
These transcripts correspond to gene models without EST and/or full-length cDNA support as well as those predicted based on gene prediction programs.
