  Background: Recent studies in a growing number of organisms have yielded
accumulating evidence that a significant portion of the non-coding region in
the genome is transcribed. We address this issue in the yeast Saccharomyces
cerevisiae.
  Results: Taking into account the absence of a significantly large yeast EST
database, we use microarray expression data collected for genomic regions
erroneously believed to be coding to study the expression pattern of non-coding
regions in the Saccharomyces cerevisiae genome. We find that at least 164 out
of 589 (28%) such regions are expressed under specific biological conditions.
In particular, looking at the probes that are located opposing other known
genes at the same genomic locus, we find that 88 out of 341 (26%) of these
genes support antisense transcription. The expression patterns of these
antisense genes are positively correlated. We validate these results using
RT-PCR on a sample of 6 non-coding transcripts.
  Conclusions: 1. The yeast genome is transcribed on a scale larger than
previously assumed. 2. Correlated transcription of antisense genes is abundant
in the yeast genome. 3. Antisense genes in yeast are non-coding.
