Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely-expressed human genes

Castelo Valdueza, Robert; Reymond, Alexandre; Wyss, Carine; Cámara, Francisco; Parra Farré, Genís; Antonarakis, Stylianos E.; Guigó Serra, Roderic; Eyras Jiménez, Eduardo

doi:http://dx.doi.org/10.1093/nar/gki328

Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely-expressed human genes

Citation

Castelo R, Reymond A, Wyss C, Cámara F, Parra G, Antonarakis S E, Guigó R, Eyras E. Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes. Nucleic acids research. 2005;33(6):1935-9. DOI: 10.1093/nar/gki328

Abstract

The recent availability of the chicken genome sequence poses the question of whether there are human protein-coding genes conserved in chicken that are currently not included in the human gene catalog. Here, we show, using comparative gene finding followed by experimental verification of exon pairs by RT–PCR, that the addition to the multi-exonic subset of this catalog could be as little as 0.2%, suggesting that we may be closing in on the human gene set. Our protocol, however, has two shortcomings: (i) the bioinformatic screening of the predicted genes, applied to filter out false positives, cannot handle intronless genes; and (ii) the experimental verification could fail to identify expression at a specific developmental time. This highlights the importance of developing methods that could provide a reliable estimate of the number of these two types of genes.