Hello everybody,
I will be giving my yearly seminar next Monday, April 5th, usuall place
and time - 8th floor conference room at 11:00 AM.

See you then,

Wojtek

HUMAN AND NEMATODE ORTHOLOGS - LESSONS FROM THE ANALYSIS OF 1800 HUMAN 
GENES AND THE PROTEOME OF CAENORHABDITIS ELEGANS

Recently we have defined and analyzed over 1800 orthologous human
and rodent genes.  Here we extend this work to compare human and
Caenorhabditis elegans coding sequences. 1,880 human proteins
were compared with about 20,000 predicted nematode proteins
presumably comprising nearly the complete proteome of  C.
elegans.  We found that 43% human/rodent orthologs have
convincing nematode counterparts. On average, the amino acid
similarity and identity between aligned human and Caenorhabditis
elegans orthologous genes are 69.3% and 49.1%, respectively, and
the nucleotide identity is 49.8%.  Detailed investigation of our
results suggests that some nematode gene predictions are
incorrect, leading to erroneous pairing with human genes (e.g.
calcineurin and polymerase II elongation factor III). 
Furthermore, other proteins (i.e. homologs of human ribosomal
proteins S20 and L41, thymosin) are missing entirely from the
nematode proteome suggesting that it may not be complete.  These
results underscore the fact that metazoan gene prediction is a
very challenging task and that most computer-predicted nematode
genes require supporting evidence of their existence from
comparative genomics and/or laboratory investigation.