tag:treefam.tenderapp.com,2013-02-16:/discussions/questions/6-conservation-of-genes-including-fungi-and-plantsTreeFam: Discussion 2013-06-14T08:56:00Ztag:treefam.tenderapp.com,2013-02-16:Comment/269380962013-05-21T09:32:27Z2013-05-21T09:32:28ZCONSERVATION OF GENES- INCLUDING FUNGI AND PLANTS<div><p>I note that Treefam includes S.cerevisiae (Sc), S.pombe (Sp),
Arabidopsis and rice as an "Outgroup" set of species. I find this a
really good idea, to give a sense of how genes have been conserved
(or not) during evolution, on a wider scale than 'just' animals.
And also, these are key model organisms of interest to a great many
researchers worldwide.</p>
<p>However in several cases where I know a (human) gene has S.pombe
or S.cerevisiae orthologues, these are often not found in
Treefam.</p>
<p>Just one example: Chk1 / CHEK1<br>
Here are links to these genes in their "home" (species-specific)
databases:<br>
Human: <a href=
"http://www.genenames.org/data/hgnc_data.php?hgnc_id=1925">http://www.genenames.org/data/hgnc_data.php?hgnc_id=1925</a><br>
Sp: <a href=
"http://www.pombase.org/spombe/result/SPCC1259.13">http://www.pombase.org/spombe/result/SPCC1259.13</a><br>
Sc: <a href=
"http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=chk1">http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=chk1</a></p>
<p>Searching Treefam for CHEK1, and opening the tree TF351441 does
not include these Sp and Sc orthologs:<br>
<a href=
"http://www.treefam.org/family/TF351441#tabview=tab1">http://www.treefam.org/family/TF351441#tabview=tab1</a></p>
<p>Oddly enough, Ensembl reports the Sc, but not the Sp
orthologue:<br>
<a href=
"http://www.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?g=CHEK1">
http://www.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?g=CHEK1</a><br>
As the chk1 gene was in fact first discovered in S.pombe (<a href=
"http://www.pubmed.org/8497322">www.pubmed.org/8497322</a>), to me
it seems rather strange not to include Sp in the list of organisms
that shares that gene!</p>
<p>In this case, the NCBI's HomoloGene correctly identifies the Sc
and Sp orthologues:<br>
<a href=
"http://www.ncbi.nlm.nih.gov/homologene?term=CHEK1">http://www.ncbi.nlm.nih.gov/homologene?term=CHEK1</a></p>
<p>Clearly these different sites (Treefam / Ensembl / HomoloGene)
use different methods and stringencies to define what is included
as being an orthologue.</p>
<p>Happily, Treefam does find Sc, Sp and At orthologues for the
well-conserved gene DNA Polymerase alpha (POLA1):<br>
<a href=
"http://www.treefam.org/family/TF103001#tabview=tab1">http://www.treefam.org/family/TF103001#tabview=tab1</a><br>
- so at the "highly conserved" end of the conservation spectrum,
this aspect of Treefam works just fine.</p>
<p>My questions related to this are:<br>
- do you think it's possible that Treefam could be missing out on
some genuine and important orthologues, by being a bit too
stringent? - what do you think of the idea of (automatically)
'cross-checking' between Treefam and Ensembl
orthologues/paralogues, to ensure some consistency between
these?</p></div>Jim Hutchinstag:treefam.tenderapp.com,2013-02-16:Comment/269380962013-06-14T08:55:59Z2013-06-14T08:55:59ZCONSERVATION OF GENES- INCLUDING FUNGI AND PLANTS<div><p>Hi Jim,<br>
thanks for your feedback.</p>
<p>You are right, there are differences between TreeFam, Ensembl
Compara and HomoloGene, which are due to the different methodology
or taxon sampling.<br>
Also, we keep our families fixed TreeFam and whereas e.g. Compara
rebuild their families with every release. There are good arguments
for either approach.</p>
<p>At some time in the near future we will be looking into ways of
testing our families. We will then also cross-check our predictions
with e.g. Ensembl. That is a good idea.</p>
<p>Thanks again for your valuable feedback!<br>
I will close the ticket for now, as we have added your suggestions
to our todo list for the evaluation of our families</p>
<p>Cheers,<br>
Fabian</p></div>Fabian