This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Homologous gene matching between mouse and human

There is a small part of mouse genes that cannot be matched to homologous human genes. For example, the Apoc1 gene:

http://www.informatics.jax.org/marker/MGI:88053

Since there is a gene, APOC1, with exactly the same symbol in human, why is this mouse Apoc1 gene not homologous to human APOC1 gene?

hgnc gene mgi
• 4,267 views • link
updated by Ram Ram • written by lovetl2002 • lovetl2002

2 answers

If you are referring to Homologene, the procedure to identify orthologs is rather conservative to minimize false positives. So, there will be false negatives and the example you cite might be one of them.

• 0 views • link
written by Siva Siva

Homologene is a database of homologs only. As far as I know it's not building any tree so can't infer orthologs and paralogs properly. A tree built out of multiple alignments would be able to resolve more distant homology than pairwise alignment-based methods. For finding orthologs and/or paralogs, have a look at TreeFam or Ensembl. Human APOC1 is clearly orthologous to mouse Apoc1 in Treefam: http://www.treefam.org/family/TF330940#tabview=tab1

• 0 views • link
written by Jean-Karim Heriche Jean-Karim Heriche

Log in to answer this question.

More posts like this