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[Geneontology-annotation] [ geneontology-Annotation issues-3073335 ] annotation problem PANTHER:PTHR11361_AN278
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From: SourceForge.net <no...@so...> - 2010-12-16 09:39:41
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Annotation issues item #3073335, was opened at 2010-09-22 13:32 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3073335&group_id=36855 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: PANTHER annotation Group: Reference Genomes >Status: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Mike Livstone (livstone) Summary: annotation problem PANTHER:PTHR11361_AN278 Initial Comment: Fission yest msh1 has a mapping to maintenance of DNA repeat elements as this protein is excusively mitochondrial in this organism, and the miotochondrial genome has negligable repeats (is involved in mis match repair) (other non-mitochondrial family members do have a role in maintaining dinucletide tract lenghth and this annotation appears to be transferred from here) As a general rule you probably shouldn't trransfer processes between nuclear and mitochondrial family members Val ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2010-12-16 09:39 Message: I think that is all for this item, so i am changing the status to closed. I think you are right, transferring annotation from nuclear to mitochondrial shouldn't be a general rule, just something to look out for. Val ---------------------------------------------------------------------- Comment By: Mike Livstone (livstone) Date: 2010-12-15 21:42 Message: Hi, Val. I reviewed this annotation, which was based on 2 annotations in the nearby MSH3 clade. One (PMID 16388310) refers to CAG repeats in an HPRT construct integrated into a human cell line. The other (PMID 11333219) refers to GT repeats in pombe ade6. Based on your point that the pombe mitochondrial genome has negligible repeats, these phenomena do not seem relevant here, so I have STOPped the annotation from propagating into the MSH1 clade as you suggest. I'm not clear on your suggestion not to transfer annotations from nuclear to mitochondrial family members. Do you mean for this family or for all families? Either way, I think this may be a factor to take into consideration, but shouldn't be a general rule. -Mike ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3073335&group_id=36855 |