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annotation check psm1 #971

Closed ValWood closed 7 years ago

ValWood commented 8 years ago

PMID: 16615890

normal vegetative cell population growth for the deletion dosn't look possible?

@Antonialock

Antonialock commented 8 years ago

According to this paper the deletion mutant is viable and grows normally

ValWood commented 8 years ago

Confused...this psm1 cohesin subunit is definitely essential. I went to double check the paper, but I can't see psm1 mentioned in here?

On 09/07/2016 18:21, Antonia wrote:

According to this paper the deletion mutant is viable and grows normally

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Antonialock commented 8 years ago

It is in the supp table of all the deletions they tested. It is also a deletion they verified.

On Sunday, 10 July 2016, Val Wood notifications@github.com wrote:

Reopened #971 https://github.com/pombase/curation/issues/971.

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Antonia Lock, PhD PomBase Biocurator, http://www.pombase.org Department of Genetics, Evolution and Environment, The Darwin Building, University College London London WC1E 6BT, UK

ValWood commented 8 years ago

I only see a table with:

: selected genes for disruption (105 genes) /d: successfully disrupted genes checked

but it doesn't tell you the disruption phenotype anywhere that I can see?

On 10/07/2016 09:00, Antonia wrote:

It is in the supp table of all the deletions they tested. It is also a deletion they verified.

On Sunday, 10 July 2016, Val Wood notifications@github.com wrote:

Reopened #971 https://github.com/pombase/curation/issues/971.

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Antonia Lock, PhD PomBase Biocurator, http://www.pombase.org Department of Genetics, Evolution and Environment, The Darwin Building, University College London London WC1E 6BT, UK

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Antonialock commented 8 years ago

I based it on We then systematically disrupted each of these genes in an S. pombe strain expressing Taz1-GFP as a fluorescent marker for the telomere; 83 strains disrupted specific genes were successfully generated. All of these gene-disrupted strains showed normal mitotic growth as expected from the meiosis-specific expression of these genes

Antonialock commented 8 years ago

I think it is a problem to make the annotations "inviable vegetative cell" from the Kim & Jacky's datasets. They made heterozygous diploids, and sporulated those. I guess from this methodology you wouldn't really know if the gene is essential for meiosis, sporulation entry into mitotic cell cycle, or vegetative growth.

That is why I asked if the annotations for these two datasets should change to "inviable cell population" rather than "inviable vegetative cell population" but I don't think you agreed at the time.

Deletions can also be made in vegetative cells, I guess that is what they did in the Chikashige publication. If you look at the expression profile of psm1 it definitely looks like it plays a role in meiosis http://128.40.79.33/cgi-bin/SPGE/geexview?group=2&scale=linear&scale_auto=on&q=SPBC29A10.04

ValWood commented 8 years ago

OK I just canted to check first. I'll check with Hiroshi.... cells without this cohesin subunit should be absolutely unequivocally dead........I wonder if its a typo?

Val

On 10/07/2016 14:04, Antonia wrote:

I based it on We then systematically disrupted each of these genes in an S. pombe strain expressing Taz1-GFP as a fluorescent marker for the telomere; 83 strains disrupted specific genes were successfully generated. All of these gene-disrupted strains showed normal mitotic growth as expected from the meiosis-specific expression of these genes

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ValWood commented 8 years ago

Re >I think it is a problem to make the annotations No I agree with you and there is a ticket for me to do this somewhere. Although its only a small subset which are lethal because they don't get through sporulation, and I think one of Henry Levin's datasets indicates which ones it is....

I have a ticket to sort this somewhere but i didn't do it yet......

This one though is definitely required for mitosis. Its one of the mitotic cohesin ATPase subunits. Without this you are f**d I'm sure.....because you couldn't form a cohesin ring.... (it is absolutely required for mitotic cohesion)

ValWood commented 8 years ago

No I agree with you and there is a ticket for me to do this somewhere.

worryingly I can't find this ticket...I'm sure there was one. Later today I'll check my to do list and e-mail folders incase it never made it onto the tracker. In my head I see a tracker ticket.....

ValWood commented 8 years ago

whan they say " showed normal mitotic growth" shouldn't this be just "viable vegetative population" rather than normal growth (no data, and we don't know if they really measured 'growth')

val

Antonialock commented 8 years ago

Yeh I was thinking the same, I'll update the annotations tomorrow.

On Sunday, 10 July 2016, Val Wood notifications@github.com wrote:

whan they say " showed normal mitotic growth" shouldn't this be just "viable vegetative population" rather than normal growth (no data, and we don't know if they really measured 'growth')

val

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Antonia Lock, PhD PomBase Biocurator, http://www.pombase.org Department of Genetics, Evolution and Environment, The Darwin Building, University College London London WC1E 6BT, UK

Antonialock commented 7 years ago

Ok I fixed it.

Did you make a new tracker ticket?

No I agree with you and there is a ticket for me to do this somewhere.

worryingly I can't find this ticket...I'm sure there was one. Later today I'll check my to do list and

e-mail folders incase it never made it onto the tracker. In my head I see a tracker ticket.....