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GenProp2003 #22

Closed LornaMGnify closed 6 years ago

LornaMGnify commented 7 years ago

4 steps listed unintegrated panthers. I have integrated 3 of these, but for SN1 I have replaced the evidence with a PIRSF model that was already integrated - IPR014394. This model is slightly more specific than the suggested unintegrated panther. However, the model also hits the homologous protein hepatocyte growth factor activator. Is this OK?

ndrawlings commented 7 years ago

No, not really. Hepatocyte growth factor activator has nothing to do with blood coagulation.

From: happy-lorna [mailto:notifications@github.com] Sent: 14 June 2017 10:47 To: rdfinn/genome-properties genome-properties@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [rdfinn/genome-properties] GenProp2003 (#22)

4 steps listed unintegrated panthers. I have integrated 3 of these, but for SN1 I have replaced the evidence with a PIRSF model that was already integrated - IPR014394. This model is slightly more specific than the suggested unintegrated panther. However, the model also hits the homologous protein hepatocyte growth factor activator. Is this OK?

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LornaMGnify commented 7 years ago

Yeah I know it doesn't, but they are in the same family by homology, and all available models hit them both so presumably they cannot be (easily) separated out. I was wondering if we should just reflect this is the threshold value - e.g. raise it by 1 to cover for the fact that this step may overhit.

ndrawlings commented 7 years ago

The sequences differ in their first 80 residues, so separating them should be relatively trivial. These represent a gene duplication present in all tetrapods, probably all vertebrates, so should be separate entities in Panther.

From: happy-lorna [mailto:notifications@github.com] Sent: 14 June 2017 11:27 To: rdfinn/genome-properties genome-properties@noreply.github.com Cc: ndrawlings ndr@ebi.ac.uk; Comment comment@noreply.github.com Subject: Re: [rdfinn/genome-properties] GenProp2003 (#22)

Yeah I know it doesn't, but they are in the same family by homology, and all available models hit them both so presumably they cannot be (easily) separated out. I was wondering if we should just reflect this is the threshold value - e.g. raise it by 1 to cover for the fact that this step may overhit.

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