From camon at ebi.ac.uk Mon Oct 8 07:00:07 2007 From: camon at ebi.ac.uk (camon at ebi.ac.uk) Date: Mon, 8 Oct 2007 15:00:07 +0100 (BST) Subject: [immunology] IFN induction to GO mapping Message-ID: <33167.81.132.77.14.1191852007.squirrel@webmail.ebi.ac.uk> Hi UniProtKB have a keyword 'Interferon induction' which they assign to proteins that are induced by interferon. They are asking if they can map this to the GO term 'immune response'. Suggestions? Its a bit of a strange kw. Here is the DEFINITION: ID Interferon induction. AC KW-0402 DE Protein induced by interferon(s). Interferons are a class of cytokines DE which mediate, by binding to specific cell-surface receptors, a broad DE range of activities such as resistance to viral infection, modulation DE of the immune response and regulation of proliferation of normal and DE malignant cells. SY IFN induction. and here are the proteins with that annotation: http://ca.expasy.org/cgi-bin/get-entries?KW=Interferon%20induction Evelyn From adiehl at informatics.jax.org Mon Oct 8 07:09:37 2007 From: adiehl at informatics.jax.org (Alexander Diehl) Date: Mon, 08 Oct 2007 14:09:37 +0000 Subject: [immunology] IFN induction to GO mapping In-Reply-To: <33167.81.132.77.14.1191852007.squirrel@webmail.ebi.ac.uk> References: <33167.81.132.77.14.1191852007.squirrel@webmail.ebi.ac.uk> Message-ID: <470A3A21.7050308@informatics.jax.org> Evelyn, The fact that their definition includes "regulation of proliferation of normal and malignant cells," makes me a bit reluctant to make this mapping. Sure interferons themselves have various roles in the immune response, but the definition provided here implies other roles which may go beyond the immune response. We would not annotate to "immune response" a gene simply because its expression level changes in a microarray experiment in response to a cytokine with a known role in the immune response, and this seems to be a similar type of proposition. I oppose this mapping. Thanks, Alex camon at ebi.ac.uk wrote: > Hi > > UniProtKB have a keyword 'Interferon induction' which they assign to > proteins that are induced by interferon. They are asking if they can map > this to the GO term 'immune response'. > > Suggestions? Its a bit of a strange kw. > > Here is the DEFINITION: > > ID Interferon induction. > AC KW-0402 > DE Protein induced by interferon(s). Interferons are a class of cytokines > DE which mediate, by binding to specific cell-surface receptors, a broad > DE range of activities such as resistance to viral infection, modulation > DE of the immune response and regulation of proliferation of normal and > DE malignant cells. > SY IFN induction. > > and here are the proteins with that annotation: > > http://ca.expasy.org/cgi-bin/get-entries?KW=Interferon%20induction > > Evelyn > > > -- Alexander Diehl, Ph.D. Senior Scientific Curator Mouse Genome Informatics The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 email: adiehl at informatics.jax.org work: +1 (207) 288-6427 fax: +1 (207) 288-6131 From camon at ebi.ac.uk Tue Oct 9 01:46:12 2007 From: camon at ebi.ac.uk (camon at ebi.ac.uk) Date: Tue, 9 Oct 2007 09:46:12 +0100 (BST) Subject: [immunology] IFN induction to GO mapping In-Reply-To: <470A3A21.7050308@informatics.jax.org> References: <33167.81.132.77.14.1191852007.squirrel@webmail.ebi.ac.uk> <470A3A21.7050308@informatics.jax.org> Message-ID: <41950.86.154.197.118.1191919572.squirrel@webmail.ebi.ac.uk> Thanks Alex for your prompt response, I also think it is a safest option not to map, Evelyn > Evelyn, > > The fact that their definition includes "regulation of proliferation of > normal and malignant cells," makes me a bit reluctant to make this > mapping. Sure interferons themselves have various roles in the immune > response, but the definition provided here implies other roles which may > go beyond the immune response. We would not annotate to "immune > response" a gene simply because its expression level changes in a > microarray experiment in response to a cytokine with a known role in the > immune response, and this seems to be a similar type of proposition. > > I oppose this mapping. > > Thanks, > > Alex > > > camon at ebi.ac.uk wrote: >> Hi >> >> UniProtKB have a keyword 'Interferon induction' which they assign to >> proteins that are induced by interferon. They are asking if they can map >> this to the GO term 'immune response'. >> >> Suggestions? Its a bit of a strange kw. >> >> Here is the DEFINITION: >> >> ID Interferon induction. >> AC KW-0402 >> DE Protein induced by interferon(s). Interferons are a class of >> cytokines >> DE which mediate, by binding to specific cell-surface receptors, a >> broad >> DE range of activities such as resistance to viral infection, >> modulation >> DE of the immune response and regulation of proliferation of normal >> and >> DE malignant cells. >> SY IFN induction. >> >> and here are the proteins with that annotation: >> >> http://ca.expasy.org/cgi-bin/get-entries?KW=Interferon%20induction >> >> Evelyn >> >> >> > > > -- > Alexander Diehl, Ph.D. > Senior Scientific Curator > Mouse Genome Informatics > The Jackson Laboratory > 600 Main Street > Bar Harbor, ME 04609 > > email: adiehl at informatics.jax.org > work: +1 (207) 288-6427 > fax: +1 (207) 288-6131 >