# HISTORY 24 Mar 2016: Updated by: TOUCHUP-v1.15 14 Mar 2016: Updated by: TOUCHUP-v1.14 # molecular_function 20140109: Euteleostomi_PTN000190053 has function cytokine activity (GO:0005125) 20140109: Euteleostomi_PTN000190053 has function type I interferon receptor binding (GO:0005132) # cellular_component 20140109: Euteleostomi_PTN000190053 is found in extracellular space (GO:0005615) # biological_process 20140109: Euteleostomi_PTN000190053 participates in cytokine-mediated signaling pathway (GO:0019221) 20140112: Euteleostomi_PTN000190053 participates in B cell differentiation (GO:0030183) 20140112: Euteleostomi_PTN000190053 participates in B cell proliferation (GO:0042100) 20140112: Euteleostomi_PTN000190053 participates in adaptive immune response (GO:0002250) 20140109: Euteleostomi_PTN000190053 participates in innate immune response (GO:0045087) 20140111: Euteleostomi_PTN000190053 participates in response to exogenous dsRNA (GO:0043330) 20140112: Euteleostomi_PTN000190053 participates in T cell activation involved in immune response (GO:0002286) 20140111: Euteleostomi_PTN000190053 participates in positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141) 20140112: Euteleostomi_PTN000190053 participates in humoral immune response (GO:0006959) 20140111: Euteleostomi_PTN000190053 participates in natural killer cell activation involved in immune response (GO:0002323) # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES from wikipedia entry: 2013-12-03 Based on the type of receptor through which they signal, human interferons have been classified into three major types. - Interferon type I: All type I IFNs bind to a specific cell surface receptor complex known as the IFN-alpha receptor (IFNAR) that consists of IFNAR1 and IFNAR2 chains.[1] The type I interferons present in humans are IFN-alpha, IFN-beta and IFN-omega. - Interferon type II: Binds to IFNGR that consists of IFNGR1 and IFNGR2 chains. In humans this is IFN-gamma. - Interferon type III: Signal through a receptor complex consisting of IL10R2 (also called CRF2-4) and IFNLR1 (also called CRF2-12). Note that this family has multiple duplications within species, which is expected for immune response proteins. Other useful references: review PMID:23046138 MF Propagate to root: cytokine activity and type I interferon receptor binding (IFNs are cytokines that bind their receptor). CC Propagate to root: extracellular space. BP Propagate to root: cytokine-mediated signaling pathway. Propagate to root: innate immune response. All IFNs are involved in the defense response to viruses and bacteria, which cannot be propagated to the root because mouse Ifna6 has a negative annotation; however those defense responses correspond to innate immune response. Propagate to root: MHC biosynthetic process, also found in fish (PMID:20660353) Propagate to root: response to exogenous dsRNA; this is also found in mouse, see PMID:18596219, as well as fish Propagate to root: positive regulation of peptidyl-serine phosphorylation of STAT protein - also found in mouse, see PMID:21044071 and fish (PMID:24244163) Propagate to root: natural killer cell activation involved in immune response; based on phylogentic conservation, it can be predicted that IFns also regulate NK cell function in fish, see PMID:19268624 Propagate to root: T cell activation involved in immune response Propagate to root: B cell proliferation and B cell differentiation, which are children of B cell activation, but that annotation was not yet available. Made annotation Jan 12 2014, TO DO: update annotations when this term is available in PAINT. Propagate to root: adaptive immune response (PMID:18953720) (although I am not sure how this is measured; seem to be inferred based on the activation of B cells and T cells) Propagate to root: humoral immune response (PMID:18953720) IFNB1 clade: - B cell proliferation: annotated in human and mouse KO has defects in B cell proliferation, see PMID:14597717 NOTE Immune response in response to exogenous dsRNA" would be better. Requested GO term https://sourceforge.net/p/geneontology/ontology-requests/10601/ TO DO Add B cell activation involved in immune response when this term is available in PAINT. DO NOT PROPAGATE - GO:0045944 positive regulation of transcription from RNA polymerase II promoter and GO:0006355 regulation of transcription, DNA-templated: too indirect; should rather annotate to "GO:0023019 signal transduction involved in regulation of gene expression". Requested annotation change. - GO:0042742 defense response to bacterium : use innate immune response instead. All IFNs are involved in the defense response to viruses and bacteria, which cannot be propagated to the root because mouse Ifna6 has a negative annotation; however those defense responses correspond to innate immune response. - GO:0051607 defense response to virus: use innate immune response instead. All IFNs are involved in the defense response to viruses and bacteria, which cannot be propagated to the root because mouse Ifna6 has a negative annotation; however those defense responses correspond to innate immune response. - GO:0046685 response to arsenic-containing substance: not found in other species. - GO:0032897 GO:0032897 negative regulation of viral transcription - Do not propagate - only evidence for mouse Ifnb1 - GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process - Requested change of annotation to GO:2001235 positive regulation of apoptotic signaling pathway. - GO:0097194 execution phase of apoptosis - result of activation of apoptosis; IFNB1 is not directly involved in execution of apoptosis. # REFERENCE Annotation inferences using phylogenetic trees The goal of the GO Reference Genome Project, described in PMID 19578431, is to provide accurate, complete and consistent GO annotations for all genes in twelve model organism genomes. To this end, GO curators are annotating evolutionary trees from the PANTHER database with GO terms describing molecular function, biological process and cellular component. GO terms based on experimental data from the scientific literature are used to annotate ancestral genes in the phylogenetic tree by sequence similarity (ISS), and unannotated descendants of these ancestral genes are inferred to have inherited these same GO annotations by descent. The annotations are done using a tool called PAINT (Phylogenetic Annotation and INference Tool).