# HISTORY 07 May 2016: Updated by: TOUCHUP-v1.18 14 Mar 2016: Updated by: TOUCHUP-v1.12 24 Mar 2016: Updated by: TOUCHUP-v1.15 # molecular_function 20110117: Ascomycota_PTN000017598 has function MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017) 20110117: Eukaryota_PTN000016644 has function phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439) 20110119: Euteleostomi_PTN000017219 has function MAP kinase phosphatase activity (GO:0033549) 20110117: Bilateria_PTN000016922 has function actin binding (GO:0003779) 20110117: Tetrapoda_PTN000016744 has function JUN kinase phosphatase activity (GO:0008579) # cellular_component 20110117: Ascomycota_PTN000017598 is found in nucleus (GO:0005634) 20110117: Euteleostomi_PTN000016649 is found in mitochondrion (GO:0005739) 20110119: Euteleostomi_PTN000017219 is found in cytosol (GO:0005829) 20110117: Bilateria_PTN000017376 is found in cytoplasm (GO:0005737) 20110117: Tetrapoda_PTN000016724 is found in nucleus (GO:0005634) 20110120: Viridiplantae_PTN000016805 is found in chloroplast (GO:0009507) 20110117: Magnoliophyta_PTN000017696 is found in nucleus (GO:0005634) 20110117: Bilateria_PTN000016922 is found in cytoplasm (GO:0005737) # biological_process 20110117: Deuterostomia_PTN000017431 participates in regulation of cell proliferation (GO:0042127) 20110117: Deuterostomia_PTN000017431 participates in positive regulation of JNK cascade (GO:0046330) 20110117: Deuterostomia_PTN000017431 participates in transforming growth factor beta receptor signaling pathway (GO:0007179) 20110117: Ascomycota_PTN000017598 participates in regulation of pheromone-dependent signal transduction involved in conjugation with cellular fusion (GO:0010969) 20110117: Ascomycota_PTN000017598 participates in adaptation of signaling pathway by response to pheromone involved in conjugation with cellular fusion (GO:0000754) 20110117: Saccharomycetaceae_PTN000017600 participates in inactivation of MAPK activity (GO:0000188) 20110117: Euteleostomi_PTN000017141 participates in negative regulation of JUN kinase activity (GO:0043508) 20110117: Euteleostomi_PTN000016832 participates in regulation of heart growth (GO:0060420) 20110117: Euteleostomi_PTN000016832 participates in regulation of fibroblast growth factor receptor signaling pathway (GO:0040036) 20110117: Euteleostomi_PTN000016832 participates in dorsal/ventral pattern formation (GO:0009953) 20110117: Euteleostomi_PTN000016832 participates in regulation of endodermal cell fate specification (GO:0042663) 20110117: Euteleostomi_PTN000016832 participates in positive regulation of apoptotic process (GO:0043065) 20110117: Euteleostomi_PTN000016832 participates in negative regulation of ERK1 and ERK2 cascade (GO:0070373) 20110117: Deuterostomia_PTN000017039 participates in endoderm formation (GO:0001706) 20110117: Euteleostomi_PTN000017042 participates in regulation of apoptotic process (GO:0042981) 20110119: Euteleostomi_PTN000017219 participates in negative regulation of T cell receptor signaling pathway (GO:0050860) 20110119: Euteleostomi_PTN000017219 participates in positive regulation of mitotic cell cycle (GO:0045931) 20110119: Euteleostomi_PTN000017219 participates in negative regulation of T cell activation (GO:0050868) 20110119: Euteleostomi_PTN000017219 participates in negative regulation of JNK cascade (GO:0046329) 20110119: Euteleostomi_PTN000017219 participates in negative regulation of ERK1 and ERK2 cascade (GO:0070373) 20110117: Euteleostomi_PTN000016701 participates in positive regulation of glucokinase activity (GO:0033133) 20110120: Euteleostomi_PTN000017379 participates in spermatogenesis (GO:0007283) 20110117: Magnoliophyta_PTN000017696 participates in negative regulation of MAP kinase activity (GO:0043407) 20110118: Bilateria_PTN000017471 participates in peptidyl-tyrosine dephosphorylation (GO:0035335) 20110117: Bilateria_PTN000016922 participates in regulation of actin polymerization or depolymerization (GO:0008064) 20110117: Bilateria_PTN000016922 participates in regulation of axonogenesis (GO:0050770) 20110117: Bilateria_PTN000016922 participates in regulation of lamellipodium assembly (GO:0010591) # PRUNED 07 May 2016: Boreoeutheria_PTN000017535 has been pruned from tree # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES 24 Mar 2016: Boreoeutheria_PTN000017535 has been pruned from tree 14 Mar 2016: Boreoeutheria_PTN000017535 has been pruned from tree . Phylogeny This is a large family with 610 members, 180 of which are RefGenome proteins. However, there are only 171 annotations in total to 81 unique terms, so it shouldn't be too complicated. This family has a small, divergent, unannotated, paralogous outgroup (AN1099), which we will ignore. The AN1094 clade is also unannotated and small, containing only 3 bacterial proteins, but the branch length between AN1094 and its parent AN1 is short and the branch length between AN1 and AN2 is even shorter, so we can consider AN1094 to be in the main part of the family. AN2 has 5 paralogous direct children: AN3, AN54, AN173, AN180, and AN183. Only the most basic and general properties will be propagated out of these 5 clades. AN173 and AN180 define very small clades with long branch lengths and no inferences will be drawn from them. AN183 defines a very large clade of 505 proteins spanning plants through humans. It has 4 paralogous descendants: AN184 (human through dicty), AN1052 (plants, treated here as an outgroup), and the unannotated non-RefGenome clades AN1004 (ciliates) and AN1046 (leishmania), both of which we will ignore. Additional details will be provided below as we crawl the clades for specific annotations. General note on approach This family consists primarily of dual-specificity phosphatases (tyrosine-serine-threonine phosphatases) and related catalytically-inactive binding proteins. The catalytic activity of these proteins is ancient and well-conserved, but their specificity -- i.e. the substrates on which they act the locations in which they are found in the cell, and the biological processes in which they are involved -- varies clade by clade. Therefore, I will begin by propagating core catalytic activities (and related processes) across the entire family (or most of it), but will then curate the more specific MF, CC, and BP of each clade individually, rather than the typical approach of curating all MF followed by CC and BP in order. Note useful references: PMID 18330678 and PMID 19228121. MF (general) -The AN2 clade is well-annotated as protein phosphatases, but the outgroup contains no annotations. While it is clear that this entire family is probably full of phosphatases, it's hard to say whether the outgroup acts on proteins. However, as noted above, the branch length between AN1 and AN2 is very short. Propagate GO:0016791 "phosphatase activity" to AN0 and GO:0004721 "phosphoprotein phosphatase activity" to AN1. -There are only 3 annotations, from only 2 papers, to GO:0008330 "protein tyrosine/threonine phosphatase activity" (PMID 11959861 and PMID 12435803). Is this a valid term, or did they just not check serine? Current understanding is that there are 2 classes of phosphatase: tyrosine and serine/threonine, so this is probably just an issue of which experiments were performed and could be curated from these papers. Ignore these 3 annotations. -***Most proteins with annotations to GO:0004725 "protein tyrosine phosphatase activity" also have annotations to GO:0008138 "protein tyrosine/serine/threonine phosphatase activity," and all proteins with annotations to 4725 have orthologs with annotations to 8138. I.E., all the phosphatases are dual-specificity phosphatases. Propagate 8138 to AN1. -PG also notes: "PMID: 19228121 MKPs extended consensus sequence {D} X26(V/L)X(V/I)H {C} XAG(I/V)S {R} SXT(I/V)XXAY(L/I) {M} where X is any amino acid and the critical residues for catalysis are in {}. From same review: bona fide MPKs are : DUSP1, 2, 4, 5, 6, 7, 8, 9, 10, 16." General comment on CC Many members of PTHR10159 are phosphatases involved in signal transduction, and they're found throughout the cell: cytoplasm, nucleus, plasma membrane. Therefore, broad high-level annotation will not be very informative, since it will cover the entire cell. Instead, examine each clade of orthologs and propagate narrowly. Also, ignore HTP localization studies without confirming data. General note on BP -Propagate GO:0006470 "protein dephosphorylation" to AN1 and GO:0016311 "dephosphorylation" to AN0 to match MF annotations. AN3 clade AN3 defines one clade with no major duplications spanning plants through humans. This clade contains 2 annotated proteins: dicty plip and mouse Ptmpt1. (There are also 2 HTP annotations on the worm protein, but they will not be used.) AN3 MF -Propagate GO:0004439 "phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity" from these 2 proteins to AN3. Despite no visible annotations supporting 8138, allow it to propagate through to AN3 because there is a reference supporting it (PMID 9256433) with 2 IDAs that does not appear in PAINT. For now, do not address the lone GO:0017120 "polyphosphoinositide phosphatase activity" annotation on Dicty plip. AN3 CC -Based on UniProt comments that Q66GT5 (mouse Ptpmt1) is located to the mitochondrial inner membrane and an HTP annotation to GO:0005739 "mitochondrion," propagate 5739 to vertebrate Ptmpt1's (AN8). Note that this is limited to vertebrates due to a Golgi annotation on dicty plip and the fact that the paper cited by UniProt (PMID 16039589) indicates that its role is in the pancreas. AN3 BP -Propagate GO:0046855 "inositol phosphate dephosphorylation" to AN3 to match the MF. -Allow "protein dephosphorylation" to persist. AN54 clade AN54 spans plants to humans and appears to have one duplication at the vertebrates (AN59), giving rise to a DUSP1 clade (AN60) and another clade (AN81) with a fish outgroup and a duplication at the quadrupeds (AN82), which in turn gives rise to a DUSP19 cade (AN103) and a divergent Laforin/EPM2A clade (AN83). It will probably be necessary to block propagation into AN60 and/or AN83 for a number of annotations. There are no propagable annotations in AN138, AN150, or AN158. Start with the Epm2a clade (AN83), which is the divergent paralog of the Dusp19 clade (AN81). AN81 is, in turn, paralogous to the Dusp12 clade; the outgroup extends from fly to plants. AN54 MF -Despite being paralogous to and divergent from DUSP19, and named differently, Epm2a ("Laforin") is believed to be a protein phosphatase. See Uniprot annotation and PMID 10092504. No change in Epm2a clade. -Propagate GO:0008579 "JUN kinase phosphatase activity" from mouse Dusp19 to rest of Dusp19 clade, AN103. -The rest of AN54 is properly annotated with 8138. AN54 CC -UniProt states that mouse Epm2a (Q9WUA5, laforin) is cytoplasmic and "Under glycogenolytic conditions localizes to the nucleus." Propagate "cytoplasm" and "nucleus" to Epm2a clade. -Propagate "cytoplasm" to Dusp19 clade (AN103). Since both paralogs AN103 and AN83 are annotated to "cytoplasm," propagate "cytoplasm" to AN81 to cover both clades and the fish outgroup. -Propagate "cytoplasm" from rat to Dusp12 clade based on PMID 10913113. Expand to AN59 to include Dusp19/Epm2a clade. -The "nucleus" annotation in DUSP12 is HTP, and the one in fly MKP-4 is based on an experiment in HeLa cells. Do not propagate these. -Propagate "chloroplast" to the plant subclade, AN164. AN54 BP -Propagate GO:0033133 "positive regulation of glucokinase activity" to Dusp12 clade. -Propagate GO:0007254 "JNK cascade" to Dusp19 clade based on PMID 11959862 and the MF annotation above. Expand to AN57 based on PMID 18456458 for fly MKP-4, but NOT/IRD to Dusp12 clade, whose target is glucokinase, not a JNK cascade protein (PMID 10913113). Also NOT/IRD to Epm2a clade. We have now covered everything outside AN183. We start with AN1052, the plant outgroup. AN1052 contains 5 Arabidopsis proteins, one of which (AT4G18593) is highly divergent, unannotated, and may be a sequence fragment. There are also a number of rice and chlamy proteins. AN1052 MF/BP -Propagate MF GO:0033549 "MAP kinase phosphatase activity" and BP GO:0043407 "negative regulation of MAP kinase activity" narrowly from IBR5 to AN1055. -33549 is also found in AN1087 (on MKP2). It is also unannotated in AN1076 (on PHS1) in PMID 19392697: "in vitro dephosphorylation assays indicated that phospho-MPK18 can be dephosphorylated by recombinant PHS1." Propagate MF 33549 to AN1052. Also propagate GO:0043405 "regulation of MAP kinase activity" (not negative regulation) to AN1052. AN1052 CC -Propagate "nucleus" narrowly from IBR5 to AN1055. -Propagate "cytoplasm" from PHS1 to AN1076. AN184 is a duplication with AN185 and AN274 as children; AN274 has a very short branch length, and AN185 is comparatively longer but still pretty short. Continue with AN185 (Dusp6, -7, and -9), which has very little sequence diversity. AN185 contains 3 paralogous vertebrate clades (DUSP6/AN191, DUSP9/AN221, and DUSP7/AN234) with outgroups that span Ciona to Entamoeba. AN185 MF -GO:0017017 "MAP kinase tyrosine/serine/threonine phosphatase activity" is found in all 3 Dusp clades. Propagate 17017 to AN190. -Fly Mkp3 has a BP annotation to GO:0043409 "negative regulation of MAPKKK cascade" and an IDA to "phosphatase activity." Expand 17017 to entire AN185 clade. AN185 CC -Propagate "cytosol" to AN185 based on multiple annotations to "cytoplasm" and a few to "cytosol," all in focused papers. -The only annotations to "nucleus" are actually to "nucleoplasm" and come from 1 paper, PMID 17322878. Can't propagate this yet. PG thinks this Reactome annotation is questionable. AN185 BP -Propagate GO:0000188 "inactivation of MAPK activity" to AN185 based on multiple annotations to this term and its parent GO:0043407 "negative regulation of MAP kinase activity" from worm lip-1 to human and in all 3 clades of DUSP6, 7, and 9. This also agrees with the MF annotation above. -There are no remaining useable terms in the DUSP7 or -9 clades. -Do not propagate anything else from the worm/fly outgroup, which is divergent compared to the rest of AN185. -Propagate GO:0070373 "negative regulation of ERK1 and ERK2 cascade" to Dusp6 clade based on 2 annotations. -Propagate these terms to the DUSP6 clade (which contains only vertebrate proteins): GO:0043065 : positive regulation of apoptosis GO:0009953 : dorsal/ventral pattern formation GO:0040036 : regulation of fibroblast growth factor receptor signaling pathway GO:0042663 : regulation of endodermal cell fate specification GO:0060420 : regulation of heart growth Continuing inward, AN274 has a Dicty/Entamoeba outgroup with one annotated member (LRDP2); the branch length is long, and there are no new annotations in this clade. The orthologous clade (AN275) is a duplication with the small unannotated clade AN276 and the large clade AN279 as children. AN279 has a fungal outgroup (AN956, with several duplications) orthologous to six paralogous metazoan clades (see below). In AN956, the AN969 clade contains only 1 annotated member (yeast YVH1, not counting 1 HTP annotation on pombe yvh1), and branch lengths are relatively long throughout. Do not propagate from YVH1. Fungal clade AN957 Paralogous to AN969, and branch lengths are long enough to consider these separately. AN957 MF -Propagate GO:0017017 "MAP kinase tyrosine/serine/threonine phosphatase activity" AN957 CC -LTP papers support propagation of "cytosol" and "nucleus." AN957 BP -There are multiple annotations to children of GO:0000188 "inactivation of MAPK activity" among the 3 cerevisiae members of the clade. Propagate 188 to AN959 to include Ashbya. Expand the parent term GO:0043405 "regulation of MAP kinase activity" to AN957 based on this statement on pombe pmp1 from PMID 12172965: "Although previously shown to regulate other MAP kinase pathways in Sz. pombe, this is the first demonstration of a role for Pmp1 in pheromone signalling." -Propagate GO:0010969 "regulation of pheromone-dependent signal transduction involved in conjugation with cellular fusion" and GO:0000754 "adaptation of signaling pathway by response to pheromone involved in conjugation with cellular fusion" to AN957. Continuing inward, AN280 has 6 paralogous children: AN281 (slingshot proteins), AN343 (DUSP1, 2, 4, 5, 8, 10, & 16), AN735 (Styx proteins, serine/threonine/tyrosine interacting proteins), AN768 (DUSP15 and DUSP22), AN830 (DUSP18, 21, 28, and 14; also contains CCDC155, which shouldn't be part of this family), and AN549 (DUSP3, -27, -26, -13, DUPD1, and STYXL1). AN281: Slingshot proteins Fly ssh (slingshot) outgroup, fish ssh homologs, paralogous clades of SSH1 and SSH2 spanning birds to humans, divergent unannotated clade SSH3 paralogous to SSH1 mammals. The SSH3 clade (AN304) is completely unannotated. However, PMID 14531860, cited at UniProt, states that all 3 mammalian SSH's may be involved in actin filament dynamics, so treat them all the same. Also, fly ssh is involved in actin filament dynamics (PMID 11832213), so treat the whole clade this way. AN281 MF -Propagate GO:0003779 "actin binding" to AN281. AN281 CC -Propagate "cytoplasm" to AN281 based on 1 annotation and multiple mentions at UniProt. AN281 BP -Propagate GO:0008064 "regulation of actin polymerization or depolymerization" to AN281. -the following terms all have to do with cell shape generated by the cytoskeleton. Propagate them to AN281: GO:0000902 : cell morphogenesis GO:0050770 : regulation of axonogenesis (subsumes 902, above) GO:0010591 : regulation of lamellipodium assembly AN343 Worm/fly outgroup with a 3-way deuterostome polytomy giving rise to a DUSP8/DUSP16 clade, a DUSP10 clade, and a DUSP1/DUSP4/DUSP5 clade. DUSP2 is a DUSP1 paralog divergent at the mammalian split. AN345: DUSP8 and 16 This clade contains only 1 annotated member, mouse Dusp16. No new MF information is available. AN345 CC mDusp16 is shown to shuttle from the cytoplasm to the nucleus upon stimulation. UniProt shows mDusp8 is also found in both the cytoplasm and nucleus (PMID 8733137). Propagate both terms to AN345 to cover both clades and the outgroup. AN345 BP mDusp16 is annotated to GO:0000188 "inactivation of MAPK activity," and InterPro IEA's show human and mouse DUSP8's as MAPK dual-specific phosphatases. Propagate 188 to AN345. AN398: DUSP1, -2, -4, and -5 The DUSP1, -4, and -5 clades are paralogs spanning the vertebrates and with Ciona and urchin as outgroups. The DUSP2 clade is mammalian and paralogous to the DUSP1 mammals. Branch lengths are relatively short throughout AN398. AN398 MF -Propagate GO:0017017 "MAP kinase tyrosine/serine/threonine phosphatase activity" to AN398 based on annotations in the DUSP4 and -5 clades and an annotation to GO:0051019 "mitogen-activated protein kinase binding" on mouse Dusp2. AN398 CC -Propagate "nucleoplasm" to AN398 based on 1 direct annotation, an annotation to "nucleus," and several annotations to "soluble fraction." -There are no annotations to "cytoplasm" available to evaluate or propagate. AN398 BP -The only signaling term in AN398 is GO:0023034 "intracellular signaling pathway." Propagate to AN398. Even though it is the natural consequence of signaling, ignore "negative regulation of transcription" for now since it is the only transcriptional term in AN398 and is kind of a downstream effect. -Propagate GO:0042981 "regulation of apoptosis" to Dusp1 clade because the rat protein is annotated to both child terms "positive regulation of apoptosis" and "positive regulation of anti-apoptosis." -Propagate GO:0001706 "endoderm formation" to AN398 based weakly on 4 annotations from 1 paper (PMID 18719100). AN499: DUSP10 clade. (no MF annotations) AN499 CC -No LTP annotations, but review article (above) says that DUSP10 is nuclear and cytoplasmic. Propagate narrowly from HTP human annotations to AN500, only among very close homologs. AN499 BP -Propagate these from mouse to AN500: GO:0046329 : negative regulation of JNK cascade GO:0043508 : negative regulation of JUN kinase activity GO:0032873 : negative regulation of stress-activated MAPK cascade Back out to AN343, parental clade of AN345, AN398, and AN499, above, plus worm/fly outgroup. AN343 MF -Based on annotation in worm vhp-1, propagate GO:0017017 "MAP kinase tyrosine/serine/threonine phosphatase activity" to AN343. For now, do not propagate the lone worm annotation to the sister term GO:0008579 "JUN kinase phosphatase activity" outside of this clade; the branch length is too long to make a broader inference without more data. AN343 CC: No additional annotations AN343 BP -Propagate GO:0000188 "inactivation of MAPK activity" to AN343 based on vhp-1 and AN345. AN735 Styx proteins, serine/threonine/tyrosine interacting proteins, worm to human.) -UniProt note for mouse Styx: "Probable pseudophosphatase. Contains a Gly residue instead of a conserved Cys residue in the dsPTPase catalytic loop which renders it catalytically inactive as a phosphatase. The binding pocket is however sufficiently preserved to bind phosphorylated substrates, and maybe protect them from phosphatases." NOT/IMR AN735. AN735 CC -Propagate "cytoplasm." AN735 BP -Propagate GO:0007283 "spermatogenesis," but only to the vertebrates (AN738). -NOT/IMR "protein dephosphorylation." AN768: Paralogous clades DUSP15 and DUSP22, urchin to human with fly outgroup. There are no useable annotations in the DUSP15 clade, AN770. Focusing on AN790 (DUSP22): AN790 (DUSP22) No new information on MF or CC. UniProt confirms this is a protein phosphatase: "Activates the Jnk signaling pathway. Dephosphorylates and deactivates p38 and stress-activated protein kinase/c-Jun N-terminal kinase (SAPK/JNK)." (cites PMID 11346645) AN790 BP -Propagate the following based on PMID 12138158 (note different PMID from UniProt): GO:0046330 : positive regulation of JNK cascade GO:0042127 : regulation of cell proliferation GO:0007179 : transforming growth factor beta receptor signaling pathway AN830 Consists of 3 paralogous vertebrate clades -- DUSP18/21, DUSP28, and DUSP14/CCDC155 -- with Ciona and worm outgroups. The DUSP28 and DUSP14 clades (AN869 and AN888) are completely unannotated and will not be considered here, EXCEPT to note that the CCDC155 clade (AN894) is paralogous to and highly divergent from mammalian DUSP14 and does not belong in this family at all; prune (CUT) AN894 from the family. There are no new MF annotations in AN830. Human DUSP18 and 21 are annotated to both nucleus and cytoplasm (CC), but these are based on overexpression in COS cells and are not corroborated; do not propagate. BP: Do propagate GO:0035335 "peptidyl-tyrosine dephosphorylation" to AN830 as the most specific term available to propagate within this clade. AN549 has an unannotated insect outgroup. AN550 is a duplication leading to the STYXL1 clade (AN551, urchin to human) and AN576 (below). AN551 (STYXL1) -UniProt note for human STYXL1: "Probable pseudophosphatase. Contains a Ser residue instead of a conserved Cys residue in the dsPTPase catalytic loop which probably renders it catalytically inactive as a phosphatase. The binding pocket may be however sufficiently preserved to bind phosphorylated substrates, and maybe protect them from phosphatases." Place NOT/IMR on AN551 for both MF and BP (1 annotation each). AN577 is a 6-way polytomy (with an urchin outgroup, AN729) giving rise to DUSP3, -27, -26, -13, and DUPD1 clades (plus one stray). DUPD1 is also a "dual-specificity phosphatase." Continuing with AN578 (DUSP3) This vertebrate clade is paralogous to AN628 and several unannotated clades. AN578 MF -Propagate GO:0033549 "MAP kinase phosphatase activity" based on 1 MF and 2 BP annotations, all from human DUSP3 and one paper (PMID 16604064). AN578 CC -Propagate "cytosol" and "nucleoplasm" based on human annotations. AN578 BP -Propagate the following terms: GO:0043409 : negative regulation of MAPKKK cascade GO:0070373 : negative regulation of ERK1 and ERK2 cascade GO:0046329 : negative regulation of JNK cascade GO:0050860 : negative regulation of T cell receptor signaling pathway GO:0050868 : negative regulation of T cell activation GO:0045931 : positive regulation of mitotic cell cycle AN603 (DUSP27) and AN692 (DUPD1): no annotations AN628 (DUSP26): only 1 annotation, an HTP "mitochondrion." Nothing to propagate. No new annotations in AN664 (DUSP13). MSL 18 Jan 2011 # 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).