{"action":"created","issue":{"url":"https://api.github.com/repos/pombase/curation/issues/1278","repository_url":"https://api.github.com/repos/pombase/curation","labels_url":"https://api.github.com/repos/pombase/curation/issues/1278/labels{/name}","comments_url":"https://api.github.com/repos/pombase/curation/issues/1278/comments","events_url":"https://api.github.com/repos/pombase/curation/issues/1278/events","html_url":"https://github.com/pombase/curation/issues/1278","id":204642782,"number":1278,"title":"evaluating regulation 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is a bit of a tangent, but I needed it to support what I believe  provide checks for what can be classed as regulation.\r\n\r\nSo we have 1161 gene products annotated to biological regulation.\r\n\r\nSo far, regulation is always \r\n\r\n1. Within process, in which case it is one MF directly regulating another molecular function\r\n2. Upstream, in which case it is  signalling or otherwise regulating  a) gene expression, or b) catabolism/stability\r\n3. regulation of a biological quality\r\n\r\nViolators below (after fixing some obvious ones and  removing those with no regulation annotation on PomBase 2) \r\n\r\n\r\nMidori @mah11 \r\ncdt1\treplication licensing factor Cdt1 \r\nmcb1\tMCM binding protein homolog Mcb1 \r\nfml1\tATP-dependent 3' to 5' DNA helicase, FANCM ortholog Fml1 \r\nrad55\tRecA family ATPase Rad55/Rhp55 \r\ndmc1\tRecA family ATPase Dmc1 \r\nrlp1\tRecA family ATPase Rlp1 \r\nbrc1\tBRCT domain protein Brc1 \r\nrdl1\tRAD51D-like protein 1  (possible mf regulator?)\r\n - [ ] ssa2\theat shock protein Ssa2 \r\n - [ ] mas5\tDNAJ domain protein Mas5 (predicted) \r\nWe identify the Ssa2-Mas5/Hsp70-Hsp40 chaperone complex as repressor of the heat shock transcription factor Hsf1 (looks like potential for mf regulator, or regulation of transcription annotation?)\r\n\r\n\r\nVal\r\n\r\nlsd2\thistone demethylase SWIRM2 (predicted) \r\n - [x] SPBC36.10\tmitochondrial intermembrane space protein....(predicted)  (Indirectly upstream, appears to be phopsholipid translocation, metabolism is indirect\"\r\n- [x] SPBC646.08c\toxysterol binding protein (predicted)  Appears to bedownstream. Primary role most likely ergosterol metabolism (is ER)\r\n- [x] scw1\tRNA-binding protein Scw1  deleted annotation in artemis, paper not curated but it would not reach our current regulation annotation guidelines, phenotype only\r\n- [x] naa20\tNatB N-acetyltransferase complex catalytic subunit Naa20 (predicted) \r\n- [x] wdr21\tWD repeat protein, human DDB1 and CUL4-associated factor 4 ortholog Wdr21 \r\npunted by GO:0070647\r\n- [x] nab2\tpoly(A) binding protein Nab2 (predicted)  issues/12991\r\n- [x] nup132\tnucleoporin Nup132 \r\n- [x] SPBC1773.17c\tglyoxylate reductase (predicted)  old IC annotation deleted. Glyoxylate cycle definitely feeds gluconeogenesis  (upstream) but I don't find any evidence that this particular step is regulatory\r\n - [x] swf1\tpalmitoyltransferase Swf1 (predicted)  indirect upstream, already removed\r\n - [x] lsd1\thistone demethylase SWIRM1  (regulation of gene expression)\r\n- [x] per1\tplasma membrane amino acid permease Per1  regulation of nitrogen utilization -> nitrogen utilization\r\n- [x] mcp1\tmicrotubule binding protein Mcp1  regulation of microtubule depolymerization -microtubule depolymerization\r\n- [x] gti1\tgluconate transmembrane transporter inducer Gti1  (signal transduction)\r\n- [x] any1\tarrestin-related endocytic adaptor Any1  (ubiquitin-dependent endocytosis can exclude this process as is regulatory ...catabolism of proteins via vacuole)\r\n- [x] hpz1\tzf-PARP type zinc finger protein, G1-S transition regulator Hpz1  (Not sure why this was in the list as it is regulation of phase transition)\r\n- [x] blt1\tubiquitin domain-like protein Blt1  (Not sure why this was in the list as it is regulation of phase transition)\r\n- [x] SPBC36B7.08c\tnucleosome assembly protein (predicted)  fixed by\r\n/GO=\"aspect=F; term=acetyltransferase activator activity; GOid=GO:0010698; evidence=ISS; db_xref=GO_REF:0000024; with=\"SGD:S000005190 date=20170203\"\r\n\r\nAntonia\r\n- [x] mfm1\tM-factor precursor Mfm1  (signal transduction presumably?)\r\n- [x] mei2\tRNA-binding protein involved in meiosis Mei2 - seems fine, see discussion\r\n- [x] csi1\tmitotic centromere-SPB clustering protein Csi1  @Antonialock should spindle elongation be phenotype only (upstream?)\r\n- [x] bob1\tprefoldin subunit 5 (predicted)  @Antonialock  is this regulating conjugation?\r\n- [x] myo51\tmyosin type V \r\n- [x] rhn1\tRNA polymerase II transcription termination factor homolog @Antonialock  is this regulating conjugation?\r\n- [ ] pac1\tdouble-strand-specific ribonuclease Pac1  @Antonialock  is this regulating conjugation?\r\n- [ ] dni1\ttetraspan protein Dni1  regulating or involved in?\r\n- [ ] hsp9\theat shock protein Hsp9 - if this is really regulating G2/M it should move down to the checkpoint. BUT if the checkpoint is active in the mutant it isn't part of the checkpoint. It is only causing a problem which  activated the checkpoint. In this case a phenotype of \"increased  activation G2-M checkpoint\" or similar is more appropriate\r\n\r\nApproved violators, via imprinting...\r\n - [x] sap1\tswitch-activating protein Sap1  (upstream regulation of where the process occurs)\r\n- [x] rtf2\treplication termination factor Rtf2  ) via imprinting...\r\n- [x] rtf1\treplication termination factor Rtf1  via imprinting...\r\n\r\n\r\n\r\nclearly regulating gene expression in some way, but not by ontology term\r\n- [ ] iss10\tMmi1-driven selective elimination factor Iss10 \r\n- [ ] mmi1\tYTH family RNA binding protein Mmi1 \r\n- [ ] msa1\tRNA-binding protein Msa1 \r\n\r\n\r\nfrom the same paper, hetrogeneous mix, (DNA repair) this paper crops up a lot as matrix outliers too:\r\n- [ ] kms1\tmeiotic spindle pole body protein Kms1 \r\n- [ ] mto1\tMT organizer Mto1 \r\n\r\n\r\n\r\n\r\n\r\nextent of heterochromatin assemlby\r\n- [ ] bdf2\tBET family double bromodomain protein Bdf2 \r\n- [ ] leo1\tRNA polymerase II associated Paf1 complex (predicted) \r\n\r\nend point of a signal transduction pathway?\r\n- [ ] hta2\thistone H2A beta \r\n- [ ] hta1\thistone H2A alpha \r\n\r\nreplication fork protection (is a child of GO:2000104 negative regulation of DNA-dependent DNA replication) is that correct.\r\nI don't even know if this should really be a term...it's one of my old ones...\r\n- [ ] nse6\tSmc5-6 complex non-SMC subunit Nse6 \r\n- [ ] nse5\tSmc5-6 complex non-SMC subunit Nse5 \r\n- [ ] swi3\treplication fork protection complex subunit Swi3 \r\n\r\nFor some they could be classified as above.\r\nFor some I'm not sure we can say \"regulation\"\r\nI'll flag some for checking, but only 62 violators currently.....\r\n\r\n\r\n\r\nLeaving these for now: \r\n - [ ] rpb7\tDNA-directed RNA polymerase complex II subunit Rpb7  and rpb7 might be phenotype only...its a tricky one. it interacts with mediator (which is gene specific regulation). perhaps mutations prevent mediator association with pol II but does  this make it a regulator?\r\n\r\n- [ ] peg1\tCLASP family microtubule-associated protein \r\n- [ ] mto2\tMT organizer Mto2 \r\nI think they are likely MF regulators... \r\n"},"comment":{"url":"https://api.github.com/repos/pombase/curation/issues/comments/277980889","html_url":"https://github.com/pombase/curation/issues/1278#issuecomment-277980889","issue_url":"https://api.github.com/repos/pombase/curation/issues/1278","id":277980889,"user":{"login":"Antonialock","id":12727506,"avatar_url":"https://avatars.githubusercontent.com/u/12727506?v=3","gravatar_id":"","url":"https://api.github.com/users/Antonialock","html_url":"https://github.com/Antonialock","followers_url":"https://api.github.com/users/Antonialock/followers","following_url":"https://api.github.com/users/Antonialock/following{/other_user}","gists_url":"https://api.github.com/users/Antonialock/gists{/gist_id}","starred_url":"https://api.github.com/users/Antonialock/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Antonialock/subscriptions","organizations_url":"https://api.github.com/users/Antonialock/orgs","repos_url":"https://api.github.com/users/Antonialock/repos","events_url":"https://api.github.com/users/Antonialock/events{/privacy}","received_events_url":"https://api.github.com/users/Antonialock/received_events","type":"User","site_admin":false},"created_at":"2017-02-07T12:10:43Z","updated_at":"2017-02-07T12:10:43Z","body":"rhn1 removed, it is a bit of stretch based on the phenotypes."}}
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