= Annotation Priorities = * 1. Issues on the curation tracker * 2. Annotation improving networks inferred from GO: * i) substrates * ii) physical interactions * iii) complexes * 3. Phenotype screens see [http://curation.pombase.org/pombe/view/list/triage_phenotype_screen_publications?model=track canto] (big bang for buck) * 4. Processes mature enough to build pathways: usually those which have a large percentage of functionally characterised genes (for example mitochondrion organization has 40 published genes/294, so is low priority, compared to cytokinesis 136/139) * chromosome segregation (Val) * DNA metabolism (Midori) * cytokinesis (Val) * regulation of mitotic cell cycle (All) * signaling pathways (Antonia) * chromatin organization (All) * cell polarity * 5. New gene characterizations -These should be sent out for community curation, but followed up == Process priorities == === Mitotic Chromosome Segregation (Val) === ||process chromosome segregation: genes 195 of which ??? published [http://www.esyn.org/builder.php?type=Graph&term=GO:0007059&interactionType=physical&source=pombase&includeInteractors=false esyN] || ||gene/complex||status||Date|| || '''Mis6-Sim4 complex (12)''' ||-||-|| ||fta1 Mis6-Sim4 complex ||annotation complete||6/1/2015|| ||fta2 Mis6-Sim4 complex ||annotation complete ||6/1/2015|| ||fta3 Mis6-Sim4 complex ||annotation complete ||6/1/2015|| ||fta4 Mis6-Sim4 complex ||annotation complete ||15/1/2015|| ||fta6 Mis6-Sim4 complex ||annotation complete ||15/1/2015|| ||fta7 Mis6-Sim4 complex ||annotation complete except CC-PMID:24789708||20/1/2015|| ||mis6 Mis6-Sim4 complex ||annotation complete except CC-PMID:24789708 CC-PMID:25375240||20/1/2015|| ||mis15 Mis6-Sim4 complex ||annotation complete ||6/1/2015|| ||mal2 Mis6-Sim4 complex || annotation complete except CC-PMID:24789708 ||9/03/2016|| ||sim4 Mis6-Sim4 complex ||annotation complete ||20/1/2015|| ||mis17 Mis6-Sim4 complex ||annotation complete ||6/1/2015|| ||cnl2 Mis6-Sim4 complex ||annotation complete except CC-PMID:24789708||-|| ||'''NMS/Ndc80 complex (10)''' ||- ||-|| ||ndc80 NMS complex/Ndc80||annotation complete||1/03/2016|| ||mis12 NMS complex||annotation complete||1/03/2016|| ||mis13 NMS complex||annotation complete ||20/1/2015|| ||mis14 NMS complex||annotation complete ||6/1/2015|| ||sos7 NMS complex ||annotation complete ||6/1/2015|| ||spc25 NMS complex/ Ndc80||annotation complete||20/1/2015|| ||spc7 NMS complex ||PMID:17035632 PMID:21664573||-|| ||nnf1 NMS complex ||annotation complete||6/10/2016|| ||nuf2 Ndc80 complex ||PMID:18411404 CC-PMID:25688135||-|| ||spc24 Ndc80 complex ||annotation complete||20/1/2015|| ||'''CENP-A recruiting complex(4)'''||- ||-|| ||mis16 CENP-A recruiting complex ||annotation complete except CC-PMID:22771823 and scm3 papers||-|| ||mis18 CENP-A recruiting complex ||annotation complete except CC-PMID:24789708 ||15/1/2015|| ||mis19 CENP-A recruiting complex ||annotation complete except CC-PMID:25375240 ||15/1/2015|| ||mis20 CENP-A recruiting complex ||annotation complete||20/1/2015|| ||'''DASH complex(10)'''||- ||-|| || dad1 DASH complex ||annotation complete||1/3/2016|| || ask1 DASH complex ||annotation complete||20/1/2015|| || dad2 DASH complex ||annotation complete ||6/5/2016|| || dad3 DASH complex ||annotation complete||17/3/2016|| || dad4 DASH complex ||annotation complete||17/3/2016|| || dad5 DASH complex ||PMID:25342311||-|| || dam1 DASH complex ||PMID:18632983 PMID:20730753 PMID:18262494 CC-PMID:23770679 CC-PMID:24239120 ||-|| || duo1 DASH complex ||annotation complete||6/5/2016|| || spc19 DASH complex ||annotation complete||17/3/2016|| || spc34 DASH complex ||annotation complete||6/5/2016|| ||'''condensin complex (5'''||- ||-|| || cnd1 condensin complex ||annotation complete except CC-PMID:25764183||23/10/2015|| || cnd2 condensin complex ||annotation complete except CC-PMID:21633354 CC-PMID:25764183||3/10/2015|| || cnd3 condensin complex ||annotation complete except CC-PMID:25764183||23/10/2015| ||cut14 condensin complex Smc2||PMID:15485909 PMID:17030601 PMID:20709788 CC-PMID:22645654 CC-PMID:25847133 ||-|| ||cut3 condensin complex Smc4||mei-PMID:12750522 PMID:15485909 PMID:19910488 PMID:20709788 PMID:26832414||-|| ||'''monopolin complex (2)'''||- ||-|| ||csm1 monopolin complex ||annotation complete||1/3/2016|| ||mde4 monopolin complex ||annotation complete||1/3/2016|| ||'''mitotic spindle checkpoint proteins (7)'''||- ||-|| ||bub1||-||-|| ||bub3||-||-|| ||dma1||-||-|| ||mad1||-||-|| ||mad2||-||-|| ||mad3||-||-|| ||mph1??||PMID:22281223||-|| ||ubc11 ubiquitin conjugating enzyme E2- ||annotation complete ||18/11/2015|| ||'''chromosome passenger complex (4)'''||- ||-|| ||ark1||Aurora B kinase is generally required for correcting improper chromosome attachment (Tanaka, 2010), and the inactivation of Ark1 (fission yeast Aurora B) provokes merotelic attachment even in chiasmate meiosis I (Hauf et al., 2007).||-|| ||bir1||-||-|| ||nbl1||-||-|| ||pic1||-||-|| ||'''kinesins/dynein (6)'''||- ||-|| ||cut7||PMID:9461438 PMID:9490630 PMID:11792803 PMID:23973085 CC-PMID:24239120 CC-PMID:25348260 CC-PMID:26031557 PMID:26909973 ||-|| ||klp2||PMID:16002618 PMID:16998477 PMID:17036054 PMID:17254972 PMID:17389875 PMID:17409356 PMID:18540083 PMID:19430466 PMID:21151990 CC-PMID:25869666||-|| ||klp5||PMID:11870212 PMID:11967147 PMID:12426374 PMID:14573463 PMID:18553361 PMID:19037096 PMID:19293830 PMID:21664573 PMID:22363481 (PMID:24239120 not sure about status) (PMID:25472718 needs GO) CC-PMID:27146110 ||-|| ||klp6||see klp5||-|| ||klp9||PMID: 22264609 ||-|| ||dlc1||PMID:14655046 PMID:15802518 ||-|| ||dhc1||PMID:15802518 PMID:16988108 PMID:17509158 CC-PMID:25688135 CC-PMID:25869666 ||-|| ||'''TACC TOG + dis(3)'''||- ||-|| ||alp7||PMID:12951601 PMID:14742702 PMID:16481403 PMID:17579515 review-PMID:17714654 PMID:19606211 PMID:19696784 PMID:19879140 PMID:21327068 CC-PMID:23770679 CC-PMID:24790093 PMID:25057016 CC-PMID:25472718 CC-PMID:26864000 ||-|| ||alp14||PMID:11369198 PMID:12426374 PMID:14742702 (connection between gtpase missing PMID:17476213) PMID:19696784 CC-PMID:22696680 CC-PMID:23770679 CC-PMID:24790093 CC-PMID:26864000||-|| ||dis1||PMID: 16920624 plus...||-|| ||'''misc mainly inner?(8)'''||- ||-|| ||clp1||PMID:11683392 PMID:14765109 PMID:16085490 PMID:16687577 PMID:18303049 PMID:18385517 PMID:19570910 PMID: 21098635 PMID: 21098641 PMID: 21965289 PMID: 22264609 PMID: 22645648 PMID: 22665807 PMID: 22918952 PMID: 23297348 PMID: 24006256 PMID: 25356547||-|| ||cnp1 ||in progress||-|| ||cnp20 ||annotation complete||6/1/2015|| ||cnp3||PMID:15791413 PMID:24449889 autonomous||-|| ||nsk1||abnormal clustering of kinetochores to spindle pole bodies||-|| ||plo1||-||-|| ||sgo2||-||-|| ||wip1||annotatio complete (no publications)||16/10/2016|| ||'''cohesin complex (5)'''||- ||-|| ||pds5 mitotic cohesin-associated protein Pds5||PMID:11598020 PMID:11861765 mei-PMID:16893973 CC-PMID:22640989 CC-PMID:26511279 CC-PMID:27084937||-|| ||psc3 mitotic cohesin-associated protein Pcs3||PMID:11780129 mei-PMID:12750522 PMID:16207082 PMID:16682348||-|| ||psm1 mitotic cohesin-associated protein Psm1||PMID:11598266 PMID:11927594 mei-PMID:12748297 PMID:15485909 PMID:16861909 PMID:17030601||-|| ||psm3 mitotic cohesin-associated protein Psm3||PMID:11927594 PMID:12711320 PMID:15485909 CC-PMID:21979813 CC-PMID:22640989||-|| ||mitotic cohesin complex, non-SMC subunit Rad21 (kleisin)||PMID:8960127 PMID:9475720 PMID:10207075 PMID:11598020 PMID:11598266 PMID:11882285 PMID:12361567 PMID:12748297 PMID:12750522 PMID:12773391 PMID:16325576 PMID:16861909 PMID:16904908 PMID:18239448 PMID:18505884 PMID:19528228 CC-PMID:21189291 CC-PMID:25778919||-|| ||'''APC complex (14)'''||- ||-|| ||cut4/apc1 APC subunit, platform subcomplex ||annotation complete except CC-PMID:24948786||12/10/2016|| ||apc4/cut5 APC subunit, platform subcomplex ||???||-|| ||apc5/cut5 APC complex subunit ||PMID:19584054||-|| ||apc15 APC, platform subcomplex ||annotation complete||24/11/2015|| ||apc8 APC TPR lobe subcomplex ||PMID:18354085 PMID:23583778||-|| ||cut9/apc6 APC TPR lobe subcomplex ||PMID:16453724 (rad PMID:8668127 PMID:947572) PMID:12653962 CC PMID:24948786||-|| ||apc3 APC TPR lobe subcomplex ||???||-|| ||apc12/hcn1 APC subunit TPR lobe accessory factor Hcn1||annotation complete |||| ||apc13 APC subunit TPR lobe accessory factor||annotation complete||24/18/2015|| ||apc10 APC substrate recognition subunit||G1-PMID:9736616 G1-PMID:10582240||-|| ||apc2 APC cullin family subunit||annotation complete||24/4/2015|| ||apc11 APC ubiquitin protein-ligase E3 subunit ||annotation complete||24/4/2015|| ||apc14 APC (might be apc16 ortholog)||annotation complete||24/4/2015|| ||'''APC activator (1)'''||- ||-|| ||slp1 substrate-specific mitotic metaphase/anaphase APC coactivator||PMID: 16453756 PMID: 9001228 PMID: 9461438(*) PMID: 10459014 PMID: 11909965 PMID: 15620645 PMID: 18556659 PMID: 24161933 PMID: 24948786 ||-|| ||mfr1/fzr1 APC/C activator ||PMID: 11493649(done) PMID: 11405625 PMID: 18644893 PMID: 11405625 PMID: 23628763||-|| ||srw1/ste9 substrate-specific mitotic G1 APC coactivator Srw1/Ste9 ||PMID: 9571240 PMID: 1934119 PMID: 9398669 (val) PMID: 9571240 PMID: 9736616(val) PMID: 11029045 PMID: 12186947 PMID: 14985109 PMID: 16627999 PMID: 19596787 PMID: 23195958(cc)||-|| ||'''APC inhibitor'''||- ||-|| ||mes1 meiotic APC inhibitor||PMID: 15791259 (done) PMID: 18331722(*) PMID: 21389117(*val) PMID: 8082199 PMID: 11459187||-|| ||'''APC targets'''||- ||-|| ||rec8|| PMID: 10207075 ||-|| ||slp1||Cdc20 OX > securin can be degraded during interphase, whereas other destruction box proteins will remain stable. In cells lacking Cdc20, securin remains stable, and sister chromatids will not separate (Visintin et al., 1997).||-|| ||'''gamma tubulin complex'''||- ||-|| ||alp4 gamma tubulin complex subunit||annotation complete CC-PMID:24704079 CC-PMID:23886939||23/10/2015|| ||alp6 gamma tubulin complex Alp6||annotation complete CC-PMID:24704079 CC-PMID:23886939||23/10/2015|| ||alp16 gamma tubulin complex Alp16||annotation complete||23/4/2015|| ||gfh1 gamma tubulin complex Gfh1||annotation complete||23/10/2015|| ||gtb1 gamma tubulin Gtb1||annotation complete||28/4/2015|| ||mod21 gamma tubulin complex||annotation complete||28/4/2015|| ||pcp1||-||-|| ||mzt1 mitotic spindle organizing protein Mzt1 ||annotation complete||23/4/2015|| ||'''proteasome complex (39)'''||- ||-|| ||'''separase securin complex'''||- ||-|| ||cut1||PMID:9635190-cut2 substrate missing REVIEW-PMID:10651900 PMID:16861909 PMID:16904908 PMID:18239448||-|| ||cut2||PMID:9312055 PMID:9755167 PMID:10459014 PMID:1052623 PMID:11029045 PMID:11598020 PMID:11967147 PMID:12783882 PMID:15146064 PMID:16303848 CC-PMID:22645648 ||-|| ||'''Msd1-Wdr8-Pkl1 complex'''||- ||-|| ||msd1 microtubule-anchoring factor Msd1||annotation complete except CC-PMID: 26031557 ||11/10/2016|| ||wdr8 mitosis-specific spindle pole body||annotation complete||11/10/2016|| ||pkl1||PMID:10749926 PMID:18984586 PMID:19838064 CC-PMID:23388459 CC-PMID:25348260 CC-PMID:26031557 ||-|| ||'''SMC loading complex'''||- ||-|| ||mis4||PMID:9808627, required in S-phase, not destroyed in G1||-|| ||ssl3 cohesin loading factor Ssl3|| PMID:24291789 PMID:19454013 PMID:18079700 PMID:16682348 ||-|| ||wpl1 Wings apart-like homolog Wpl1||-||-|| ||'''? remaining 51? including (list on desktop):'''||- ||-|| ||'''misc kinase/phosphatase'''||- ||-|| ||ppe1 ||to do PMID:12773390 ||-|| ||sds22 phosphatase||PMID:1846086 PMID:15335873 PMID:8374168 ||-|| ||sds23 PP2A-type phosphatase inhibitor||-||-|| ||cdc13 G2/M B-type cyclin Cdc13||-||-|| ||dis2 serine/threonine protein phosphatase PP1||PMID: 19592249 ||-|| ||cdc2 cyclin-dependent protein kinase Cdk1/Cdc2||-||-|| ||fin1 serine/threonine protein kinase||- ||-|| ||cek1 serine/threonine protein kinase Cek1 ||-||-|| ||gsk3 serine/threonine protein kinase Gsk3 ||-||-|| ||ekc1 protein phosphatase regulatory subunit ||- ||-|| ||'''ubiquitin related'''||- ||-|| ||ubc4|| PMID: 7698660 PMID: 8972853 PMID: 19423874 PMID:19584054 PMID_21389117 CC PMID: 24454826 ||-|| ||cut8 tethering factor for nuclear proteasome ||PMID:12653962 (more about repair, mah PMID:17178839)||-|| ||pop1||PMID:14970237||-|| ||pop2||PMID:14970237||-|| ||pop3||-||-|| ||mlo2 ubiquitin protein ligase E3 component human N-recognin 7 homolog Mlo2 ||-||-|| ||cdc48 AAA family ATPase ||-||-|| ||'''cohesion'''||- ||-|| ||dfp Hsk1-Dfp1 kinase complex regulatory subunit Dfp1||-||-|| ||eso1 sister chromatid cohesion protein||-||-|| ||swi6 HP1 family chromodomain protein Swi6 ||-||-|| ||prw1 Clr6 histone deacetylase complex subunit||-||-|| ||clr6 histone deacetylase (class I) Clr6 ||-||-|| ||rmi1 RecQ mediated genome instability protein Rmi1||-||-|| ||hta2 histone H2A beta||-||-|| ||hta1 histone H2A alpha||-||-|| ||'''spindle'''||- ||-|| ||mto1 MT organizer Mto1||-||-|| ||mal3 ||PMID: 11086011???||-|| ||ppc89 spindle pole body protein ||-||-|| ||SUMO ||-||-|| ||alp11 tubulin specific chaperone cofactor B||annotation complete ||01/3/2016|| ||alp21 tubulin specific chaperone cofactor E||annotation complete ||01/3/2016|| ||alp31 tubulin specific chaperone cofactor A||annotation complete ||01/3/2016|| ||alp1 tubulin specific chaperone cofactor D||annotation complete ||9/3/2016|| ||alp41 GTP-binding protein (beta-tubulin folding)||annotation complete ||01/3/2016|| ||'''misc cenp'''||- ||-|| ||cbh1 CENP-B homolog Cbh1|| PMID:10733588 PMID: 12130537 PMID: 17940212 PMID: 21151105 PMID: 22042869 -|| ||cbh2 CENP-B homolog Cbh2||-|| ||cbp1 CENP-B homolog Cbp1||-|| ||'''misc'''||- ||-|| ||scm3 ||PMID:19217404 PMID:15316103 PMID:24186062 (also mis16) CC PMID:24789708 PMID: 26921242||-|| ||csi1||annotation complete||01/3/2016|| ||top2||-||-|| ||ase1||-||-|| ||pcs1||PMID:20935472 plus... ||-|| ||orc5 origin recognition complex subunit Orc5 ||-|| ||cdc31 centrin ||-|| ||nud3 nuclear distribution protein NUDC homolog ||-|| ||dcc1 Ctf18 RFC-like complex subunit Dcc1 ||-|| ||sfc3 transcription factor TFIIIC complex B box binding subunit Sfc3 ||-|| ||top1 DNA topoisomerase I ||-|| ||ctf8 DNA replication factor C complex subunit Ctf8 ||-|| ||gpn2 conserved ATP binding protein ||-|| ||rna1 Ran GAP Rna1 ||-|| ||top3 DNA topoisomerase III ||-|| ||sfi1||annotation complete except CC-PMID: 25031431 CC-PMID:25736294 ||-|| ||mfh1||annotation complete except CC-PMID: 24026537||10/10/2016|| ||mfh2||annotation complete except CC-PMID: 24026537||10/10/2016|| === ||dis1 ||PMID:16920624 plus…XMAP215/ TOG/Stu2-family homolog, binds microtubules and localizes to kinetochores (Nakaseko et al., 2001). Mutants in dis1 lack the chromosome alignment phase in metaphase and arrest with elongated spindles and segregated but unseparated chromosome pairs (Nabe- shima et al., 1998; Ohkura et al., 1988).dis1 mutants arrest with an activated spindle checkpoint and appear to experience an increase in sister chromatid cosegregation (70%) at full restrictive temperature. Such cosegregation results when mono-oriented attachment of sister kineto- chores to microtubules from the same SPB is not corrected. Since dis1 mutants lack the phase of constant spindle length when chromosomes are properly aligned ||-|| || dis2 phosphatase || (PMID:14765108 - describes checkpoint termination Dis2 abrogates Chk1 phosphorylation and activation in vivo, ) PMID:2245912 PMID:8389306 PMID:8305731 PMID:7983142 PMID:7957097 PMID:9264466 PMID:9790575 PMID:10668632 PMID:11085271 PMID:16411888 PMID:17895368 PMID:19592249 PMID:21664573 (Out for CC PMID:21703453 PMID:21965289 PMID:23333317) (Iain Hagan PMID:25487150) || -|| ||cut7||In the temperature-sensitive cut7 mutant, spindle formation is blocked shortly after duplication of the SPB. The mitotic spindle radiating from the opposite poles cannot interdigitate and thus remains as a V shape (Hagan and Yanagida, 1992). The cut7- specific defect generates a condition whereby the bipolar attachment of the spindle to kinetochores is not achieved. Previously, we demonstrated that this defect causes an arrest in a mad2+-dependent manner (Kim et al., 1998). At the restrictive temperature the majority of Mad2-GFP was found on condensed chromosomes as one or more speckles (Fig. 4).|| ||skp1||PMID:15147872||-|| === Notes and annotation questions on chromosome segregation === * read review PMID: 23512483 * is CENP-A containing nucleosome assembly part of kinetochore assembly? Although the outer repeats play an important role in sister centromere cohesion and possibly help to properly orient the multiple kinetochore microtubule attachment sites (Pidoux and Allshire, 2004 * Centromeres: getting a grip of chromosomes. Curr. Opin. Cell Biol. 12, 308–319., the central region is needed for the assembly of the kinetochore per se and the interaction with the mitotic spindle fibers * what is the relationship between kinetochoe assembly, spindle elongation and chromosome segregation (currently disjoint) * reannotate ndc80 and MIND subcomplexes annotate PAS complex * ask expert to look at CENP_A assembly vs CENP-A assembly phenotype * no substrates currently annotated for APC, look for motifs ABBA, KENm D-Box, C-BOX, F-box, 2BR, LRRL * I think from humanUbc11 is the APC E2, has some substrates assigned (cdc13 direct, slp1 indirect), but sc imlies ubc4 and ubc1 (amybe all) * possible substrates to annotate mitotic securin and cylin; late mitosis cdh1 , cytokinesis aurora, cyclins, cdc29; G1 geminin, cdc6, skp2,ubcH10(ubc11) * check all know APC targets annotated == Cytokinesis but feel free to do any genes or complexes that I haven't started == ||process cytokinesis: 139 of which 136 published [http://www.esyn.org/builder.php?type=Graph&term=GO:0000910&interactionType=physical&source=pombase&includeInteractors=false esyN] || ||gene/complex||status|| date|| ||lsk1 ||in progress||-|| || mac1 || annotation complete || 22/1/2014|| ||lkh1|| chained 12565823 || -|| === Notes and annotation questions on cytokinesis === * previously considered to be linear assembly mid1- rng2- others. But if you can ectopically localize rng2 you can get all of the others (any one of the 3 will work) * check should mid1 be ring assemlby or localization only? * check mid1 NOT assembly? positioning || main target of mid1 is rng2 || rng3- myosin specific chaperone add to wiki with mohan paper details == Regulation of mitotic cell cycle == ||process regulation of mitotic cell cycle: l genes 258 of which 231 published [http://www.esyn.org//builder.php?type=Graph&term=GO:0007346&interactionType=physical&source=pombase&includeInteractors=false esyN] || ||gene/complex||status|| date|| ||psk1 || annotation complete (except PMID: 22976295 out for CC) ||16/2/2015|| === Notes and annotation questions on cell cycle regulation === * Only include gene products here not covered in chromosome segregation, cytokinesis or DNA metabolism * genes which should be annotated to "signalling" based on the signalling components of the cell cycle regulation network * Need to do cytokinesis checkpoint, G1 cell size control checkpoint, DNA damage checkpoint (ask experts to check specific checkpoint lists) || Misc other annotation complete || ||gene/complex||status|| date|| ||mcp60 || annotation complete ||16/2/2015||