= 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 PMID25375240||20/1/2015||
||mis15 Mis6-Sim4 complex ||annotation complete ||6/1/2015||
||mal2  Mis6-Sim4 complex || annotation complete except  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 ||-||-||
||'''NMS/Ndc80 complex (10)'''  ||- ||-||
||ndc80 NMS complex/Ndc80  ||annotation complete needs annotation to ndc80 complex ||-||
||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 complex||annotation complete  needs annotation to ndc80 complex||20/1/2015||
||spc7 NMS complex ||in progress IS THIS TURNING SAC SIGNALLING OFF?  PMID:17035632||-||
||nnf1  NMS complex ||PMID:17035632 ||-||
||nuf2 Ndc80 complex ||2 plus PMID:23770679 (out for CC) needs annotation to ndc80 complex||-||
||spc24 Ndc80 complex ||annotation complete needs annotation to ndc80 complex||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  ||PMID: 16079915||-||
|| dad2 DASH complex  ||PMID: 9748434 PMID: 11193425  PMID: 17352737 ||-||
|| dad3 DASH complex  ||annotation complete||17/3/2016||
|| dad4 DASH complex  ||annotation complete||17/3/2016||
|| dad5 DASH complex  ||PMID: 9748434 PMID: 10879493 PMID: 25342311??? ||-||
|| dam1 DASH complex  ||  PMID: 18029449 PMID: 18256284 PMID: 18262494 PMID: 18632983  PMID: 19037096  PMID: 20624975 PMID: 20730753 PMID: 22084306 PMID: 22375062 PMID: 23770679 PMID: 24239120 ||-||
|| duo1 DASH complex  ||PMID: 16079915 PMID: 21901484||-||
|| spc19 DASH complex  ||annotation complete||17/3/2016||
|| spc34 DASH complex  ||PMID: 16079915 ||-||
||'''condensin complex (5'''||- ||-||
|| cnd1 condensin complex non-SMC subunit ||annotation complete CC-PMID:25764183||23/10/2015||
|| cnd2 condensin complex non-SMC subunit ||annotation complete CC PMID:21633354,PMID:25764183||3/10/2015||
|| cnd3 condensin complex non-SMC subunit ||annotation complete CC-PMID:25764183||23/10/2015||
||cut14 condensin complex SMC subunit Smc2||PMID: 8395535 PMID: 7957061 PMID: 9285594  PMID: 9802907  PMID: 10485849  PMID: 12966087  PMID: 15331764  PMID: 15485909   PMID: 17030601  PMID: 20709788   PMID: 21540296    PMID: 22645654  CC PMID: 25847133 ||-||
||cut3 condensin complex SMC subunit Smc4|| PMID: 7957061  PMID: 9285594  PMID: 10485849  PMID: 11927594   PMID: 12750522  PMID: 12966087   PMID: 15148393  PMID: 15485909  PMID: 19910488  PMID: 20709788  PMID: 24362309 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||-||
||'''chromosome passenger complex (4)'''||- ||-||
||ark1||-||-||
||bir1||-||-||
||nbl1||-||-||
||pic1||-||-||
||'''kinesins/dynein (6)'''||- ||-||
||cut7||-||-||
||klp2||-||-||
||klp5||-||-||
||klp6||-||-||
||pkl1||-||-||
||dlc1||-||-||
||dhc1||-||-||
||'''TACC TOG + dis(3)'''||- ||-||
||alp7||-||-||
||alp14||-||-||
||dis1||-||-||
||'''misc mainly inner?(8)'''||- ||-||
||clp1||-||-||
||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||-||-||
||'''cohesin complex (5)'''||- ||-||
||pds5 mitotic cohesin-associated protein Pds5||-||-||
||psc3 mitotic cohesin-associated protein Pds5||-||-||
||psm1 mitotic cohesin-associated protein Pds5||-||-||
||psm3 mitotic cohesin-associated protein Pds5||-||-||
||mitotic cohesin complex, non-SMC subunit Rad21 (kleisin)||-||-||
||'''APC complex (14)'''||- ||-||
||cut4/apc1 APC subunit, platform subcomplex ||CC-PMID:24948786  PMID:8918880||-||
||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 Apc10||PMID: 9736616  PMID: 12653962 only||-||
||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 APC/C activator||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||-||
||mes1||PMID: 15791259 (done) PMID: 18331722(*)  PMID: 21389117(*val)  PMID: 8082199 PMID: 11459187||-||
||srw1/ste9 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||-||-||
||'''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||
||'''proteasome complex (39)'''||- ||-||
||'''separase securin complex'''||- ||-||
||cut1||PMID: 9635190 (HIGH PRIORITY cut2 substrate)        PMID: 9649518  PMID: 9802907   PMID: 10651900 REVIEW PMID: 12653962  screen     PMID: 15161942   PMID: 15329725   PMID: 15507118   PMID: 16483313  PMID: 16861909  PMID: 16904908  PMID: 18239448||-||
||cut2|| PMID: 8632802  PMID: 9264466  PMID: 9312055  PMID: 9755167  PMID: 10459014  PMID: 1052623  PMID: 11029045 PMID: 11084332  PMID: 11598020  PMID: 11967147 PMID: 12390246 PMID: 12553909 PMID: 12783882 PMID: 15146064 PMID: 15791259  PMID: 16303848  PMID: 16483313  PMID: 19117951  PMID: 22084378  PMID: 22645648 ||-||
||'''? remaining 54 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'''||- ||-||
||ubc11 ubiquitin conjugating enzyme E2- ||annotation complete ||18/11/2015||
||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'''||- ||-||
||mis4||PMID:9808627, required in S-phase, not destroyed in G1||-||
||dfp Hsk1-Dfp1 kinase complex regulatory subunit Dfp1||-||-||
||ssl3 cohesin loading factor Ssl3|| PMID:24291789  PMID:19454013  PMID:18079700 PMID:16682348 ||-||
||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||-||-||
||wpl1 Wings apart-like homolog Wpl1||-||-||
||hta2 histone H2A beta||-||-||
||hta1 histone H2A alpha||-||-||
||'''spindle'''||- ||-||
||mto1 MT organizer Mto1||-||-||
||msd1 microtubule-anchoring factor Msd1||-||-||
||mal3 ||PMID: 11086011???||-||
||wdr8 mitosis-specific spindle pole body WD repeat protein||-||-||
||klp9 kinesin-like protein||-||-||
||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||
||mzt1 mitotic spindle organizing protein Mzt1 ||annotation complete||23/4/2015||
||'''misc cenp'''||- ||-||
||cbh1 CENP-B homolog Cbh1|| -||
||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||
||hos2||PMID:17352737 plus||-||
||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|| -||-||
||mfh1|| one paper ||-||
||mfh2|| one paper ||-||
===
||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 ex- perience 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||