Version 245 (modified by vw253, 6 years ago) (diff)


Annotation Priorities

  • Processes relevant to the most , (especially anything related to cell cycle regulation, cancer, broadly conserved)
  • Have large percentage of functionally characterised genes (for example mitochondrion organization has 40 published genes/294, so is low priority compared to cytokinesis 136/139)
  • Are mature enough to be able to construct pathways/networks
  • New gene characterizations -These should be sent out for community curation, but followed up
  • phenotype screens see canto
  • Process priorities : chromosome segregation, DNA metabolism, cytokinesis, regulation of mitotic cell cycle, any signaling pathway, chromatin organization, , cytokinesis, establishment or maintenance of cell polarity, protein modification by small protein conjugation or removal
  • kinases, phosphatases, GTPAses, ubiquitin ligases, protein methylases (anything with direct substrate to improve networks)

HIGHEST priority genes/complexes/papers

Tel1 PMID:21098122 Tel1 phosphorylation of histone H2A at DSBs depends on its interaction with the Nbs1 subunit of MRN complex (52). (add tel1 targets as histones)
All histones????These are often not annotated with their roles in cell cycle regulation and repair, and so they are excluded from the graphs (also need to have specific nucleosome terms, 'what do you call a normal nucleosome?l' and 'centromere specific'
plo1??? priority papers for G2/M network, need to annotate papers which capture plo1 role in mitotic G2/M transition AND cdc25 target, and plo1 as a target of MAPK signalling

Process priorities

Chromosome segregation (Val, but feel free to do any genes or complexes that I haven't started)

process chromosome segregation: genes 207 of which 183 published esyN
gene/complexstatus date
fta1 Mis6-Sim4 complex annotation complete6/1/2015
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: 2478970820/1/2015
mis6 Mis6-Sim4 complex annotation complete except CC PMID:24789708 PMID2537524020/1/2015
mis15 Mis6-Sim4 complex annotation complete 6/1/2015
mal2 Mis6-Sim4 complex PMID: 12242294 + others -
sim4 Mis6-Sim4 complex annotation complete 20/1/2015
sos7 NMS complex annotation complete 6/1/2014
spc25 NMS complex/ Ndc80 complexannotation complete needs annotation to ndc80 complex20/1/2015
spc7 NMS complex in progress IS THIS TURNING SAC SIGNALLING OFF? PMID: 17035632-
ndc80 NMS complex/Ndc80 annotation complete needs annotation to ndc80 complex -
mis12 NMS complexto do PMID:15930132 check biorientation ann-
mis13 NMS complexannotation complete 20/1/2015
mis14 NMS complexannotation complete 6/1/2014
nnf1 NMS complex to do PMID:17035632 -
mis16 CENP-A recruiting complex complete except CC PMID:22771823 and scm3* papers-
mis18 CENP-A recruiting complex complete except CC PMID:24789708 15/1/2015
mis19 CENP-A recruiting complex complete except CC PMID:25375240 15/1/2015
mis20 CENP-A recruiting complex annotation complete 20/1/2015
nuf2 Ndc80 complex 2 plus PMID:23770679 (out for CC) needs annotation to ndc80 complex-
spc24 Ndc80 complex annotation complete needs annotation to ndc80 complex20/1/2015
dad1 DASH complex to do PMID:16079914 PMID:16079915 -
csm1 monopolin complex in progress PMID: 20935472 PMID:12689592 plus…-
mde4 monopolin complex TODO ONLY PMID:19523829 PMID:20723757 PMID: 22264609-
mis17 annotation complete 6/1/2015
cnp20 annotation complete 6/1/2015
ppe1 to do PMID: 12773390 -|
scm3 to do PMID: 19217403 PMID: 19217404 (also mis16)-
cnp1 in progress-
mal3 in progress-
dad1 PMID:17352737 -
cnp3PMID:15791413 PMID: 24449889 autonomous-
sds22 phoshatase PMID: 1846086 PMID: 15335873 PMID: 8374168 -
cnd1 condensin complex non-SMC subunit annotation complete CC-PMID:2576418323/10/2015
cnd2 condensin complex non-SMC subunit PMID:21633354-
cnd3 condensin complex non-SMC subunit CC-PMID:2576418323/10/2015
hos2 PMID:17352737 plus -
pcs1PMID:20935472 plus... -
ams12chen et al, cenp-a loading -
nsk1abnormal clustering of kinetochores to spindle pole bodies-
cut4/apc1 anaphase-promoting complex subunit, platform subcomplex CC-PMID:24948786 PMID:19117951 PMID:12615927 PMID:10582241 PMID:10526233 PMID:10082519 PMID:8918880-
apc4/cut5 anaphase-promoting complex subunit, platform subcomplex ???-
apc5/cut5 anaphase-promoting complex subunit, platform subcomplex TPR ???-
apc15 anaphase-promoting complex subunit, platform subcomplex ???-
apc8 anaphase-promoting complex TPR lobe subcomplex ???-
cut9/apc6 anaphase-promoting complex TPR lobe subcomplex ???-
apc3 anaphase-promoting complex TPR lobe subcomplex ???-
apc12 anaphase-promoting complex subunit TPR lobe accessory factor Hcn1???-
apc13 anaphase-promoting complex subunit TPR lobe accessory factorannotation complete23/10/2015
apc10 anaphase-promoting complex substrate recognition subunit Apc10PMID: 9736616 PMID: 10526233 PMID: 12653962 only-
apc2 anaphase-promoting complex cullin family subunitannotation complete24/4/2015
apc11 anaphase-promoting complex ubiquitin protein-ligase E3 subunit annotation complete24/4/2015
apc14 anaphase-promoting complex (might be apc16 ortholog)annotation complete24/4/2015
alp4 gamma tubulin complex Spc97/GCP2 subunit Alp4annotation complete CC-PMID:24704079 CC-PMID:2388693923/10/2015
alp6 gamma tubulin complex Alp6annotation complete CC-PMID:24704079 CC-PMID:2388693923/10/2015
alp16 gamma tubulin complex Alp16annotation complete 23/4/2015
gfh1 gamma tubulin complex Gfh1annotation complete23/10/2015
gtb1 gamma tubulin Gtb1annotation complete 28/4/2015
mod21 gamma tubulin complex Mod21annotation complete28/4/2015
mzt1 mitotic spindle organizing protein Mzt1 annotation complete23/4/2015
mad2 & SCC mad2 targets slp1 acting as a mitotic anaphase-promoting complex inhibitor activity---
cdc20Cdc20 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).-


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).

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 esyN
gene/complexstatus 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 esyN
gene/complexstatus 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/complexstatus date
mcp60 annotation complete 16/2/2015