Version 81 (modified by vw253, 7 years ago) (diff)


Annotation Priorities

Overall annotation priorities

Think about processes which are:

  • Relevant to the majority of pombe labs
  • More interest to researchers from other organisms, (especially humans, and cancer), anything related to cell cycle regulation
  • 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 aggressively (most of these come back fairly quickly as they are usually easy to annotate)

phenotype screens

  • see canto (big bang for buck, ups numbers)

Anything with gene products as "has_substrate" (for improving networks) priority papers

Prioritise all published kinases/ phosphatases/ GTPases/ ubiquitin ligases/ protein methylases

  • Mus81-T239A disrupts the ability of Cds1 to bind and phosphorylate Mus81 and causes hyper-recombination upon hydroxyurea-induced replication arrest (Kai et al., 2005) PMID: 15805465 .
  • mcs6 substrate cdc2 PMID: 8557037
  • Cytoplasmic Clp1 in turn dephosphorylates the essential F-BAR scaffold protein Cdc15 (Clifford et al. 2008), CR assembly
  • Indeed, Sid2 phosphorylates the nonessential Cdc14 phosphatase Clp1 to foster Clp1’s cytoplasmic retention (Chen et al. 2008) cytoplasmic retention
  • mid1 is a plo1 substrate
  • from 21008122 In humans and both yeasts, DSBs are initially detected and processed by the Mre11-Rad50-Nbs1Xrs2 (MRN) nucleolytic protein complex in association with the Tel1ATM checkpoint kinase and the Ctp1CtIP/Sae2 DNA-end processing factor;...implies tel1 /rad50/nbs1 should be annotated to GO:0000729
  • HIGH PRIORITY from 21098122 :The functions of ATM and ATR orthologs are intimately tied to the detection and nucleolytic processing of DSBs. ATMTel1 localizes at DSBs by interacting with Mre11-Rad50- Nbs1Xrs2 (MRN) protein complex, which directly binds DNA ends (12, 20, 24, 50, 52). use these papers to annotate the missing connection between tel1 and the mre11 complex
  • PMID: 14739927 Finally, we show direct interaction between Rad3 and Crb2, which is inhibitory to Rad3 activity (direct enzyme regulator substrate)
  • HIGH PRIORITY from 21098122 There are two pathways that lead to Crb2 localization at sites of DNA damage (10). One pathway requires two inde- pendent histone modifications: (i) phosphorylation of the C- terminal tail of histone H2A
  • HIGH PRIORITY from 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)
  • find physical interaction between rad9 and crb2
  • HIGH PRIORITY 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'
  • cdc2 PMID: 6526270 uniprot has this paper for allele cdc2-4w C67F (we have 'unspecified')
  • cdc2 Millar JB et al. (1991) Moreno S et al. (1989) Moreno S et al. (1989) Simanis V et al. (1986) Booher RN et al. (1989) Noguchi E et al. (2002)

KW searches canto list of pubs

activitycuratable pub w/out sessionpubs w/ new sesspubs w/ active sessNot done due to access

anything which pins down the cell cycle annotations to the specific phase/transition they regulate

  • srw1 has no mitotic cell cycle regulation annotation prioritise PMID: 9571240, PMID: 9736616 PMID: 10921878

Process priorities

Chromosome segregation

Process priorities : chromosome segregation, DNA metabolism, cytokinesis, regulation of mitotic cell cycle, any signaling pathway (especially glucose mediated signalling after multigene phenotypes), chromatin organization, autophagy (quick and good GO terms), cytokinesis, establishment or maintenance of cell polarity. protein modification by small protein conjugation or removal, genes which should be annotated to "signalling" based on the signalling components of the cell cycle regulation network

process chromosome segregation: main curator val genes 207 of which 183 published esyN
gene/complexstatus date
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 PMID: 24789708 out for CC -
mis6 Mis6-Sim4 complex in progress (sessions created PMID: 12719471 ) (out for CC PMID: 24789708 PMID: 25375240) PMID: 10766735 PMID: 12928332 PMID: 11553715 -
mis15 Mis6-Sim4 complex annotation complete 6/1/2015
mal2 Mis6-Sim4 complex PMID: 12242294 + others -
sim4 Mis6-Sim4 complex in progress-
sos7 NMS complex annotation complete 6/1/2014
spc25 NMS complex/ Ndc80 complexto do PMID:15728720 -
spc7 NMS complex in progress IS THIS TURNING SAC SIGNALLING OFF? PMID: 17035632-
ndc80 NMS complex/Ndc80 to do PMID:21256022 PMID:15728720 -
mis12 NMS complexto do to do   PMID:10761928  PMID: 15502821 PMID: 15930132-
mis13 NMS complexto do PMID:18362178 -
mis14 NMS complexannotation complete 6/1/2014
nnf1 NMS complex to do PMID:17035632 -
mis16 CENP-A recruiting complex complete except PMID:22771823 (out for CC) and scm3 papers-
mis18 CENP-A recruiting complex complete except PMID:24789708 (out for CC) -
mis19 CENP-A recruiting complex complete except PMID:25375240 (out for CC) -
mis20 CENP-A recruiting complex in progress -
nuf2 Ndc80 complex in progress-
spc24 Ndc80 complex annotation complete (when the ndc80 done) -
dad1 DASH complex to do PMID:16079914 PMID:16079915 -
csm1 monopolin complex in progress PMID: 20935472 plus…-
mde4 monopolin complex in progress-
hhp1 monopolin complex in progress-
hhp2 monopolin complex in progress-
mis17 annotation complete 6/1/2014
cnp20 annotation complete 6/1/2014
dis1 PMID:16920624 plus… -
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 PMID: 18362178-
cnd2 condensin complex non-SMC subunit --
cnd3 condensin complex non-SMC subunit --
dis2 phosphatase PMID:3409871 PMID: 2544292 PMID: 2544298 PMID:2245912 PMID:2170029 PMID:1846086 PMID:1944266 PMID:1314161 PMID:8387356 PMID:8389306 PMID:8305731 PMID:7983142 PMID:7957097 PMID:9264466 PMID:9790575 PMID:10668632 PMID:11085271 PMID:16411888 PMID:17895368 PMID:19592249 PMID:21664573 PMID:21703453 PMID:21965289 PMID:23333317 PMID:24554432 PMID:24945319 PMID:25487150 -

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


process cytokinesis: main curator val genes 139 of which 136 published esyN
gene/complexstatus date
lsk1 in progress-
mac1 annotaion complete 22/1/2014

Notes and annotation questions on cytokinesis

Regulation of mitotic cell cycle

Only include gene products not included in chromosome segregation, cytokinesis or DNA metabolism

process regulation of mitotic cell cycle: l genes 258 of which 231 published esyN
gene/complexstatus date