| Version 265 (modified by , 5 years ago) (diff) |
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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 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
Chromosome Segregation (Val)
| process chromosome segregation: genes 207 of which 183 published esyN | ||
| gene/complex | status | 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 | 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 | PMID: 12242294 + others | - |
| sim4 Mis6-Sim4 complex | annotation complete | 20/1/2015 |
| sos7 NMS complex | annotation complete | 6/1/2014 |
| 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 | - |
| ndc80 NMS complex/Ndc80 | annotation complete needs annotation to ndc80 complex | - |
| mis12 NMS complex | to do PMID:15930132 check biorientation ann | - |
| mis13 NMS complex | annotation complete | 20/1/2015 |
| mis14 NMS complex | annotation 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 complex | 20/1/2015 |
| 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 | - |
| cnp3 | PMID:15791413 PMID: 24449889 autonomous | - |
| sds22 phoshatase | PMID: 1846086 PMID: 15335873 PMID: 8374168 | - |
| cnd1 condensin complex non-SMC subunit | annotation complete CC-PMID:25764183 | 23/10/2015 |
| cnd2 condensin complex non-SMC subunit | PMID:21633354 | - |
| cnd3 condensin complex non-SMC subunit | CC-PMID:25764183 | 23/10/2015 |
| hos2 | PMID:17352737 plus | - |
| pcs1 | PMID:20935472 plus... | - |
| ams12 | chen et al, cenp-a loading | - |
| nsk1 | abnormal clustering of kinetochores to spindle pole bodies | - |
| cut4/apc1 APC subunit, platform subcomplex | CC-PMID:24948786 PMID:19117951 PMID:12615927 PMID:10582241 PMID:10526233 PMID:10082519 PMID:8918880 | - |
| apc4/cut5 APC subunit, platform subcomplex | ??? | - |
| apc5/cut5 APC complex subunit, platform subcomplex TPR | ??? | - |
| apc15 APC, platform subcomplex | ??? | - |
| apc8 APC TPR lobe subcomplex | ??? | - |
| cut9/apc6 APC TPR lobe subcomplex | ??? | - |
| apc3 APC TPR lobe subcomplex | ??? | - |
| apc12 APC subunit TPR lobe accessory factor Hcn1 | ??? | - |
| apc13 APC subunit TPR lobe accessory factor | annotation complete | 23/10/2015 |
| apc10 APC substrate recognition subunit Apc10 | PMID: 9736616 PMID: 10526233 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 |
| alp4 gamma tubulin complex Spc97/GCP2 subunit Alp4 | 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 Mod21 | annotation complete | 28/4/2015 |
| mzt1 mitotic spindle organizing protein Mzt1 | annotation complete | 23/4/2015 |
| mad2 & SCC | mad2 targets slp1 acting as a mitotic anaphase-promoting complex inhibitor activity | --- |
| cdc20 | 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). | - |
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| 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/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?
| 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/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 |
