Cell Cycle
Summary
The cell cycle terms in GO haven't been touched for a while. There's a number of problems with the current arrangement since the cell cycle is largely based on timing. Along with cell cycle experts, we need to find a better way to model the cell cycle in GO.
Personnel
GO
- Val
- GOEds (Jane, Paola, David, Tanya)
- Rachael Huntley (UniProt-GOA)
- Mary Dolan (MGI)
Reactome
- Bijay Jassal
- Lisa Matthews
External experts
- Jacqueline Hayles
- Takashi Toda
- Rob De Bruin
Key Issues
Summary from Val:
I had a read through most of the SF items and this is a general flavour of the problems. Problems include:
- General inconsistencies: [1] identifies some inconsistencies under cell cycle, and raises the questions
- Where does the cell cycle begin and end what do we mean by cell cycle as a process?
- Should we separate "cell cycle events " like DNA replication, chromosome segregation, from the cell cycle control system[2]
- Problems linking events to timing, because events occur in different phases in different organisms [3]
- Should we have phases (S-phase, M-phase, G1 phase which are currently in the process ontology), OR should we only have regulation of cell cycle phase transitions?
- A lot of issues arise because we don't have a clear idea where sub processes begin and end. So for instance is spindle elongation part of chromosome segregation? [4] e.g. Chromosome segregation occurs in two phases: chromosomes move towards spindle poles during anaphase A, and spindle poles separate from each other during anaphase B.(PMID: 11309422). But the definition of chromosome segregation in GO ends when the chromosomes reach the spindle poles, suggesting that spindle elongation comes after:
Viruses and the host cell cycle
Currently two separate cell cycle grouping terms in the viral node. Should they be merged or related? (once sorted out what processes are part of the cell cycle, and what processes regulate the cell cycle):
- modification by virus of host cell cycle regulation ; GO:0019055
- modulation by virus of host cell cycle ; GO:0060153
SF items
- New term Flemming body (resolved)
- CELL CYCLE: cell separation parentage
- meiotic telomere clustering terms
- missing parent (resolved)
- CELLCYCLE MP GO:0031573 intra-S DNA damage checkpoint
- G2 M transition (resolved)
- Response to G2/M transition checkpoint signal (resolved)
- quiescence
- CELLCYCLE Cell cycle checkpoint definitions
- add: cytokinesis has_part membrane fission and related (resolved)
- CELLCYCLE interphase between meiosis I and meiosis II
- CELLCYCLE reg. of cell cycle timing vs reg. of CC processes
- cell cycle arrest in response to nitrogen starvation (resolved but partly open)
- cell cycle vs regulation of cell cycle
- endoreplication
- premeiotic DNA replication
- meiosis and mitosis cell cycle terms
- S to G2/M transition (resolved)
- missing relationship for chromosome segregation?
- G0 phase
- involved_in versus during
- NTR-positive regulation of protein export from nucleus during meiotic anaphase II (resolved)
- pre-replicative complex assembly
- mitotic spindle elongation
Resources
Cell Cycle Ontology
- The CCO is a metaontology, which pulls in cell cycle terms from other ontologies (GO).
- PMID 19480664
- https://sourceforge.net/projects/cellcycleonto/
- For browsing the CCO: http://bioportal.bioontology.org/ontologies/1507
Papers
Meetings
Cell Cycle Content Meeting (EBI, Hinxton, UK)
Feb. 28th and March 1st 2013.
Link to meeting page: http://wiki.geneontology.org/index.php/Cell_Cycle_Content_Meeting_Feb_2013
Cell Cycle Content Meeting follow-up 27 March 2013