Difference between revisions of "How WormBase writes a concise description"
From WormBaseWiki
Jump to navigationJump to searchLine 14: | Line 14: | ||
'''Molecular identity''' | '''Molecular identity''' | ||
<Gene> encodes .....; | <Gene> encodes .....; | ||
+ | |||
'''Orthology/Similarity''' | '''Orthology/Similarity''' | ||
<Gene> is <orthologous, similar) to .....; | <Gene> is <orthologous, similar) to .....; | ||
+ | |||
'''Process/Pathway''' | '''Process/Pathway''' | ||
<Gene> is <required, functions, regulates, is involved in, is part of> .....; | <Gene> is <required, functions, regulates, is involved in, is part of> .....; | ||
+ | |||
'''Genetic interaction with respect to Process or Pathway''' | '''Genetic interaction with respect to Process or Pathway''' | ||
<Gene> interacts genetically with <gene1, gene2> ..... in <Process, Pathway>; | <Gene> interacts genetically with <gene1, gene2> ..... in <Process, Pathway>; | ||
+ | |||
'''Physical interaction''' | '''Physical interaction''' | ||
<Protein> physically interacts with <protein, DNA, RNA) .....; | <Protein> physically interacts with <protein, DNA, RNA) .....; | ||
+ | |||
'''Molecular Function''' | '''Molecular Function''' | ||
<Protein> has ..... activity in <in vitro, in vivo> assays; | <Protein> has ..... activity in <in vitro, in vivo> assays; | ||
+ | |||
'''Tissue Expression''' | '''Tissue Expression''' | ||
<Gene/Protein> is expressed in ..... and expression in ..... is (positively, negatively) | <Gene/Protein> is expressed in ..... and expression in ..... is (positively, negatively) | ||
regulated by .....; | regulated by .....; | ||
+ | |||
'''Sub-cellular localization''' | '''Sub-cellular localization''' | ||
<Protein> is localized to <cellular component> and expression in <cellular component> | <Protein> is localized to <cellular component> and expression in <cellular component> |
Revision as of 22:03, 5 February 2015
Writing a concise description for a C. elegans gene
The following key facts are captured in a concise description, when this information is available in the published literature. Please do not use information from meeting abstracts, Worm Breeder Gazette articles and personal observations/communications.
- Molecular identity
- Orthology
- Process/Pathway
- Genetic interactions
- Physical interactions
- Function/Molecular Activity
- Tissue Expression
- Sub cellular localization
So, the template for a concise description would look like:
Molecular identity <Gene> encodes .....; Orthology/Similarity <Gene> is <orthologous, similar) to .....; Process/Pathway <Gene> is <required, functions, regulates, is involved in, is part of> .....; Genetic interaction with respect to Process or Pathway <Gene> interacts genetically with <gene1, gene2> ..... in <Process, Pathway>; Physical interaction <Protein> physically interacts with <protein, DNA, RNA) .....; Molecular Function <Protein> has ..... activity in <in vitro, in vivo> assays; Tissue Expression <Gene/Protein> is expressed in ..... and expression in ..... is (positively, negatively) regulated by .....; Sub-cellular localization <Protein> is localized to <cellular component> and expression in <cellular component> is <positively, negatively> regulated by .....
Note that the above template is to be used as a guide, and not all descriptions may follow the exact order or choice of words.
Examples of concise descriptions written by WormBase:
Example: lin-10
lin-10 encodes a PDZ and PTB domain-containing protein that is homologous to mammalian Munc interacting proteins (Mint1) and is required for polarized protein localization; LIN-10 is required for proper localization of the LET-23 EGF receptor to the basolateral membrane of the vulval precursor cells and for proper postsynaptic localization of GLR-1, an AMPA-type glutamate receptor in interneurons; LIN-10 is detected in the cytoplasm, membrane, and at particularly high levels in the Golgi.
Example: lon-2
The lon-1 gene encodes a protein belonging to the PR-protein superfamily that is a target of DBL-1 (TGF-beta) signaling, and that regulates polyploidization and body length.