Difference between revisions of "How WormBase writes a concise description"

From WormBaseWiki
Jump to navigationJump to search
Line 25: Line 25:
  <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'''  

Revision as of 17:17, 24 June 2013

Writing a concise description for a C. elegans gene

Curators as a general rule make sure that 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, personal observations, etc.):

  • Molecular identity
  • Orthology
  • Process/Pathway
  • Genetic interactions
  • Physical interactions
  • Function/Molecular Activity
  • Tissue Expression
  • Sub cellular localization

So, the template for a concise description will look like:

Molecular identity
<Gene> encodes .....;
<Gene> is <orthologous, similar) to .....;
<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.