JAN 08 2010

From DictyWiki

Jump to: navigation, search

Contents

Bob's gene model curation

  • Continuing to work from human ortholog list and also seeking out unknowns; all curated genes documented in Bob's curated genes

SOP and other wiki updates

Subunit nomenclature

  • Question: We decided that large or small subunit should be lower case, eg moc2l. What about regulatory or catalytic subunit?
  1. ppp2r4 where ppp2r = PhosPhotyrosyl Phosphatase 2A Regulator
  2. ppp4C where ppp4C = Protein PhosPhatase 4 Catalytic subunit
  3. Note that ppp4C appears in the literature (PMID:17353263) whereas ppp2r4 does not.
  • For longer regulatory "r" and "catalytic" "c" should be lower case.
  • Question: check rfa1, rfc1, rfc2, etc. According to dictybase, rfc = Replication Factor C with gene product "replication factor C subunit"; however SP gene name is "rfc1" with gene product name "Probable replication factor C subunit 1". So does the C refer to replication factor or the subunit? If this is "replication factor C subunit" the C should be capitalized in the gene name, but if this is "replication factor C subunit 1", should the C should be lower case? Also sf3a1 (splicing factor 3A subunit 1)
  • replication factor A, B, C is the name of the parent grouping, so this should be rfa, rfc1. These should be, for example, gene name "rfc1", gene product "replication factor C subunit 1"; also modify name description
  1. done: replication factors
  • The dicty gene names differ from the SP gene names for most RNA polymerase subunits: eg, dicty has gene product "RNA polymerase I, largest subunit", gene name "rpa1"; SP has gene product "DNA-directed RNA polymerase I subunit rpa1" , gene name "polr1a". Did we agree to disagree with them on these? Do we want to retain gene product names like "xxxx largest subunit"?
  • Look to see if there is a nomenclature paper for RNA polymerases.
  1. Failed to find a good nomenclature paper for RNA polymerases in pubmed search using various combinations of the search terms "RNA polymerase" "nomenclature" "gene name" "review", etc.
  • Search at Swissprot shows:
  1. plants have gene names rpoA/B/C
  2. yeast use rpc/b/a followed by a number
  3. human, mouse, etc use "polr(letter)(number)-dicty is included in this group at swissprot.
  • May want to add the SP gene names as gene name synonyms.
  • Reached the end, but now need to review my notes and questions in my spreadsheet
  • Add the excel spreadsheet in main folder in dicty curators

Protein/gene product nomenclature

  • Follow-up to ensure that the protein synonym field is displayed on the gene summary page

Miscellaneous

  • Are two letter gene names OK? Check DDB_G0280371 which has been assigned gene name "gk" by SWISSPROT. Human ortholog is "GK"; S. cerevisiae ortholog is "GUT1".
  • No, we prefer not to have two letter gene names-as this makes searching difficult. Send an email to Silvia to ask her to change, but first need to look into and suggest an alterative-possibly gut1.
  • Question: should we approve of use "putative secreted protein" as a gene product name in cases where signalP predicts a signal peptide, or is this too assertive? DDB_G0289285 is an example.
  • Leave gene product as "unknown", but put note about signal peptide in the description.

New items

  1. Enhance the main page, with for example, link to papers and gene models curated in a month
  2. Amoeboid blast server on our site
Personal tools