3 March 2015 PAINT Conference Call

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PAINT conference call minutes, March 3rd, 2015

Participants: Rama, Karen, Pascale, Suzi, Marc, Janos, Huaiyu Paul T.

Agenda

Touchup script

  • Touch up script now running: (Chris? Suzi?) can you explain what is being done ? Is there anything curators should be checking for potential bugs ?
  • It seems to run every day (?) with a message ' undo touchup commit, revision' (at least that's be the message in the last 3-4 days); this means we cannot obtain curation stats the way we used to, since everything is updated all the time. Can we have another way for doing the stats ?

Minutes:

  • Pasclae: We used to use the GO-SVN page to track curation status/progress. The touch up script changes the author and the order of the families, so it is difficult to track anymore. Is there a different for us to do it?
  • Suzi suggested to use the Notes file. However, not everyone put down their name in the file. The dates can be retrieved from the Notes file in order to know when the tree was last curated.
  • Pascale: Can this be done globally?
  • Suzi: There should be some command-line function to do it.
  • This topic will be discussed further in the future.

Family presentation

Pascale

PTHR24264 - Trypsin and other proteases

  • Main clades:
    1. PLAU: Urokinase-type plasminogen activator; function (Swiss-Prot): Specifically cleaves the zymogen plasminogen to form the active enzyme plasmin.
    2. Trypsin (PRSS1, 2, 3)
  • MF: Propagated serine-type endopeptidase activity to root
  • CC: Propagated extracellular space to root
  • BP: Propagated proteolysis to root
    • PLAU clade:
      • plasminogen activation
      • fibrolysis
      • regulation of cell adhesion mediated by integrin
    • Trypsin clade (PRSS*)
      • zymogen activation
      • Digestion

Open questions

  • regulation of smooth muscle cell-matrix adhesion

http://www.ncbi.nlm.nih.gov/pubmed/8837777

  • regulation of endothelial cell migration (cancer paper)

http://www.ncbi.nlm.nih.gov/pubmed/15313892

  • regulation of cell (hepatocyte) proliferation:

http://www.ncbi.nlm.nih.gov/pubmed/17587687 http://www.ncbi.nlm.nih.gov/pubmed/16899994 http://www.ncbi.nlm.nih.gov/pubmed/17893885 (tumorigenesis paper)

  • angiogenesis

http://www.ncbi.nlm.nih.gov/pubmed/15854129 "Involvement of urokinase-type plasminogen activator in sphingosylphosphorylcholine-induced angiogenesis." Data is in Figure 5: when authors apply PLAU (uPA) onto HUVEC cells, it induces angiogenesis.

      • Is that role direct enough for propagation ?