19 May 2015 PAINT Conference Call

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PAINT conference call minutes, May 19th, 2015

Participants: Donghui, Karen, Rama, Marc, Huaiyu, Moni, Li

Agenda and Minutes

PAINT still writing "GO Central" instead of "GO_Central"(Karen)

  • The touch-up script corrects the term of "GO Central" to "GO_Central", but the PAINT software still writes "GO Central".
  • This was reported in the GitHub [see issue in GitHub]. Chris responded with a short perl script, which works.
  • Since Suzi is not at the call, this is postponed again.

PAINT curation progress update (Huaiyu)

A progress statistics were generated, and available at the google spreadsheet:

Family Presentation (Li) - PTHR14332

PTHR14332 - A simple tree, animal kingdom only, human to Triad- Eumetazoa

Tree:

PMID:21852244 - Predicts DISC1 orthologues in diverse eukaryotic organisms, including early-branching animals such as amphioxus, sea anemone, amoebas and Trichoplax, and in plants and algae. DISC1 thus is widespread among eukaryotes, although it remains absent from fungi, nematodes and Diptera, including fruit flies

  • dictyostelium Q550K0: Uncharacterized protein
  • Arabidopsis thaliana DISC1 ortholog Q8L4Q6; At5g25070: located in cytoplasm (ISS), cytosol (IDA)

Gene:

  • DISC1 (disrupted in schizophrenia 1) whose gene locus has been associated with many psychiatric conditions including schizophrenia, clinical depression and bipolar disorder.
  • After four generations of studying a Scottish family for, in 2000, this gene was given the name "DISC1". Disrupted in schizophrenia 1; a translocation directly disrupts the gene.

Function:

  • The DISC1 protein function appears to be highly diverse
  • DISC1 is proposed to interact with many proteins, including those implicated in neuropsychiatric disorders and/or that localize to the centrosome.
  • Interact with motor proteins to transport/localize various cellular cargo to centrosome and axon
  • DISC1 directly interacted with kinesin heavy chain of Kinesin-1.
  • DISC1 interact with microtubule-associated dynein motor complex and is essential for maintaining the complex at the centrosome

=> Propagate cytoskeletal protein binding to the root

PMID:2195721, a review that talks about Disc1 as a scaffold protein => Read more papers and add annotation of “protein complex scaffold” and propagate to the root.

  • protein complex scaffold
  • GO id: GO:0032947
  • Definition: Functions to provide a physical support for the assembly of a multiprotein complex.

Cellular Component:

  • Propagate to:
    • GO:0005813
    • GO:0005739
  • Additional propagations?
    • GO:0005634?
      The arginine-rich motif conforms to a known nuclear localization signal
      Human to F. rubripes
  • Challenge existing annotations?
    • Dynein complex?
    • Kinesin complex?
      Though the paper says DISC1 is a component of the microtubule-associated dynein motor complex and is essential for maintaining the complex at the centrosome, it really about Disc1 as a scaffold protein bind and localizing the complex.
      Change complex annotations to Dnein binding and Kinesin binding?

Process:

  • PMID:19828788
    • shows that zebrafish and human DISC-1 function is conserved
    • DISC1 regulates canonical Wnt signalling via an interaction with GSK3beta; DISC-1 as a crucial positive modulator of the canonical Wnt pathway
  • DISC1 directly interacted with kinesin heavy chain of Kinesin-1. Interaction with DISC1/Ndel1 in vivo is required for neuronal migration, * DISC1 regulates the localization of NUDEL/LIS1/14-3-3epsilon complex into the axons as a cargo receptor for axon elongation.
  • Characteristics of eumetazoans include true tissues organized into germ layers, the presence of neurons, and an embryo that goes through a gastrula stage.

So propagate the below terms to root:

  • GO:0001764
  • GO:0030177
  • GO:0045773
  • GO:0000226
  • Go:0034613

Minor PAINT related issuers:

  • Duplicate read for human annotation in the annotation panel
  • “with” field links are very helpful, but didn’t work when multiple entrees.