WormBase-Caltech Weekly Calls

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GoToMeeting link: https://www.gotomeet.me/wormbase1

2019 Meetings












December 5, 2019

New interaction Venn diagram tool

  • daf-16 interactions
  • Venn diagram shows how various interactors have multiple interaction types with a common focus gene
  • For a given selected gene set, you can copy to clipboard, download CSV, TSV, and link to enrichment analysis or WormMine
  • Very nice! It would be great to have the gene list options here available wherever lists are provided in WormBase (Sibyl working on it)
  • Request: add SimpleMine as another link out (go to SimpleMine with the gene list prepopulated)
  • Request: could there be a toggle to include/exclude high-throughput interactions?
  • Request: The Venn circle labels sometimes get in the way of seeing the diagram; can they be moved to the side or possibly replace simply with single letters like "P", "G" and "R" for "physical", "genetic" and "regulatory" respectively? Might still need a legend?
  • Request: Change the wording "Browse selection" to something like "View/analyze gene list"
  • Where else could we implement a similar type of Venn diagram tool? Disease or phenotype annotations?

New round of phenotype requests

  • GMail really throttling email sending
  • Chris will reach out to Google/GMail to see if we can:
    • A) get a clear explanation about what their restrictions are and how they work and
    • B) see if we can get a paid plan to help expedite the email process (see how much cost)

Aligning interaction data with GO and GO-CAM

  • The Alliance interactions working group is considering proposing a greater alignment between GO interaction annotations (like "binding" annotations with IPI evidence codes, for example) and Alliance molecular interaction annotations
  • Also, would like to propose a pipeline for possibly automatically generating GO-CAM annotations/networks based on inferences made from phenotype annotations, genetic interactions, regulatory interactions, and molecular interactions
  • Much of this depends on genetic perturbation (e.g. allele/variant) annotation to effects, like loss-of-function or gain-of-function annotations
    • Would be good to get a sense from other Alliance members the extent to which we could rely on the presence of such annotations
  • Chris and Kimberly will meet to discuss further

Short SObA talk at Alliance meeting

  • Raymond prepared to give short talk on SObA to the Alliance group

Single cell data visualization tool

  • Eduardo will present to Paul's lab meeting tomorrow
  • Will discuss at Alliance expression working group pre-meeting