WormBase-Caltech Weekly Calls

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September 1, 2016

Working group discussions

  • More clear about issues surrounding orthology sets
  • ZFIN has protein curation that may be becoming a bit out of date

Single-cell RNA profiling

  • We've been curating some data, but not clear how to display the data
  • Some data sets, like tiling arrays, might conclude genes that are expressed in a cell/tissue
  • Genes that are detected at convincing levels (present call) in cell/tissue
  • Should we display expression data that we do not (or cannot) update differently from other data
  • Simply: is a gene in a cell/tissue or not; is it enriched in a cell/tissue or not
  • Could capture quantitative assessments; transcripts per million, etc.
  • Should we provide an analysis of raw data to users to perform their own comparative analyses
  • Bob Goldstein's group prepared software tools in their paper; could we make use of them?
  • Big question: how do we handle divergent (expression) data?
  • David (Angeles) working on an expression data analysis pipeline
  • Single-cell RNA-Seq data: should it be merged with expression pattern data? Ideally, yes
  • There's difficulty in reconciling small and large datasets (or different data types)
  • Would we want to apply some type of weighting to each type of evidence for a gene-anatomy association, for example
  • In general for expression, it would be great to consolidate data to directly connect genes to anatomy/life stage

September 8, 2016


  • TransgeneOme import -Daniela:

adding a Community_curator tag or Curator tag in the Expression model to acknowledge the community curators that annotated/will annotate the data.

documentation on the import here -for the records http://wiki.wormbase.org/index.php/TransgeneOme_import