WormBase-Caltech Weekly Calls

From WormBaseWiki
Jump to navigationJump to search

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings









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  • ZFIN has protein curation that may be becoming a bit out of date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.

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