WormBase-Caltech Weekly Calls

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


2018 Meetings

January

February 1, 2018

Automated gene descriptions - orthology

  • Some genes have human orthology mentioned in automated descriptions, even though the orthology call has not been called in DIOPT
  • WormBase uses EnsemblCompara and other methods (not aggregate method like DIOPT)
  • Orthology synchrony is a challenge; WormBase and FlyBase may need to pay special attention to orthology calls and discrepancies
  • DIOPT is purely automated, does not consider other information about orthology evidence
  • We should be clear about how the orthology calls are made

Next upload

  • Unclear of exact date
  • Probably end of March

SimpleMine issue

  • Redundant genes in input list are merged
  • Should SimpleMine provide an option to keep redundancies?
    • Give option up front? Provide submission step to point out redundancies? Ask for choice?
  • We can default to show row-by-row correspondence, and display the number of redundant entries
  • Conclusion: Make an option for users to indicate if they want row-by-row correspondence or a merged list

Cell type expression

  • Waterston paper
  • 40,000 random cells, clusters sequenced individually to a depth of 20,000 reads; ~1000 genes per cell; cluster data; make judgement call as to what cell types they likely are
  • For now, we can do a simple annotation: significantly expressed genes for each cell type
  • Supplemental table S5 for neurons
  • Maybe just ignore the hybrid calls like AQM/PVM, etc.
  • It may be good to isolate the single cell data from other expression data
  • We should annotate/capture the expression clusters
  • Would be good to be able to do enrichment analysis on the clusters
  • Data has not been placed in SPELL yet, Gary considered the data a work in progress
  • We can communicate with Waterston group; are they collecting more data?
  • Wen will take another look at the data
  • Gary W. concerned about the reported/assumed/inferred identity of the cells in the paper
  • Probably cannot curate to individual cells, but we can annotate to a higher level term