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

Single cell expression

• Waterston paper
• 40,000 random cells, sequenced individually to a depth of 20,000 reads; ~1000 genes per cell; cluster data; make judgement call as to what cell 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