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Datasets

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Malachi Griffith edited this page May 1, 2017 · 1 revision

Ideas for datasets

Expression / differential expression

  • Used for DE visualization (Volcano plot, heatmaps, etc.)
  • Used for pathway analysis
  • HCC1395 tumor/normal pair
  • HBR/UHR replicates
  • BRC Traz paper.

Copy Number AND LOH

  • Used for GenVisR visualizations (showing segments for copy number and variant VAFs for LOH)
  • We want a cohort of segment data (e.g. 20 tumors). A selection of ClinSeq cases with good WGS data?
  • Individual tumor normal to demonstrate zoomed in copy number view with per base resolution of the data. ALL1? or HCC1395?

Mutations

  • Used for GenVisR visualizations (Waterfall plot, lolliplot, mutation spectrum).
  • Used for St. Jude's PECAN browser.
  • From supplement materials of a paper. Cohort level.
  • BRC Traz paper (https://www.ncbi.nlm.nih.gov/pubmed/28327926). Basically reproduce the concepts of Figure 2, Figure 3.
  • FL Lymphoma paper.

Mutation spectrum (comparison to know mutation patterns)

  • HCC1395 + 5 OSCC + 5 SCLC + 5 HCC + 5 Melanoma
  • Sample across each cohort above to create a contrived mutation spectrum experiment

Raw read data

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