changed 5 years ago  
Linked with GitHub

GGG 298 - Week 9

Wednesday lab - 3/4

Integrating all the things - a sourmash project!

Friday Discussion - 3/6

Assignment (due 11am, Friday, 3/6)

(Due Friday 3/6 at 11am, entered into this form.)

Read "Functionally Enigmatic Genes: A Case Study of the Brain Ignorome", and answer this question in 2-3 sentences: Assuming you're a professor running your own research lab, how would you study the "ignorome" in a biology subfield of your choice?

Paper notes

  • top 5% of genes have 70% of literature
  • 20% of genes have essentially no literature
  • these 20% have same coexpression network connectivity, number of orthologs/paralogs.
  • main difference: date of discovery

Discussion questions and notes

Why is the brain ignorome an interesting topic? Are any of these genes likely to be important?

The authors claim that "intensely expressed and highly selective" genes are likely to have greater impact on brain function. True? False?

How are annotations for genes conveyed into the database(s), anyway?

How does guilt by association work? How useful is it? What did this paper do? How should we represent these findings in databases?

How do you revisit no-longer-hot topics in science? (e.g. "Rosetta stone" approach in microbes…)

Imagine that you find a bunch of largely unannotated/"unknown" genes in your RNAseq study. What do you do with them?

Approaches suggested by students:

  • narrow our focus - look at cell-type specific expression (scRNA). But does this necessarily connect with phenotype?
  • look for covariations with phenotype, e.g. Huntington's (but what if there are none?)
  • do targeted knockouts or other experiments (but $$$)
  • study the ignorome systematically across tissues, and work to focus attention on it. (but must still result in discoveries of some kind.)

A few points:

  • you could describe this situation as a terrible outcome of human attention bias
  • alternatively, perhaps we should recognize that humans construct relevance and community through participation, and that's what happened here.
  • is this an opportunity, or not? How would we take advantage of this opportunity?

Titus often uses the "known knowns", "known unknowns", and "unknown unknowns" framework that Rumsfeld popularized during Iraq War. This could be one framework to diversify funding?

Select a repo