Orthology conjecture rotation project

The following is just a rough list of my immediate and stretch goals for the upcoming project:

Primary goals

  • use ensembl compara to determine orthologs and paralogs for zebra fish and mouse

  • Stick to pipeline outlined by Vilella et al. paper

  • use Gene ontology to obtain Biological process and Molecular function info for mouse and zebrafish?

  • use same cutoffs to include only experimentally inferred annotations

  • rework clark code and then use it on my data set

  • create similar graphs and compare results to clark paper

  • my theory: a purely mouse to zebrafish comparison should eliminate the experimental bias found in human vs mouse since mouse and zebrafish can be used for more similar experiments

Stretch goals

  • Find RNA seq data to work with (if its already out there) as a further check

  • Fully eliminate authorship bias

  • normalize measures of function similarity with respect to background similarity

  • estimate frequencies of GO terms separately for each species?

  • Find a way to incorporate phenoscape data into comparison

  • find good source of similar data for m