The following is just a rough list of my immediate and stretch goals for the upcoming project:
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
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 mice
figure out how to accurately and consistently compare features in an automated fashion
The above goals were created in early January 2014, they changed during the course of the
project. The final goals, set around early february, were:
Obtain a sample set of genes that relate a mouse ortholog to a set of zebrafish paralogs that resulted from the teleost duplication
obtain a full set of that data (possibly from Yves Van De Peer)
use phenoscape to obtain ontological annotations for each gene
use scripts from Prishanti to calculate the functional similarity between orthologs and each paralog set, as well as between the paralogs.
I have had all of the orthologs mouse to zebrafish orthologs for a while. Recently I did
a bit of processing and narrowed the list down to just one to one orthologs since
that seems to be what the Clark paper wants.