Use of DAVID algorithms for clustering custom annotated gene lists in a non-model organism, rainbow trout.

ABSTRACT:

Objective

The DAVID gene functional classification tool requires adaptations for use in non-model species and there is little available information to guide selection of a kappa score. Our objective was to develop an R-script that allows custom gene identifiers and novel annotation information to be incorporated into analyses, then use such data to evaluate the number of differentially expressed genes (DEGs) in a comparison based on kappa score selection.

Results

Using an R-script we developed and multiple data sets ranging from 555 to 3340 annotated DEGs from a study in rainbow trout, we found the percentage of DEGs harbored within a module and the number of genes shared among multiple modules decreased with increasing kappa score regardless of the number of DEGs in the com

SUBMITTER: Ma H 

PROVIDER: S-EPMC5781295 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature