Supplementary Material for: DoriTool: A Bioinformatics Integrative Tool for Post-Association Functional Annotation

The emergence of high-throughput data in biology has increased the
need for functional in silico analysis and prompted the development of
integrative bioinformatics tools to facilitate the obtainment of
biologically meaningful data. In this paper, we present DoriTool, a
comprehensive, easy, and friendly pipeline integrating biological data
from different functional tools. The tool was designed with the aim to
maximize reproducibility and reduce the working time of the researchers,
especially of those with limited bioinformatics skills, and to help
them with the interpretation of the results. DoriTool is based upon an
integrative strategy implemented following a modular design pattern.
Using scripts written in Bash, Perl and R, it performs a functional in
silico analysis annotation at mutation/variant level, gene level,
pathway level and network level by combining up-to-date functional and
genomic data and integrating also third-party bioinformatics tools in a
pipeline. DoriTool uses GRCh37 human assembly and online mode. DoriTool
provides nice visual reports including variant annotation, linkage
disequilibrium proxies, gene annotation, gene ontology analysis,
expression quantitative trait loci results from Genotype-Tissue
Expression (GTEx) and coloured pathways. Here, we also show DoriTool
functionalities by applying it to a dataset of 13 variants associated
with prostate cancer. Project development, released code libraries,
GitHub repository (https://github.com/doritool) and documentation are
hosted at https://doritool.github.io/. DoriTool is, to our knowledge,
the most complete bioinformatics tool offering functional in silico
annotation of variants previously associated with a trait of interest,
shedding light on the underlying biology and helping the researchers in
the interpretation and discussion of the results.