Examples
We provide a set of examples for each type of omics data that can be processed by PathwayMatcher:
Single-nucleotide polymorphisms (SNP) represented with the RsId identifiers defined in dbSNP[1] were obtained from the GIANT (Genetic Investigation of ANthropometric Traits) consortium. BMI Data association results for Models Adjusting for Smoking Status as obtained here were downloaded and matched to pathways using PathwayMatcher. The results allows categorizing variants at the exome wide scale according to possible effects in pathways.
Manhattan plot of the association results with the markers matched to a specific top level pathway in blue.
It is therefore possible to inspect association results focusing on specific top-level pathways, related to major biological functions.
QQ plot of the association results with markers segregated according to possible effect on top level pathways in blue.
The multiple levels of the pathway database allow zooming in on specific functions and reactions.
Manhattan plot of the association results with markers possibly affecting the Signal Transduction pathway in blue and within this top level pathway, markers possibly affecting cAMP signalling in red.
- The illustrations can be reproduced using the BMI dataset below. Other examples are available as obtained from DisGeNET[1], using the curated variant-disease association list:
[1] dbSNP
[2] Janet Piñero, Àlex Bravo, Núria Queralt-Rosinach, Alba Gutiérrez-Sacristán, Jordi Deu-Pons, Emilio Centeno, Javier García-García, Ferran Sanz, Laura I. Furlong; DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants, Nucleic Acids Research, Volume 45, Issue D1, 4 January 2017, Pages D833–D839
[3] VCF v4.3