Examples

We provide a set of examples for each type of omics data that can be processed by PathwayMatcher:

• Genetic Variants
• Genes
• Peptides
• Proteins
• Proteoforms

Genetic Variants

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 pathway in blue.

• Other examples can be obtained from DisGeNET^[1], using the curated variant-disease association list:
  • Cystic fibrosis
  • Diabetes
  • Diabetes in the Youth
  • Huntington disease
  • Hypoglycemia
  • Ulcerative colitis

Genes

• Cystic fibrosis
• Diabetes
• Diabetes in the Youth
• Huntington disease
• Hypoglycemia
• Ulcerative colitis

Peptides

• Insulin related signaling peptides

Proteins

• Cystic fibrosis
• Diabetes
• Diabetes in the Youth
• Huntington disease
• Hypoglycemia
• Ulcerative colitis

References

[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