FunCoup: Pathway analysis of a gene set
A demo of pathway analysis using PathBIX with a gene set. The example gene set comes from “an Alzheimer study”: psen1 psen2 apoe flnb. Submitting these to PathBIX gives no significant pathways in KEGG, either by network crosstalk or gene overlap. We therefore use FunCoup to find the closest neighbors and submit the extended gene set to PathBIX, which yields 14 significant pathways, of which most are linked to Alzheimer’s disease, such as Notch signaling, Wnt signaling, Neurotrophin signaling, and Focal Adhesion. Also Arrhythmogenic cardiomyopathy and Endometrial & Gastric cancer were found, which are linked to Wnt signaling. FunCoup website: https://funcoup.org/ PathBIX website: https://pathbix.sbc.su.se/ Group website: https://sonnhammer.org/ Reference: FunCoup 5: Functional Association Networks in All Domains of Life, Supporting Directed Links and Tissue-Specificity. Emma Persson, Miguel Castresana-Aguirre, Davide Buzzao, Dimitri Guala, Erik L.L. Sonnhammer. Journal of Molecular Biology, 433:166835. https://doi.org/10.1016/j.jmb.2021.166835
A demo of pathway analysis using PathBIX with a gene set. The example gene set comes from “an Alzheimer study”: psen1 psen2 apoe flnb. Submitting these to PathBIX gives no significant pathways in KEGG, either by network crosstalk or gene overlap. We therefore use FunCoup to find the closest neighbors and submit the extended gene set to PathBIX, which yields 14 significant pathways, of which most are linked to Alzheimer’s disease, such as Notch signaling, Wnt signaling, Neurotrophin signaling, and Focal Adhesion. Also Arrhythmogenic cardiomyopathy and Endometrial & Gastric cancer were found, which are linked to Wnt signaling. FunCoup website: https://funcoup.org/ PathBIX website: https://pathbix.sbc.su.se/ Group website: https://sonnhammer.org/ Reference: FunCoup 5: Functional Association Networks in All Domains of Life, Supporting Directed Links and Tissue-Specificity. Emma Persson, Miguel Castresana-Aguirre, Davide Buzzao, Dimitri Guala, Erik L.L. Sonnhammer. Journal of Molecular Biology, 433:166835. https://doi.org/10.1016/j.jmb.2021.166835