Orthoscape aimed to analyze evolutionary information in the gene networks and gene sets
Orthoscape is a Cytoscape application aimed to perform evolutionary analysis of gene networks and visualize the results. Orthoscape can perform the following actions either for a gene network/metabolic pathway or simple set of genes: 1) Calculate evolutionary indices for every gene and analyze distributions of these indices in a network: a) Phylostratigraphic Age Index (PAI). PAI indicates the evolutionary age of a gene by searching the last common ancestor for a species representing the original gene and every species representing the orthologous genes; b) Divergency index (DI). DI reflects the influence of natural selection on gene evolution. It is based on Ka/Ks (dN/dS) ratio between gene and every ortholog. To calculate Ka/Ks we use KaKs Calcultor and PAML. 2) Group genes into clusters according to their homology level calculated using a) Nucleotide sequences identity value; b) Smith-Waterman's algorithm score; c) Similarity of protein domains. 3) Rearrange/layout/color gene networks and metabolic pathways according to evolutionary indices PAI and DI as well as homology groups. The Orthoscape input is either data from KEGG/Pathway Commons pathway databases or result from network reconstruction plugin GeneMANIA. More information in the paper: [https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1427-5 Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles]


Works with Cytoscape 3.10


Version 2.0.0

Released 29 Nov 2023

Works with Cytoscape 3.10

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