psSubpathway: a software package for flexible identification of phenotype-specific subpathways in cancer progression

• DOI: 10.1093/bioinformatics/btz894
• Publication Date: 2019-12-07T12:12:39Z
• Authors: Junwei Han; Xudong Han; Qingfei Kong; Liang Cheng
• Keywords: Identification; R package

Subpathways, which are defined as local gene subregions within a biological pathway, have been reported to be associated with the occurrence and development of cancer. The recent subpathway identification tools generally identify differentially expressed subpathways between normal cancer samples. psSubpathway is novel systems biology R-based software package that enables flexible phenotype-specific in dataset multiple categories (such subtypes developmental stages cancer). operation modes include extraction from pathway networks, inference activities context expression data, subtype-specific subpathways, dynamic-changed stage visualization samples different phenotypes. Its capabilities enable find specific abnormal datasets multi-phenotype fill gaps tools. may more biomarkers facilitate tailored treatment for patients cancer.The implemented R available under GPL-2 license CRAN website (https://cran.r-project.org/web/packages/psSubpathway/).Supplementary data at Bioinformatics online.