minepath.org: a free interactive pathway analysis web server

Abstract

Minepath (www.minepath.org) is a web-based platform that elaborates on, and radically extends the identification of differentially expressed sub-paths in molecular pathways. Besides the network topology, the underlying MinePath algorithmic processes exploit exact gene-gene molecular relationships (e.g. activation, inhibition) and are able to identify differentially expressed pathway parts. Each pathway is decomposed into all its constituent sub-paths, which in turn are matched with corresponding gene expression profiles. The highly ranked, and phenotype inclined sub-paths are kept. Apart from the pathway analysis algorithm, the fundamental innovation of the MinePath web-server concerns its advanced visualization and interactive capabilities. To our knowledge, this is the first pathway analysis server that introduces and offers visualization of the underlying and active pathway regulatory mechanisms instead of genes. Other features include live interaction, immediate visualization of functional sub-paths per phenotype and dynamic linked annotations for the engaged genes and molecular relations. The user can download not only the results but also the corresponding web viewer framework of the performed analysis. This feature provides the flexibility to immediately publish results without publishing source/expression data, and get all the functionality of a web based pathway analysis viewer.

Chip-seq and gene expression data for the identification of functional sub-pathways: a proof of concept in lung cancer

“…According to MinePath the most significant pathway for the differentially expressed sub-pathways based on the gene expression data is the p53 with a p-value less than 10-8. Looking at the p53 pathway ( Figure 2) in the MinePath viewer [31] we can conclude that p53 pathway is mainly functional for lung cancer samples (green relation between genes) as we expected.…”

P5 eHealth: An Agenda for the Health Technologies of the Future

“…Access to external biobanks can be established and freely available data from the web can be stored in the data warehouse with the aid of literature mining (Potamias et al 2005). Depending on the scenario, users are able to execute models (Sfakianakis et al 2009), use the p-medicine Oncosimulator (Stamatakos et al 2014), systems biology models (Koumakis et al 2016a;Koumakis et al 2017;Mehta et al 2016) or they can use the Decision Support System . In all cases results lead to personalized medicine via decision support.…”

Participatory Aspects of ICT Infrastructures for Cancer Management

“…Access to external biobanks can be established and freely available data from the web can be stored in the data warehouse with the aid of literature mining (Potamias et al 2005). Depending on the scenario, users are able to execute models (Sfakianakis et al 2009), use the p-medicine Oncosimulator (Stamatakos et al 2014), systems biology models (Koumakis et al 2016a;Koumakis et al 2017;Mehta et al 2016) or they can use the Decision Support System (Bucur et al 2016). In all cases results lead to personalized medicine via decision support.…”