PathVisio 3: An Extendable Pathway Analysis Toolbox

Abstract

PathVisio is a commonly used pathway editor, visualization and analysis software. Biological pathways have been used by biologists for many years to describe the detailed steps in biological processes. Those powerful, visual representations help researchers to better understand, share and discuss knowledge. Since the first publication of PathVisio in 2008, the original paper was cited more than 170 times and PathVisio was used in many different biological studies. As an online editor PathVisio is also integrated in the community curated pathway database WikiPathways.Here we present the third version of PathVisio with the newest additions and improvements of the application. The core features of PathVisio are pathway drawing, advanced data visualization and pathway statistics. Additionally, PathVisio 3 introduces a new powerful extension systems that allows other developers to contribute additional functionality in form of plugins without changing the core application.PathVisio can be downloaded from http://www.pathvisio.org and in 2014 PathVisio 3 has been downloaded over 5,500 times. There are already more than 15 plugins available in the central plugin repository. PathVisio is a freely available, open-source tool published under the Apache 2.0 license (http://www.apache.org/licenses/LICENSE-2.0). It is implemented in Java and thus runs on all major operating systems. The code repository is available at http://svn.bigcat.unimaas.nl/pathvisio. The support mailing list for users is available on https://groups.google.com/forum/#!forum/wikipathways-discuss and for developers on https://groups.google.com/forum/#!forum/wikipathways-devel.

Mitochondrial Citrate Transporter-dependent Metabolic Signature in the 22q11.2 Deletion Syndrome

“…To avoid algorithm bias, the same analysis was carried out by importing metabolite data into REACTOME (29). This analysis confirmed previous conclusions obtained with PathVisio (30) in which the main pathways were related to transport of small molecules, tRNA aminoacylation, and metabolic genetic diseases (methylmalonic aciduria, 5-oxoprolinase deficiency, and multiple carboxylase deficiency among others; not shown). Proteins, mapped as 1.…”

Addition of carbonic anhydrase 9 inhibitor SLC-0111 to temozolomide treatment delays glioblastoma growth in vivo

“…Using the normalized data, MetaboAnalyst 3.0 (55) was used to analyze the processed data using the initial parameters: missing value estimation, KNN estimation for missing values, normalization by sum, and autoscaling. PathViso 3 (56, 57) and adapted WikiPathways (56,58) were used for the visualization of pathway map. P values were based on 1-way ANOVA results (MetaboAnalyst 3.0).…”

Obese diet-induced mouse models of nonalcoholic steatohepatitis-tracking disease by liver biopsy

“…Whereas all mice experienced slight weight loss following the biopsy, they returned expression analysis was performed with edgeR [17] and genes with a P ≤ 0.05 after correction for multiple testing using the Benjamini and Hochberg method was regarded as significantly regulated. Pathway analysis of WikiPathways [18] was performed using the statistics module in PathVisio [19] .…”