Presenting and exploring biological pathways with PathVisio

Abstract

Background: Biological pathways are a useful abstraction of biological concepts, and software tools to deal with pathway diagrams can help biological research. PathVisio is a new visualization tool for biological pathways that mimics the popular GenMAPP tool with a completely new Java implementation that allows better integration with other open source projects. The GenMAPP MAPP file format is replaced by GPML, a new XML file format that provides seamless exchange of graphical pathway information among multiple programs.

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

“…Biological Pathways Affected in 22qDS-To gain insight into the metabolic pathways in 22qDS that are different from controls, metabolomics data were analyzed by using PathVisio software (Table 3) and filtered by the false discovery rate p value Յ0.05 (28). This analysis revealed that solute-mediated transmembrane transport of small molecules was overrepresented in 22qDS.…”

An integrated map of corticotropin‐releasing hormone signaling pathway

“…Based on these confident set of reactions, we developed the pathway map using PathVisio software (van Iersel et al 2008). The topological arrangement of the molecules in the map was based on the information obtained from, i) inhibitor-based assays; ii) mutation-based assays; iii) knockout studies; iv) canonical pathways; and v) review articles.…”

Immunophenotyping and Transcriptomic Outcomes in PDX-Derived TNBC Tissue

“…For comparison with other breast cancer gene expression profiles, a collection of 1,033 breast cancer samples was used as reference dataset (38). Pathway analysis based on the RNASeq data for the two cell populations sorted with CD184 was performed using PathVisio3 (39,40). Significant biological functions were determined using the elim method of …”