Table 2.
Visualization tools for pathways
| Standalone applications | ||
|---|---|---|
| Tool and references | Description | URL |
| BiNA [190] | Drawings of metabolic networks supporting hiding of cofactors and drawing of chemical structures | http://bina.unipax.info/ |
| BioTapestry [191] | Interactive tool for building, visualizing and sharing gene regulatory network models over the web | http://www.biotapestry.org/ |
| Caleydo [192] | Visual analysis framework targeted at biomolecular data. Visualization of interdependencies between multiple datasets | http://www.caleydo.org/ |
| CellDesigner [193] | A modeling tool for biochemical networks | http://www.celldesigner.org/ |
| Edinburgh Pathway Editor [194] | Edit and draw pathway diagrams | http://epe.sourceforge.net/SourceForge/EPE.html |
| GenMAPP [195] | Visualization of gene expression and other genomic data on maps representing biological pathways and groupings of genes | http://www.genmapp.org/ |
| Ingenuity IPA | Data integration platform and manually annotated pathways | http://tinyurl.com/IngenuityPath |
| JDesigner [196] | Graphical modeling environment for biochemical reaction networks | http://jdesigner.sourceforge.net/Site/JDesigner.html |
| KaPPA View [197] | Plant pathways | http://kpv.kazusa.or.jp/ |
| KEGG Atlas [198] | Interactive Kyoto Encyclopedia of Genes and Genomes pathways | http://www.genome.jp/kegg/ |
| Omix [199] | Visualizing multi-omics data in metabolic networks | https://www.omix-visualization.com |
| PathVisio [52] | Biological pathway analysis software that allows drawing, editing and analysis of biological pathways | http://www.pathvisio.org/ |
| VitaPad [200] | Application to visualize biological pathways and map experimental data to them | http://tinyurl.com/vitapad/ |
| Web tools for pathways | ||
| ArrayXPath [201] | Mapping and visualizing microarray gene-expression data and integrated biological pathway resources using SVG | http://tinyurl.com/ArrayXPath/ |
| GEPAT [202] | Integrated analysis of transcriptome data in genomic, proteomic and metabolic contexts | http://gepat.sourceforge.net/ |
| iPath [50, 203] | Web-based tool for the visualization, analysis and customization of pathway maps | http://pathways.embl.de/ |
| Kegg-Based Viewer [204] | KEGG-based pathway visualization tool for complex high-throughput data | http://www.g-language.org/data/marray/ |
| MapMan [61] | User-driven tool that displays large datasets onto diagrams of metabolic pathways or other processes | http://mapman.gabipd.org/web/guest/mapman |
| MetPA [205] | Analysis and visualization of metabolomic data within the biological context of metabolic pathways | http://metpa.metabolomics.ca |
| Omics Viewer [206] | Data mapping on BioCyc pathways (collection of 5500 pathway/genome databases) | http://www.biocyc.org/ |
| Pathway Explorer [207] | Interactive Java drawing tool for the construction of biological pathway diagrams in a visual way and the annotation of the components and interactions between them | http://genome.tugraz.at/pathwayexplorer/pathwayexplorer_description.shtml |
| Pathway projector [208] | Zoomable pathway browser using KEGG atlas and Google Maps API | http://www.g-language.org/PathwayProjector/ |
| PATIKA [51] | Integrated environment composed of a central database and a visual editor, built around an extensive ontology and an integration framework | http://www.cs.bilkent.edu.tr/~patikaweb/ |
| Reactome SkyPainter [62] | Visualization of over-represented pathways and reactions from gene lists | http://www.reactome.org/skypainter-2 |
| WikiPathways [209] | Wiki-based, open, public platform dedicated to the curation of biological pathways by and for the scientific community | http://www.wikipathways.org/ |