Category Cross-Omics>Pathway Analysis/Tools

Abstract PathVisio is a tool for displaying and editing biological pathways in the GPML format.

In a sense PathVisio lets you draw pathways as though you are drawing them in PowerPoint. But the difference is that PathVisio can understand the biological context of a pathway, because you can link 'biological components' (genes or proteins) in your pathways to biological data using database identifiers.

This will let you map experimental data (e.g. microarray data) and visualize it on top of the pathway drawing.

Note: Mapping experimental data is Not yet a feature of PathVisio 1.1, but you can do this in combination with GenMAPP or with additional plug-ins for PathVisio.

The available GPML (see below) pathways are converted directly from GenMAPP (see G6G Abstract Number 20219) pathways and should appear exactly the same.

GPML stands for 'GenMAPP Pathway Markup Language'. Originally this file format was named GMML, for Gen-MAPP Markup Language.

GMML was renamed to GPML to make it more distinct from both GML and XGMML, two (2) markup languages used extensively by the Cytoscape (see G6G Abstract Number 20092) community.

Existing features/capabilities in PathVisio 1.0 --

1) The ability to edit pathways.

2) Importing and exporting to / from GenMAPP.

3) Searching pathways for genes --

4) Browsing search results.

5) Retrieving Databases and Pathways --

The supported databases are:

1) SGD (S.cerevisiae); 2) EMBL; 3) Ensembl; 4) HUGO; 5) InterPro; 6) Entrez Gene; 7) MGI (M. musculus); 8) OMIM; 9) PDB;

10) Pfam; 11) RefSeq; 12) RGD (R. norvegicus); 13) Uniprot/TrEMBL; 14) Gene Ontology (GO); 15) UniGene; 16) Affymetrix Probe Set ID.

New features/capabilities in PathVisio 1.1 --

1) Mac OS X and Linux compatibility.

2) The ability to add literature references and comments more easily by double-clicking and searching on PubMed Id.

3) The ability to connect lines to shapes more easily with drag and drop.

4) Elbow and curved connectors.

5) Line anchors and the possibility to make arrows point to other lines.

6) Multi-line labels.

7) Re-designed group selection model and appearance to make it easier to find grouped items.

8) Easier database references: search for genes and metabolites by name instead of database identifier.

9) Modeless editor (removed edit mode button).

Experimental features/capabilities being worked on for PathVisio 2.0 --

1) Importing and displaying 'microarray expression' data.

2) Visualizing other data types.

3) Pathway statistics.

System Requirements

Contact manufacturer.


Manufacturer Web Site BiGCaT Bioinformatics PathVisio

Price Contact manufacturer.

G6G Abstract Number 20243

G6G Manufacturer Number 100401