PathVisio
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 --
- a) Search by gene symbol;
- b) Search by gene identifier.
4) Browsing search results.
5) Retrieving Databases and Pathways --
- a) Pathways converted from GenMAPP.
- b) Synonym databases - Gene Databases provide PathVisio with cross references between gene identifiers in pathways and other database identifiers.
- c) Available synonym databases - PathVisio synonym databases contain the latest information from Ensembl. A synonym database for any species that is in Ensembl can be generated.
- d) Supported database systems - Each supported public database supported in PathVisio synonym databases has a specific system code that is used to identify which system a particular identifier belongs to in PathVisio.
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
- BiGCaT Bioinformatics
- Department of Bioinformatics - BiGCaT
- P.O. Box 616
- UNS50 Box19
- NL-6200 MD Maastricht
- The Netherlands
- Phone: +31 (0)43 3881231 or +31 (0)43 3881417
- Fax: +31 (0)43 3884149
Manufacturer Web Site BiGCaT Bioinformatics PathVisio
Price Contact manufacturer.
G6G Abstract Number 20243
G6G Manufacturer Number 100401