What is PathJam?

PathJam is a public tool which provides an intuitive and user-friendly framework for biological pathway analysis of human gene lists. This server integrates pathway-related annotations from several public sources (Reactome, KEGG, Biocarta, etc) making easier the understanding of gene lists of interest.

Using PathJam you will obtain interactive graphs linking genes and pathway annotations, exportable tables (.txt, .xls) including the annotations for your lists and useful plots showing the connectivity, in terms of pathways activity, for the genes.

PathJam has been thought to produce compatible outputs with well-established analysis methods (i.e. GSEA .gmx format) and can be used as a widget in CARGO server.

Currently,  genes are indexed from  pathways, available from

The Pathjam's index was updated on: Wed Oct 13 10:24:00 CEST 2010

Requirements

PathJam has been developed under Java techonology. This application is distributed as a Java applet inside a web page. So, in order to be able to execute PathJam, your browser should support Java 1.5 or later.

At this point, IE Explorer (6 and 7), Mozilla Firefox (2 and 3) and Apple Safari are known to work.

Acknowledgements

PathJam displays information from different sources. We are thankful to the developers and Institutions for providing freely available services:

• REACTOME
• KEGG Pathway DB
• NCI Pathway Interaction DB

Quick start

To understand how PathJam works, in the following steps we have a fast look at some of the available funcionalities:

1. Search for a single gene or list of gene identifiers. The following gene identifiers can be used for searching purpouses: Gene Symbol, Entrez Gene, Ensembl, SwissProt and OMIM.

2. Once PathJam has executed your query, search results are inmediately showed in a Java Applet.

3. Click on one of the genes (or a group of them) from the list and the tab Pathways for selected genes will show you the pathways where each of selected genes are involved.

4. Click on one of the pathways (or a group of them) from the list and the tab Genes for selected pathways will show you the genes which each of selected pathways contains.

5. In both cases, different views showing the relations between genes and pathways become available: graph view, tabular view and cross table view. In addition, you can save the current view as image (if graph view is selected) or as cvs file (if tabular view is selected).

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