What is the Cancer Cell Map?

The Cancer Cell Map is a collection of selected human-focused cellular pathways implicated in cancer that are linked to visualization and analysis tools.

Is the Cancer Cell Map free?

Yes, it's free! It is available under a Creative Commons license which allows you to use the Cancer Cell Map data completely free for any purpose as long as you clearly attribute the data as originating from the Cancer Cell Map (cancer.cellmap.org).

How were the Cancer Cell Map pathways selected?

Cancer Cell Map pathways were selected based on the scientific interests of research labs at Memorial Sloan-Kettering Cancer Center. Effort was made not to duplicate information in other public pathway databases.

What are the future plans for the cancer cell map?

We hope to expand the number of cancer cell map pathways and analysis tools that are available. Contact us if you are interested in collaborating!

Who do I contact for additional information about the Cancer Cell Map?

You should send an e-mail to . The Cancer Cell Map was created by Gary Bader, Ethan Cerami, Benjamin Gross and Chris Sander. Pathways are curated at the Institute of Bioinformatics.

What other pathway databases exist?

We have compiled a comprehensive list of pathway databases at Pathguide

What can I do with this information?

You can view your own Human Affymetrix gene expression data in the context of Cell Map Pathways using the Expression Viewer software built using the Cytoscape network visualization and analysis software.

How were the pathways collected?

A team of M.Sc. and Ph.D. biologists at the Institute of Bioinformatics in Bangalore, India read original research papers and hand-entered the pathway data into our database.

What kind of information is part of each pathway?

Each pathway contains proteins and their cellular locations, different types of physical interactions, such as molecular interaction, biochemical reaction, catalysis and transport, post-translational protein modifications, original citations, experimental evidence and links to other databases. Some information is only available in the downloaded BioPAX files.

How do you define a pathway?

A pathway is a collection of all genes/proteins that have been described as pathway members in any publication and all the interactions between them that can be found described in the literature.

How good is the quality of the Cancer Cell Map?

The quality of the Cancer Cell Map pathways is very high. Half of the pathways were reviewed by experts at Memorial Sloan-Kettering Cancer Center and were found to contain only a few errors, which were subsequently fixed.

Pathway	Reviewers
Alpha6-Beta4 Integrin	Wenjun Guo in Filippo Giancotti's lab
Androgen Receptor	Liying Zhang and William Gerald
Delta-Notch	Institute of Bioinformatics
EGFR1	Institute of Bioinformatics
Hedgehog	Institute of Bioinformatics
Id	Jonathan Perk and other members of Robert Benezra's lab
Kit receptor	Imke Ehlers in Peter Besmer's lab
TGFR	Van Le Hong, Wei He and other members of Joan Massague's lab
TNF-alpha	Institute of Bioinformatics
Wnt	Institute of Bioinformatics

Are there any known issues with the pathway data in the Cancer Cell Map?

The catalysis controller cellular location may be different than the cellular location of the participants in the controlled conversion. Complex components are not guaranteed to have correct cellular location data and the cellular compartments could be different for different subunits.

How can I contribute?

We are looking for funding to expand the Cancer Cell Map. Pathway reviewers are most welcome.

What can I do with this information?

You can download the pathways in BioPAX Level 2 format for global analysis. Details about the BioPAX format.

How many pathways are part of the Cancer Cell Map?

The pathways currently available are listed on the Cancer Cell Map homepage. Each pathway has around 100-400 interactions.

How can I download this information?

You can download the information in one convenient download.

What is cPath?

cPath is open source database software that runs the Cancer Cell Map website. You can download it for your own use from the cPath developer site.

Main features include:

• Import pipeline capable of aggregrating pathway and interaction data sets from multiple sources, including: MINT, IntAct, HPRD, DIP, BioCyc, KEGG, PUMA2 and Reactome.
• Import/Export support for the Proteomics Standards Initiative Molecular Interaction (PSI-MI) and the Biological Pathways Exchange (BioPAX) XML formats.
• Data visualization and analysis via Cytoscape.
• Simple HTTP URL based XML web service.
• Complete software is freely available for local install. Easy to install and administer.
• Partly funded by the U.S. National Cancer Institute, via the Cancer Biomedical Informatics Grid (caBIG), and aims to meet "silver-level" requirements for software interoperability and data exchange.

What is Cytoscape?

Cytoscape is open-source network visualization and analysis software. Cancer Cell Map uses it to display expression data in the context of our pathways. You can download it for your own use from cytoscape.org

How can I access Cancer Cell Map data via a web service?

The Cancer Cell Map, via the cPath pathway database software, provides a Web Services API for programmatically accessing data. Details are available at the Web Services API Help Page. For instance, you could create a Cancer Cell Map query feature in your own software to automatically load pathways over the web.