PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data.
BACKGROUND
While existing network visualization tools enable the exploration of cancer genomics data, most biologists prefer simplified, curated pathway diagrams, such as those featured in many manuscripts from The Cancer Genome Atlas (TCGA). These pathway diagrams typically summarize how a pathway is altered in individual cancer types, including alteration frequencies for each gene.


RESULTS
To address this need, we developed the web-based tool PathwayMapper, which runs in most common web browsers. It can be used for viewing pre-curated cancer pathways, or as a graphical editor for creating new pathways, with the ability to overlay genomic alteration data from cBioPortal. In addition, a collaborative mode is available that allows scientists to co-operate interactively on constructing pathways, with support for concurrent modifications and built-in conflict resolution.


METHODS
The PathwayMapper tool is accessible at http://pathwaymapper.org and the code is available on Github ( https://github.com/iVis-at-Bilkent/pathway-mapper ).


BACKGROUND
ivis@cs.bilkent.edu.tr.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Computer Engineering, Bilkent University, Ankara, Turkey.
Istemi
I
Bahceci
Department of Computer Engineering, Bilkent University, Ankara, Turkey.
Ugur
U
Dogrusoz
Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA.
Konnor C
KC
La
Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA.
Özgün
Ö
Babur
Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Jianjiong
J
Gao
Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.|Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Nikolaus
N
Schultz
D023281:Genomics / Q000379:methods*; D006801:Humans; D053858:Metabolic Networks and Pathways; D009369:Neoplasms / Q000378:metabolism*; D015398:Signal Transduction; D012984:Software