TY - JOUR
T1 - PathwayMapper
T2 - A collaborative visual web editor for cancer pathways and genomic data
AU - Bahceci, Istemi
AU - Dogrusoz, Ugur
AU - La, Konnor C.
AU - Babur, Özgün
AU - Gao, Jianjiong
AU - Schultz, Nikolaus
N1 - Funding Information:
This work was supported by the Marie-Josee and Henry R. Kravis Center for Molecular Oncology, a National Cancer Institute Cancer Center Core Grant (P30-CA008748), the Robertson Foundation, and the Prostate Cancer Foundation. We are also grateful for the support of the Google Summer of Code program.
Publisher Copyright:
© 2017 The Author. Published by Oxford University Press. All rights reserved.
PY - 2017/7/15
Y1 - 2017/7/15
N2 - Motivation: 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.
AB - Motivation: 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.
UR - http://www.scopus.com/inward/record.url?scp=85024490501&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85024490501&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btx149
DO - 10.1093/bioinformatics/btx149
M3 - Article
C2 - 28334343
AN - SCOPUS:85024490501
SN - 1367-4803
VL - 33
SP - 2238
EP - 2240
JO - Bioinformatics
JF - Bioinformatics
IS - 14
ER -