Knowledge of the hallmark networks of cancer has been key to interpreting the molecular heterogeneity seen within and across tumors. NDEx, the Network Data Exchange (www.ndexbio.org), is an online commons where scientists can upload, share, and publicly distribute molecular networks and pathway models. We are currently two years into a three-year grant from the National Cancer Institute (U24 CA184427A), during which time we have created the NDEx open-source platform; released NDEx as a public website; and begun to link NDEx to applications such as Cytoscape. Having built this initial system, our goals for the next funding period are to rapidly develop NDEx network content and communities and the means by which these resources impact cancer research and treatment. In particular, we will (1) Connect NDEx networks to next-generation cancer genome analysis; (2) Enable the direct publishing of interactive networks on journal websites; (3) Develop hallmark cancer pathway content via social organization and automation; and (4) Scale the NDEx framework to support a growing community of users and analysis tools. Through these aims, the emphasis of the NDEx Project transitions from core infrastructure to genome analysis workflows, cancer-relevant network content, publishing, and community building. These developments address a strong and immediate need in cancer research for a cyberinfrastructure that can analyze genome-scale information in the context of molecular networks.

Public Health Relevance

NDEx (www.ndexbio.org) is an online commons in which biological networks can be shared, published and used by cancer researchers. Informatics applications for analysis and visualization can use NDEx as a hub to exchange networks, facilitating modular workflows. NDEx is a step towards new forms of scientific publication and collaboration in which networks bearing data, hypotheses, and findings flow easily between scientists.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Resource-Related Research Projects--Cooperative Agreements (U24)
Project #
5U24CA184427-06
Application #
9692560
Study Section
Special Emphasis Panel (ZCA1)
Program Officer
Li, Jerry
Project Start
2014-05-01
Project End
2022-04-30
Budget Start
2019-05-01
Budget End
2020-04-30
Support Year
6
Fiscal Year
2019
Total Cost
Indirect Cost
Name
University of California, San Diego
Department
Internal Medicine/Medicine
Type
Schools of Medicine
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093
Zhang, Wei; Ma, Jianzhu; Ideker, Trey (2018) Classifying tumors by supervised network propagation. Bioinformatics 34:i484-i493
Auer, Florian; Hammoud, Zaynab; Ishkin, Alexandr et al. (2018) ndexr-an R package to interface with the network data exchange. Bioinformatics 34:716-717
Zhang, Wei; Bojorquez-Gomez, Ana; Velez, Daniel Ortiz et al. (2018) A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nat Genet 50:613-620
Huang, Justin K; Jia, Tongqiu; Carlin, Daniel E et al. (2018) pyNBS: a Python implementation for network-based stratification of tumor mutations. Bioinformatics 34:2859-2861
Bui, Nam; Huang, Justin K; Bojorquez-Gomez, Ana et al. (2018) Disruption of NSD1 in Head and Neck Cancer Promotes Favorable Chemotherapeutic Responses Linked to Hypomethylation. Mol Cancer Ther 17:1585-1594
Huang, Justin K; Carlin, Daniel E; Yu, Michael Ku et al. (2018) Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. Cell Syst 6:484-495.e5
Marty, Rachel; Kaabinejadian, Saghar; Rossell, David et al. (2017) MHC-I Genotype Restricts the Oncogenic Mutational Landscape. Cell 171:1272-1283.e15
Carter, Hannah; Marty, Rachel; Hofree, Matan et al. (2017) Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. Cancer Discov 7:410-423
Pratt, Dexter; Chen, Jing; Pillich, Rudolf et al. (2017) NDEx 2.0: A Clearinghouse for Research on Cancer Pathways. Cancer Res 77:e58-e61
Hofree, Matan; Carter, Hannah; Kreisberg, Jason F et al. (2016) Challenges in identifying cancer genes by analysis of exome sequencing data. Nat Commun 7:12096

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