TumorMap: Exploring the molecular similarities of cancer samples in an interactive portal

Cancer Research

Volumn 77, Issue 21, 2017, Pages e111-e114

  Newton, Yulia ^a   Novak, Adam M ^a   Swatloski, Teresa ^a   McColl, Duncan C ^a   Chopra, Sahil ^a,b   Graim, Kiley ^a   Weinstein, Alana S ^a   Baertsch, Robert ^a   Salama, Sofie R ^a   Ellrott, Kyle ^a,c   Chopra, Manu ^a,d   Goldstein, Theodore C ^a,e   Haussler, David ^a   Morozova, Olena ^a   Stuart, Joshua M ^a  

^a University of California   (United States)

^b STANFORD UNIVERSITY   (United States)

^c OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^d Pacific Collegiate School   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; BIOINFORMATICS; CANCER CLASSIFICATION; CANCER GENETICS; CANCER RESEARCH; GENETIC DATABASE; INFORMATION PROCESSING; MOLECULAR GENETICS; PRIORITY JOURNAL; SYSTEM ANALYSIS; TUMORMAP DATABASE; WEB BROWSER; BIOLOGY; CHROMOSOMAL MAPPING; COMPUTER INTERFACE; GENE REGULATORY NETWORK; GENETIC PREDISPOSITION; GENETICS; GENOMICS; HUMAN; HUMAN GENOME; MUTATION; NEOPLASM; PATHOLOGY; PROCEDURES; REPRODUCIBILITY; SOFTWARE;

CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; GENE REGULATORY NETWORKS; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOMICS; HUMANS; MUTATION; NEOPLASMS; REPRODUCIBILITY OF RESULTS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 85035028333     PISSN: 00085472     EISSN: 15387445     Source Type: Journal    
DOI: 10.1158/0008-5472.CAN-17-0580     Document Type: Article

References (14)

1. Nielsen CB, Cantor M, Dubchak I, Gordon D, Wang T. Visualizing genomes: techniques and challenges. Nat Methods 2010;7:S5–15.
2. Kim SK. A gene expression map for Caenorhabditis elegans. Science 2001;293:2087–92.
3. MacArthur BD, Lachmann A, Lemischka IR, Ma'ayan A. GATE: software for the analysis and visualization of high-dimensional time series expression data. Bioinformatics 2010;26:143–4.
4. Bolouri H, Zhao LP, Holland EC. Big data visualization identifies the multidimensional molecular landscape of human gliomas. Proc Natl Acad Sci U S A 2016;113:5394–9.
5. Lee S-I. A generalized significance testing method for global measures of spatial association: an extension of the Mantel test. Environ Plan A 2004;36:1687–703.
6. Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Shaw KRM, Ozenberger BA, et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 2013;45:1113–20.
7. Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, et al. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell 2014;158:929–44.
8. Melamed RD, Wang J, Iavarone A, Rabadan R. An information theoretic method to identify combinations of genomic alterations that promote glioblastoma. J Mol Cell Biol 2015;7:203–13.
9. Prat A, Adamo B, Fan C, Peg V, Vidal M, Galvan P, et al. Genomic analyses across six cancer types identify basal-like breast cancer as a unique molecular entity. Sci Rep 2013;3:3544.
10. Knuutila S, Bjorkqvist AM, Autio K, Tarkkanen M, Wolf M, Monni O, et al. DNA copy number amplifications in human neoplasms: review of comparative genomic hybridization studies. Am J Pathol 1998;152: 1107–23.
11. An G, Xu Y, Shi L, Shizhen Z, Deng S, Xie Z, et al. Chromosome 1q21 gains confer inferior outcomes in multiple myeloma treated with bortezomib but copy number variation and percentage of plasma cells involved have no additional prognostic value. Haematologica 2014; 99:353–9.
12. Yoshihara K, Shahmoradgoli M, Martínez E, Vegesna R, Kim H, Torres-Garcia W, et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun 2013; 4:2612.
13. Aytes A, Mitrofanova A, Lefebvre C, Alvarez MJ, Castillo-Martin M, Zheng T, et al. Cross-species regulatory network analysis identifies a synergistic interaction between FOXM1 and CENPF that drives prostate cancer malignancy. Cancer Cell 2014;25: 638–51.
14. Google Maps JavaScript API V3 Reference. Google Developers.