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Grant Details

Grant Number: 5U24CA199461-04 Interpret this number
Primary Investigator: Weinstein, John
Organization: University Of Tx Md Anderson Can Ctr
Project Title: Next-Generation Clustered Heat Maps for Fluent, Interactive Exploration of Omic Data
Fiscal Year: 2018
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Abstract

? DESCRIPTION (provided by applicant): Clustered Heat Maps (CHMs) have been called the ubiquitous visual icons of post-genomic biology, having appeared in many thousands of publications. We introduced CHMs in the early 1990s for visualization and analysis of patterns of similarity and difference in molecular profile data at the DNA, RNA, protein, metabolite, and pharmacological levels. However, those CHMs were static images. What we wanted was an interactive CHM-based environment for deep exploration of patterns in omic data - CHMs in which one could zoom and navigate as in a Google map, link out to a variety of external information sources, re-color on the fly, invoke a statistical toolbox, save all metadata necessary to reproduce the map months or years later, and produce high- resolution graphics that meet the standards of all major journals. Accordingly, we have developed interactive "Next-Generation" Clustered Heat Maps (NG-CHMs) with those and many other capabilities. The NG-CHMs have (i) received extensive user feedback; (ii) been used for studies in multiple preclinical and clinical departments at MD Anderson Cancer Center; (iii) been provided publicly in three public web portals associated with The Cancer Genome Atlas (TCGA) -- with, in aggregate, >1,000 maps; (iv) served as the principal analytic and interpretive tools for proteomic data in TCGA; and (v) been employed in almost all of TCGA's Disease Working Groups. However, they have not yet permeated the cancer research community. We now propose to mature and harden the NG-CHM development, introducing additional toolbox features, increasing user-friendliness, increasing "share ability," and refining the environment to fit the needs and workflows of cancer biologists and clinical researchers who are not specialists in informatics. The end product will be a suite of interactive visualization resources that can easily be shared among members of a research team, distributed to colleagues, and/or serve as interactive graphics linked to the static print versions in journal pages. Extensive written documentation and tutorial videos are currently provided; hands-on workshops will be held at multiple meetings and institutions.

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Publications

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers.
Authors: Berger A.C. , Korkut A. , Kanchi R.S. , Hegde A.M. , Lenoir W. , Liu W. , Liu Y. , Fan H. , Shen H. , Ravikumar V. , et al. .
Source: Cancer Cell, 2018-04-09 00:00:00.0; 33(4), p. 690-705.e9.
EPub date: 2018-04-02 00:00:00.0.
PMID: 29622464
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Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas.
Authors: Liu Y. , Sethi N.S. , Hinoue T. , Schneider B.G. , Cherniack A.D. , Sanchez-Vega F. , Seoane J.A. , Farshidfar F. , Bowlby R. , Islam M. , et al. .
Source: Cancer Cell, 2018-04-09 00:00:00.0; 33(4), p. 721-735.e8.
EPub date: 2018-04-02 00:00:00.0.
PMID: 29622466
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Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer.
Authors: Hoadley K.A. , Yau C. , Hinoue T. , Wolf D.M. , Lazar A.J. , Drill E. , Shen R. , Taylor A.M. , Cherniack A.D. , Thorsson V. , et al. .
Source: Cell, 2018-04-05 00:00:00.0; 173(2), p. 291-304.e6.
PMID: 29625048
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Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas.
Authors: Campbell J.D. , Yau C. , Bowlby R. , Liu Y. , Brennan K. , Fan H. , Taylor A.M. , Wang C. , Walter V. , Akbani R. , et al. .
Source: Cell Reports, 2018-04-03 00:00:00.0; 23(1), p. 194-212.e6.
PMID: 29617660
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Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas.
Authors: Cancer Genome Atlas Research Network. Electronic address: elizabeth.demicco@sinaihealthsystem.ca , Cancer Genome Atlas Research Network .
Source: Cell, 2017-11-02 00:00:00.0; 171(4), p. 950-965.e28.
PMID: 29100075
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A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data.
Authors: Broom B.M. , Ryan M.C. , Brown R.E. , Ikeda F. , Stucky M. , Kane D.W. , Melott J. , Wakefield C. , Casasent T.D. , Akbani R. , et al. .
Source: Cancer Research, 2017-11-01 00:00:00.0; 77(21), p. e23-e26.
PMID: 29092932
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Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer.
Authors: Robertson A.G. , Kim J. , Al-Ahmadie H. , Bellmunt J. , Guo G. , Cherniack A.D. , Hinoue T. , Laird P.W. , Hoadley K.A. , Akbani R. , et al. .
Source: Cell, 2017-10-19 00:00:00.0; 171(3), p. 540-556.e25.
EPub date: 2017-10-05 00:00:00.0.
PMID: 28988769
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Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma.
Authors: Cancer Genome Atlas Research Network. Electronic address: wheeler@bcm.edu , Cancer Genome Atlas Research Network .
Source: Cell, 2017-06-15 00:00:00.0; 169(7), p. 1327-1341.e23.
PMID: 28622513
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Integrated genomic and molecular characterization of cervical cancer.
Authors: Cancer Genome Atlas Research Network , Albert Einstein College of Medicine , Analytical Biological Services , Barretos Cancer Hospital , Baylor College of Medicine , Beckman Research Institute of City of Hope , Buck Institute for Research on Aging , Canada's Michael Smith Genome Sciences Centre , Harvard Medical School , Helen F. Graham Cancer Center &Research Institute at Christiana Care Health Services , et al. .
Source: Nature, 2017-03-16 00:00:00.0; 543(7645), p. 378-384.
EPub date: 2017-01-23 00:00:00.0.
PMID: 28112728
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Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles.
Authors: Farshidfar F. , Zheng S. , Gingras M.C. , Newton Y. , Shih J. , Robertson A.G. , Hinoue T. , Hoadley K.A. , Gibb E.A. , Roszik J. , et al. .
Source: Cell Reports, 2017-03-14 00:00:00.0; 18(11), p. 2780-2794.
PMID: 28297679
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Integrated Molecular Characterization of Uterine Carcinosarcoma.
Authors: Cherniack A.D. , Shen H. , Walter V. , Stewart C. , Murray B.A. , Bowlby R. , Hu X. , Ling S. , Soslow R.A. , Broaddus R.R. , et al. .
Source: Cancer Cell, 2017-03-13 00:00:00.0; 31(3), p. 411-423.
PMID: 28292439
Related Citations

Multiplatform-based molecular subtypes of non-small-cell lung cancer.
Authors: Chen F. , Zhang Y. , Parra E. , Rodriguez J. , Behrens C. , Akbani R. , Lu Y. , Kurie J.M. , Gibbons D.L. , Mills G.B. , et al. .
Source: Oncogene, 2017 Mar; 36(10), p. 1384-1393.
EPub date: 2016-10-24 00:00:00.0.
PMID: 27775076
Related Citations

Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma.
Authors: Fishbein L. , Leshchiner I. , Walter V. , Danilova L. , Robertson A.G. , Johnson A.R. , Lichtenberg T.M. , Murray B.A. , Ghayee H.K. , Else T. , et al. .
Source: Cancer Cell, 2017-02-13 00:00:00.0; 31(2), p. 181-193.
EPub date: 2017-02-02 00:00:00.0.
PMID: 28162975
Related Citations

Characterization of Human Cancer Cell Lines by Reverse-phase Protein Arrays.
Authors: Li J. , Zhao W. , Akbani R. , Liu W. , Ju Z. , Ling S. , Vellano C.P. , Roebuck P. , Yu Q. , Eterovic A.K. , et al. .
Source: Cancer Cell, 2017-02-13 00:00:00.0; 31(2), p. 225-239.
PMID: 28196595
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Integrated genomic characterization of oesophageal carcinoma.
Authors: Cancer Genome Atlas Research Network , Analysis Working Group: Asan University , BC Cancer Agency , Brigham and Women?s Hospital , Broad Institute , Brown University , Case Western Reserve University , Dana-Farber Cancer Institute , Duke University , Greater Poland Cancer Centre , et al. .
Source: Nature, 2017-01-12 00:00:00.0; 541(7636), p. 169-175.
EPub date: 2017-01-04 00:00:00.0.
PMID: 28052061
Related Citations

Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas.
Authors: Campbell J.D. , Alexandrov A. , Kim J. , Wala J. , Berger A.H. , Pedamallu C.S. , Shukla S.A. , Guo G. , Brooks A.N. , Murray B.A. , et al. .
Source: Nature Genetics, 2016 Jun; 48(6), p. 607-16.
PMID: 27158780
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Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma.
Authors: Zheng S. , Cherniack A.D. , Dewal N. , Moffitt R.A. , Danilova L. , Murray B.A. , Lerario A.M. , Else T. , Knijnenburg T.A. , Ciriello G. , et al. .
Source: Cancer Cell, 2016-05-09 00:00:00.0; 29(5), p. 723-36.
PMID: 27165744
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PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning.
Authors: Melott J.M. , Weinstein J.N. , Broom B.M. .
Source: Bioinformatics (oxford, England), 2016-01-15 00:00:00.0; 32(2), p. 312-4.
EPub date: 2016-01-15 00:00:00.0.
PMID: 26400039
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Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.
Authors: Cancer Genome Atlas Research Network , Linehan W.M. , Spellman P.T. , Ricketts C.J. , Creighton C.J. , Fei S.S. , Davis C. , Wheeler D.A. , Murray B.A. , Schmidt L. , et al. .
Source: The New England Journal Of Medicine, 2016-01-14 00:00:00.0; 374(2), p. 135-45.
EPub date: 2016-01-14 00:00:00.0.
PMID: 26536169
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The Molecular Taxonomy of Primary Prostate Cancer.
Authors: Cancer Genome Atlas Research Network .
Source: Cell, 2015-11-05 00:00:00.0; 163(4), p. 1011-25.
PMID: 26544944
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Invasive Bladder Cancer: Genomic Insights and Therapeutic Promise.
Authors: Kim J. , Akbani R. , Creighton C.J. , Lerner S.P. , Weinstein J.N. , Getz G. , Kwiatkowski D.J. .
Source: Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research, 2015-10-15 00:00:00.0; 21(20), p. 4514-24.
PMID: 26473186
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