ArticleiScience2019
Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines.
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Article in iScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32citing papers in PubMed
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32 citing papers in PubMed.
- Integrated multi-dimensional comparison of proteomic profiles across 54 cancer cell lines.iScience · 2025Article
- Establishment of cell size-dependent growth rate via differential scaling of metabolite uptake and release.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Receptor-binding proteins from animal viruses are broadly compatible with human cell entry factors.Nature microbiology · 2025Article
- iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control.Nature communications · 2025Article
- Cilengitide sensitivity is predicted by overall integrin expression in breast cancer.Breast cancer research : BCR · 2024Article
- AI-empowered perturbation proteomics for complex biological systems.Cell genomics · 2024Article
- Proteome-wide copy-number estimation from transcriptomics.Molecular systems biology · 2024Article
- B Cell Lymphocytes as a Potential Source of Breast Carcinoma Marker Candidates.International journal of molecular sciences · 2024Article
- Multiplexed quantitative proteomics in prostate cancer biomarker development.Advances in cancer research · 2024Review
- Histone methyltransferase activity affects metabolism in human cells independently of transcriptional regulation.PLoS biology · 2023Article
- CellMinerCDB: NCATS Is a Web-Based Portal Integrating Public Cancer Cell Line Databases for Pharmacogenomic Explorations.Cancer research · 2023Article
- Single-cell proteo-genomic reveals a comprehensive map of centrosome-associated spliceosome components.iScience · 2023Article
- Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics.Nature communications · 2023Article
- Article
- Identifying the genes impacted by cell proliferation in proteomics and transcriptomics studies.PLoS computational biology · 2022Article
- Experimental reproducibility limits the correlation between mRNA and protein abundances in tumor proteomic profiles.Cell reports methods · 2022Article
- Saturation of the mitochondrial NADH shuttles drives aerobic glycolysis in proliferating cells.Molecular cell · 2022Article
- Pan-cancer proteomic map of 949 human cell lines.Cancer cell · 2022Article
- Reducing Peptide Sequence Bias in Quantitative Mass Spectrometry Data with Machine Learning.Journal of proteome research · 2022Article
- Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas.Scientific data · 2022Article
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Authors and funding
39 authors.
Tiannan GuoKey Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland. Electronic address: guotiannan@westlake.edu.cn.
Augustin LunacBio Center, Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
Vinodh N RajapakseDevelopmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Ching Chiek KohDepartment of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
Zhicheng WuKey Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
Wei LiuKey Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China.
Yaoting SunKey Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
Huanhuan GaoKey Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
Michael P MendenRWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany; Bioscience, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK.
Chao XuFaculty of Software, Fujian Normal University, Fuzhou, China.
Laurence CalzoneInstitut Curie, PSL Research University, INSERM, U900, Mines Paris Tech 75005, Paris, France.
Loredana MartignettiInstitut Curie, PSL Research University, INSERM, U900, Mines Paris Tech 75005, Paris, France.
Chiara AuwerxDepartment of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
Marija BuljanDepartment of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
Amir Banaei-EsfahaniDepartment of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland.
Alessandro OriLeibniz Institute on Aging, Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany.
Murat IskarStructural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
Ludovic GilletDepartment of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
Ran BiDepartment of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China.
Jiangnan ZhangDepartment of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China.
Huanhuan ZhangKey Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China.
Chenhuan YuKey Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China.
Qing ZhongInstitute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; Cancer Data Science Group, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia.
Sudhir VarmaHiThru Analytics, Laurel, MD 20707, USA.
Uwe SchmittScientific IT Services, ETH Zurich, Zurich, Switzerland.
Peng QiuDepartment of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Dr., Atlanta, GA 30332, USA.
Qiushi ZhangKey Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
Yi ZhuKey Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
Peter J WildInstitute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland.
Mathew J GarnettSanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Peer BorkStructural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.
Martin BeckStructural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
Kexin LiuDepartment of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China.
Julio Saez-RodriguezRWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany.
Fathi ElloumiDevelopmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
William C ReinholdDevelopmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Chris SandercBio Center, Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
Yves PommierDevelopmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: yves.pommier@nih.gov.
Ruedi AebersoldDepartment of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland. Electronic address: aebersold@imsb.biol.ethz.ch.
Funding
Wellcome Trust 102696
Abstract
Here we describe a proteomic data resource for the NCI-60 cell lines generated by pressure cycling technology and SWATH mass spectrometry. We developed the DIA-expert software to curate and visualize the SWATH data, leading to reproducible detection of over 3,100 SwissProt proteotypic proteins and systematic quantification of pathway activities. Stoichiometric relationships of interacting proteins for DNA replication, repair, the chromatin remodeling NuRD complex, β-catenin, RNA metabolism, and prefoldins are more evident than that at the mRNA level. The data are available in CellMiner (discover.nci.nih.gov/cellminercdb and discover.nci.nih.gov/cellminer), allowing casual users to test hypotheses and perform integrative, cross-database analyses of multi-omic drug response correlations for over 20,000 drugs. We demonstrate the value of proteome data in predicting drug response for over 240 clinically relevant chemotherapeutic and targeted therapies. In summary, we present a novel proteome resource for the NCI-60, together with relevant software tools, and demonstrate the benefit of proteome analyses.
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Biological SciencesCancer Systems BiologyProteomicsSystems Biology
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