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A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses.
Gross, Sean M; Dane, Mark A; Smith, Rebecca L; Devlin, Kaylyn L; McLean, Ian C; Derrick, Daniel S; Mills, Caitlin E; Subramanian, Kartik; London, Alexandra B; Torre, Denis; Evangelista, John Erol; Clarke, Daniel J B; Xie, Zhuorui; Erdem, Cemal; Lyons, Nicholas; Natoli, Ted; Pessa, Sarah; Lu, Xiaodong; Mullahoo, James; Li, Jonathan; Adam, Miriam; Wassie, Brook; Liu, Moqing; Kilburn, David F; Liby, Tiera A; Bucher, Elmar; Sanchez-Aguila, Crystal; Daily, Kenneth; Omberg, Larsson; Wang, Yunguan; Jacobson, Connor; Yapp, Clarence; Chung, Mirra; Vidovic, Dusica; Lu, Yiling; Schurer, Stephan; Lee, Albert; Pillai, Ajay; Subramanian, Aravind; Papanastasiou, Malvina; Fraenkel, Ernest; Feiler, Heidi S; Mills, Gordon B; Jaffe, Jake D; Ma'ayan, Avi; Birtwistle, Marc R; Sorger, Peter K; Korkola, James E; Gray, Joe W; Heiser, Laura M.
Afiliação
  • Gross SM; Department of Biomedical Engineering, OHSU, Portland, OR, USA.
  • Dane MA; Department of Biomedical Engineering, OHSU, Portland, OR, USA.
  • Smith RL; Department of Biomedical Engineering, OHSU, Portland, OR, USA.
  • Devlin KL; Department of Biomedical Engineering, OHSU, Portland, OR, USA.
  • McLean IC; Department of Biomedical Engineering, OHSU, Portland, OR, USA.
  • Derrick DS; Department of Biomedical Engineering, OHSU, Portland, OR, USA.
  • Mills CE; Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.
  • Subramanian K; Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.
  • London AB; Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  • Torre D; Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  • Evangelista JE; Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  • Clarke DJB; Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  • Xie Z; Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  • Erdem C; Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA.
  • Lyons N; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Natoli T; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Pessa S; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Lu X; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Mullahoo J; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Li J; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
  • Adam M; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
  • Wassie B; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
  • Liu M; Department of Biomedical Engineering, OHSU, Portland, OR, USA.
  • Kilburn DF; Department of Biomedical Engineering, OHSU, Portland, OR, USA.
  • Liby TA; Department of Biomedical Engineering, OHSU, Portland, OR, USA.
  • Bucher E; Department of Biomedical Engineering, OHSU, Portland, OR, USA.
  • Sanchez-Aguila C; Department of Biomedical Engineering, OHSU, Portland, OR, USA.
  • Daily K; Sage Bionetworks, Seattle, WA, USA.
  • Omberg L; Sage Bionetworks, Seattle, WA, USA.
  • Wang Y; Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.
  • Jacobson C; Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.
  • Yapp C; Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.
  • Chung M; Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.
  • Vidovic D; Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, 33136, USA.
  • Lu Y; Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
  • Schurer S; Institute for Data Science & Computing, University of Miami, Miami, FL, 33136, USA.
  • Lee A; Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Pillai A; Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, 33136, USA.
  • Subramanian A; Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
  • Papanastasiou M; Institute for Data Science & Computing, University of Miami, Miami, FL, 33136, USA.
  • Fraenkel E; Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, USA.
  • Feiler HS; Human Genome Research Institute, National Institutes of Health, Bethesda, USA.
  • Mills GB; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Jaffe JD; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Ma'ayan A; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Birtwistle MR; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
  • Sorger PK; Department of Biomedical Engineering, OHSU, Portland, OR, USA.
  • Korkola JE; Knight Cancer Institute, OHSU, Portland, OR, USA.
  • Gray JW; Knight Cancer Institute, OHSU, Portland, OR, USA.
  • Heiser LM; Division of Oncological Sciences, OHSU, Portland, OR, USA.
Commun Biol ; 5(1): 1066, 2022 10 07.
Article em En | MEDLINE | ID: mdl-36207580
The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, and extracellular matrix proteins. While these signals are normally tightly controlled, their dysregulation leads to phenotypic and molecular states associated with diverse diseases. To develop a detailed understanding of the linkage between molecular and phenotypic changes, we generated a comprehensive dataset that catalogs the transcriptional, proteomic, epigenomic and phenotypic responses of MCF10A mammary epithelial cells after exposure to the ligands EGF, HGF, OSM, IFNG, TGFB and BMP2. Systematic assessment of the molecular and cellular phenotypes induced by these ligands comprise the LINCS Microenvironment (ME) perturbation dataset, which has been curated and made publicly available for community-wide analysis and development of novel computational methods ( synapse.org/LINCS_MCF10A ). In illustrative analyses, we demonstrate how this dataset can be used to discover functionally related molecular features linked to specific cellular phenotypes. Beyond these analyses, this dataset will serve as a resource for the broader scientific community to mine for biological insights, to compare signals carried across distinct molecular modalities, and to develop new computational methods for integrative data analysis.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Proteômica / Fator de Crescimento Epidérmico Idioma: En Ano de publicação: 2022 Tipo de documento: Article
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Proteômica / Fator de Crescimento Epidérmico Idioma: En Ano de publicação: 2022 Tipo de documento: Article