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Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics.
Deng, Eden Z; Marino, Giacomo B; Clarke, Daniel J B; Diamant, Ido; Resnick, Adam C; Ma, Weiping; Wang, Pei; Ma'ayan, Avi.
Affiliation
  • Deng EZ; Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA.
  • Marino GB; Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA.
  • Clarke DJB; Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA.
  • Diamant I; Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA.
  • Resnick AC; Center for Data Driven Discovery in Biomedicine, Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
  • Ma W; Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY 10029, USA.
  • Wang P; Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY 10029, USA.
  • Ma'ayan A; Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA. Electronic address: avi.maayan@mssm.edu.
Cell Rep Methods ; 4(8): 100839, 2024 Aug 19.
Article in En | MEDLINE | ID: mdl-39127042
ABSTRACT
The availability of data from profiling of cancer patients with multiomics is rapidly increasing. However, integrative analysis of such data for personalized target identification is not trivial. Multiomics2Targets is a platform that enables users to upload transcriptomics, proteomics, and phosphoproteomics data matrices collected from the same cohort of cancer patients. After uploading the data, Multiomics2Targets produces a report that resembles a research publication. The uploaded matrices are processed, analyzed, and visualized using the tools Enrichr, KEA3, ChEA3, Expression2Kinases, and TargetRanger to identify and prioritize proteins, genes, and transcripts as potential targets. Figures and tables, as well as descriptions of the methods and results, are automatically generated. Reports include an abstract, introduction, methods, results, discussion, conclusions, and references and are exportable as citable PDFs and Jupyter Notebooks. Multiomics2Targets is applied to analyze version 3 of the Clinical Proteomic Tumor Analysis Consortium (CPTAC3) pan-cancer cohort, identifying potential targets for each CPTAC3 cancer subtype. Multiomics2Targets is available from https//multiomics2targets.maayanlab.cloud/.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Phosphoproteins / Proteomics / Transcriptome / Neoplasms Limits: Humans Language: En Journal: Cell Rep Methods Year: 2024 Document type: Article Affiliation country: Estados Unidos Country of publication: Estados Unidos
Fulltext
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Phosphoproteins / Proteomics / Transcriptome / Neoplasms Limits: Humans Language: En Journal: Cell Rep Methods Year: 2024 Document type: Article Affiliation country: Estados Unidos Country of publication: Estados Unidos