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DRPPM-EASY: A Web-Based Framework for Integrative Analysis of Multi-Omics Cancer Datasets.
Obermayer, Alyssa; Dong, Li; Hu, Qianqian; Golden, Michael; Noble, Jerald D; Rodriguez, Paulo; Robinson, Timothy J; Teng, Mingxiang; Tan, Aik-Choon; Shaw, Timothy I.
Afiliación
  • Obermayer A; Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA.
  • Dong L; Computational Biology Department, St Jude Children's Research Hospital, Memphis, TN 38105, USA.
  • Hu Q; Department of Drug Discovery, Moffitt Cancer Center, Tampa, FL 33612, USA.
  • Golden M; University of Central Florida, Orlando, FL 32816, USA.
  • Noble JD; Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL 33612, USA.
  • Rodriguez P; Department of Immunology, Moffitt Cancer Center, Tampa, FL 33612, USA.
  • Robinson TJ; Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL 33612, USA.
  • Teng M; Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA.
  • Tan AC; Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA.
  • Shaw TI; Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA.
Biology (Basel) ; 11(2)2022 Feb 08.
Article en En | MEDLINE | ID: mdl-35205126
ABSTRACT
High-throughput transcriptomic and proteomic analyses are now routinely applied to study cancer biology. However, complex omics integration remains challenging and often time-consuming. Here, we developed DRPPM-EASY, an R Shiny framework for integrative multi-omics analysis. We applied our application to analyze RNA-seq data generated from a USP7 knockdown in T-cell acute lymphoblastic leukemia (T-ALL) cell line, which identified upregulated expression of a TAL1-associated proliferative signature in T-cell acute lymphoblastic leukemia cell lines. Next, we performed proteomic profiling of the USP7 knockdown samples. Through DRPPM-EASY-Integration, we performed a concurrent analysis of the transcriptome and proteome and identified consistent disruption of the protein degradation machinery and spliceosome in samples with USP7 silencing. To further illustrate the utility of the R Shiny framework, we developed DRPPM-EASY-CCLE, a Shiny extension preloaded with the Cancer Cell Line Encyclopedia (CCLE) data. The DRPPM-EASY-CCLE app facilitates the sample querying and phenotype assignment by incorporating meta information, such as genetic mutation, metastasis status, sex, and collection site. As proof of concept, we verified the expression of TP53 associated DNA damage signature in TP53 mutated ovary cancer cells. Altogether, our open-source application provides an easy-to-use framework for omics exploration and discovery.
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Texto completo: 1 Banco de datos: MEDLINE Idioma: En Revista: Biology (Basel) Año: 2022 Tipo del documento: Article País de afiliación: Estados Unidos

Texto completo: 1 Banco de datos: MEDLINE Idioma: En Revista: Biology (Basel) Año: 2022 Tipo del documento: Article País de afiliación: Estados Unidos