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Protocol for using Multiomics2Targets to identify targets and driver kinases for cancer cohorts profiled with
Giacomo B Marino1, Eden Z Deng1, Daniel J B Clarke1
1Department 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.
Abstract:
The availability of multi-omics data applied to profile cancer cohorts is rapidly increasing. Here, we present a protocol for Multiomics2Targets, a computational pipeline that can identify driver cell signaling pathways, protein kinases, and cell-surface targets for immunotherapy. We describe steps for preparing the data, uploading files, and tuning parameters. We then detail procedures for running the workflow, visualizing the results, and exporting and sharing reports containing the analysis. For complete details on the use and execution of this protocol, please refer to Deng et al.1.
Insights
This study introduces Multiomics2Targets, a computational pipeline for analyzing multi-omics cancer data. It identifies key cancer targets, including cell signaling pathways and protein kinases, for potential immunotherapy treatments.
Area of Science:
- Computational biology
- Cancer research
- Immunotherapy
Background:
- Multi-omics data for cancer profiling is increasingly available.
- Identifying actionable targets from complex datasets remains a challenge.
Purpose of the Study:
- To present a computational pipeline, Multiomics2Targets, for analyzing multi-omics cancer data.
- To enable the identification of driver cell signaling pathways, protein kinases, and cell-surface targets for immunotherapy.
Main Methods:
- The protocol details data preparation and file uploading.
- It includes steps for parameter tuning and workflow execution.
- Visualization, export, and sharing of analysis reports are described.
Main Results:
- The pipeline facilitates the identification of critical molecular targets within cancer cohorts.
- It provides a structured approach to translating multi-omics data into potential therapeutic strategies.
Conclusions:
- Multiomics2Targets offers a standardized protocol for leveraging multi-omics data in cancer research.
- The pipeline aids in discovering novel targets for developing effective cancer immunotherapies.
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