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Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Web-based multi-omics integration using the Analyst software suite.

Jessica D Ewald1, Guangyan Zhou1, Yao Lu2

  • 1Institute of Parasitology, McGill University, Montreal, Quebec, Canada.

Nature Protocols
|February 14, 2024
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Summary
This summary is machine-generated.

This protocol introduces a user-friendly software suite for multi-omics analysis, integrating single-omics, knowledge-driven, and data-driven approaches for efficient data interpretation.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Multi-omics studies are increasing, requiring integrated analysis workflows and accessible software tools.
  • Current multi-omics integration methods often lack user-friendliness and comprehensive functionality.
  • Efficient analysis and interpretation of complex multi-omics data are crucial for biological discovery.

Purpose of the Study:

  • To present a comprehensive protocol for multi-omics data analysis and integration.
  • To demonstrate the utility of the Analyst software suite for various omics data types.
  • To enable researchers to perform knowledge-driven and data-driven integration using biological networks and dimensionality reduction.

Main Methods:

  • Single-omics data analysis using ExpressAnalyst (transcriptomics/proteomics) and MetaboAnalyst (lipidomics).
  • Knowledge-driven integration of significant features using OmicsNet and biological networks.
  • Data-driven integration via joint dimensionality reduction using OmicsAnalyst.

Main Results:

  • The protocol successfully integrates transcriptomics, proteomics, and lipidomics data from human pancreatic islet and plasma samples.
  • The Analyst software suite facilitates both knowledge-driven and data-driven multi-omics integration.
  • The complete workflow can be executed efficiently within approximately 2 hours.

Conclusions:

  • The Analyst software suite provides a user-friendly web interface for diverse multi-omics data analysis tasks.
  • This protocol offers a streamlined approach to multi-omics integration, enhancing biological data interpretation.
  • The presented workflow empowers researchers to conduct advanced multi-omics analyses with ease.