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Methods Mol Biol. 2018;1849:227-242. doi: 10.1007/978-1-4939-8728-3_15.

Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions.

Author information

1
College of Pharmacy, Oregon State University, Corvallis, OR, USA. rodrrich@oregonstate.edu.
2
College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA.
3
College of Pharmacy, Oregon State University, Corvallis, OR, USA. andriy.morgun@oregonstate.edu.

Abstract

Improvements in sequencing technologies and reduced experimental costs have resulted in a vast number of studies generating high-throughput data. Although the number of methods to analyze these "omics" data has also increased, computational complexity and lack of documentation hinder researchers from analyzing their high-throughput data to its true potential. In this chapter we detail our data-driven, transkingdom network (TransNet) analysis protocol to integrate and interrogate multi-omics data. This systems biology approach has allowed us to successfully identify important causal relationships between different taxonomic kingdoms (e.g., mammals and microbes) using diverse types of data.

KEYWORDS:

Causal relationships; Network analysis; Omics; Transkingdom

PMID:
30298258
PMCID:
PMC6557635
DOI:
10.1007/978-1-4939-8728-3_15
[Indexed for MEDLINE]
Free PMC Article

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