The MultiOmics Explainer: explaining omics results in the context of a pathway/genome database

High-throughput experiments can bring to light associations between genes, proteins and/or metabolites, many of which will be explainable by existing knowledge. Our aim is to speed elucidation of such explanations and, in some cases, find explanations that scientists might otherwise overlook. We des...

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Bibliographic Details
Published inBMC bioinformatics Vol. 20; no. 1; p. 399
Main Authors Paley, Suzanne, Karp, Peter D
Format Journal Article
LanguageEnglish
Published England BioMed Central Ltd 18.07.2019
BioMed Central
BMC
Subjects
Computational biology
Genes
Metabolites
Metabolomics
Methods
Multiomics analysis
Network analysis
Pathfinding
Pathway visualization
Pathway/genome database
Proteomics
Scientists
Software
Suites (Software)
Transcription (Genetics)
United States
Multiomics analysis
Pathfinding
Pathway visualization
Pathway/genome database
Network analysis
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Summary:High-throughput experiments can bring to light associations between genes, proteins and/or metabolites, many of which will be explainable by existing knowledge. Our aim is to speed elucidation of such explanations and, in some cases, find explanations that scientists might otherwise overlook. We describe the MultiOmics Explainer, a new tool within the Pathway Tools software suite that leverages what is known about an organism's metabolic and regulatory network to suggest explanations for the results of omics experiments. Querying a database such as EcoCyc, the MultiOmics Explainer searches the organism's network of metabolic reactions, transporters, cofactors, enzyme substrate-level activation and inhibition relationships, and transcriptional and translational regulation relationships to identify paths of influence among input genes, proteins and metabolites. Results are presented in a combined metabolic and regulatory diagram. We present several examples of explanations generated for associations found in the Escherichia coli literature. The MultiOmics Explainer is a valuable tool that helps researchers understand and interpret the results of their omics experiments in the context of what is known about an organism's metabolic and regulatory network. It showcases the rich set of computational inferences that can be drawn from a database such as EcoCyc that encodes a diverse range of biological interactions.
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-019-2971-6