Dataset Information

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

ABSTRACT:

Background

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.

Results

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.

Conclusions

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.

SUBMITTER: Paley S

PROVIDER: S-EPMC6637615 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Publications

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

Paley Suzanne S Karp Peter D PD

BMC bioinformatics 20190718 1

<h4>Background</h4>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.<h4>Results</h4>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 t ...[more]

PMID: 31319812

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Dataset Information

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

Background

Results

Conclusions

Publications

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

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