Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 Apr 18;9(4):76.
doi: 10.3390/metabo9040076.

Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

Farhana R Pinu  1 , David J Beale  2 , Amy M Paten  3 , Konstantinos Kouremenos  4   5 , Sanjay Swarup  6 , Horst J Schirra  7 , David Wishart  8   9
Affiliations

Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

Farhana R Pinu et al. Metabolites. .

Abstract

The use of multiple omics techniques (i.e., genomics, transcriptomics, proteomics, and metabolomics) is becoming increasingly popular in all facets of life science. Omics techniques provide a more holistic molecular perspective of studied biological systems compared to traditional approaches. However, due to their inherent data differences, integrating multiple omics platforms remains an ongoing challenge for many researchers. As metabolites represent the downstream products of multiple interactions between genes, transcripts, and proteins, metabolomics, the tools and approaches routinely used in this field could assist with the integration of these complex multi-omics data sets. The question is, how? Here we provide some answers (in terms of methods, software tools and databases) along with a variety of recommendations and a list of continuing challenges as identified during a peer session on multi-omics integration that was held at the recent 'Australian and New Zealand Metabolomics Conference' (ANZMET 2018) in Auckland, New Zealand (Sept. 2018). We envisage that this document will serve as a guide to metabolomics researchers and other members of the community wishing to perform multi-omics studies. We also believe that these ideas may allow the full promise of integrated multi-omics research and, ultimately, of systems biology to be realized.

Keywords: data analysis; data integration; databases; experimental design; mathematical modeling; metabolic networks; pathway analysis; quantitative omics; translational metabolomics.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
A conceptual model for designing a systems biology experiment.
Figure 2
Figure 2
Top-down and bottom-up data reduction integration approaches used in system biology.
Figure 3
Figure 3
Principal differences between post-analysis data integration (left) and integrated data analysis (right) for handling multi-omics data sets.
See this image and copyright information in PMC

References

    1. Breitling R. What is systems biology? Front. Physiol. 2010;1:9. doi: 10.3389/fphys.2010.00009. - DOI - PMC - PubMed
    1. Hillmer R.A. Systems biology for biologists. PLoS Pathog. 2015;11:e1004786. doi: 10.1371/journal.ppat.1004786. - DOI - PMC - PubMed
    1. Cho C.R., Labow M., Reinhardt M., van Oostrum J., Peitsch M.C. The application of systems biology to drug discovery. Curr. Opin. Chem. Biol. 2006;10:294–302. doi: 10.1016/j.cbpa.2006.06.025. - DOI - PubMed
    1. Cisek K., Krochmal M., Klein J., Mischak H. The application of multi-omics and systems biology to identify therapeutic targets in chronic kidney disease. Nephrol. Dial. Transplant. 2016;31:2003–2011. doi: 10.1093/ndt/gfv364. - DOI - PubMed
    1. Hagemann M., Hesse W.R. Systems and synthetic biology for the biotechnological application of cyanobacteria. Curr. Opin. Biotechnol. 2018;49:94–99. doi: 10.1016/j.copbio.2017.07.008. - DOI - PubMed