A practical data processing workflow for multi-OMICS projects

• Published in: Biochimica et biophysica acta Vol. 1844; no. 1; pp. 52 - 62
• Main Authors: Kohl, Michael, Megger, Dominik A., Trippler, Martin, Meckel, Hagen, Ahrens, Maike, Bracht, Thilo, Weber, Frank, Hoffmann, Andreas-Claudius, Baba, Hideo A., Sitek, Barbara, Schlaak, Jörg F., Meyer, Helmut E., Stephan, Christian, Eisenacher, Martin
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.01.2014
• Subjects: Biomarker; Biomarkers - metabolism; Chromatography, Liquid; Data processing workflow; Mass Spectrometry; Multi-OMICS; Proteomics; Quantitative Proteomics; Quantitative Transcriptomics; Regression analysis; Transcriptome; Workflow; Biomarker; CRAN; Data processing workflow; BG; BC-FC; XPlatCom; HCC; MeSH; ASCII; OLDLCT; Regression analysis; RAID; Deucl; Multi-OMICS; Quantitative Proteomics; HGNC; Quantitative Transcriptomics; LD; KEGG; GUI; FC; (X)PlatCom; fold change; The Comprehensive R Archive Network; CrossPlatformCommander; Box–Cox-transformed fold changes; Medical Subject Headings; hepatocellular carcinoma; D(eucl); liver disease; graphical user interface; Kyoto Encyclopedia of Genes and Genomes; bio-molecule group; DIGE-LC-MS-Transcriptomics overlap; American Standard Code for Information Interchange; Euclidean distance; redundant array of independent disks; HUGO Gene Nomenclature Committee; OL(DLCT)
• ISSN: 1570-9639; 0006-3002; 1878-1454
• DOI: 10.1016/j.bbapap.2013.02.029

Multi-OMICS approaches aim on the integration of quantitative data obtained for different biological molecules in order to understand their interrelation and the functioning of larger systems. This paper deals with several data integration and data processing issues that frequently occur within this context. To this end, the data processing workflow within the PROFILE project is presented, a multi-OMICS project that aims on identification of novel biomarkers and the development of new therapeutic targets for seven important liver diseases. Furthermore, a software called CrossPlatformCommander is sketched, which facilitates several steps of the proposed workflow in a semi-automatic manner. Application of the software is presented for the detection of novel biomarkers, their ranking and annotation with existing knowledge using the example of corresponding Transcriptomics and Proteomics data sets obtained from patients suffering from hepatocellular carcinoma. Additionally, a linear regression analysis of Transcriptomics vs. Proteomics data is presented and its performance assessed. It was shown, that for capturing profound relations between Transcriptomics and Proteomics data, a simple linear regression analysis is not sufficient and implementation and evaluation of alternative statistical approaches are needed. Additionally, the integration of multivariate variable selection and classification approaches is intended for further development of the software. Although this paper focuses only on the combination of data obtained from quantitative Proteomics and Transcriptomics experiments, several approaches and data integration steps are also applicable for other OMICS technologies. Keeping specific restrictions in mind the suggested workflow (or at least parts of it) may be used as a template for similar projects that make use of different high throughput techniques. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. •A workflow for integrating multi-OMICS data is presented.•The suggested workflow may serve as a template for similar projects.•The suggested CrossPlatformCommander software facilitates several workflow steps.•Capturing multi-OMICS correlations requires sophisticated statistical approaches.