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Omics Data Complementarity Underlines Functional Cross-Communication in Yeast

Malod-Dognin, N; Pržulj, N; (2017) Omics Data Complementarity Underlines Functional Cross-Communication in Yeast. Journal of Integrative Bioinformatics , 14 (2) , Article 20170018. 10.1515/jib-2017-0018. Green open access

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Abstract

Mapping the complete functional layout of a cell and understanding the cross-talk between different processes are fundamental challenges. They elude us because of the incompleteness and noisiness of molecular data and because of the computational intractability of finding the exact answer. We perform a simple integration of three types of baker’s yeast omics data to elucidate the functional organization and lines of cross-functional communication. We examine protein–protein interaction (PPI), co-expression (COEX) and genetic interaction (GI) data, and explore their relationship with the gold standard of functional organization, the Gene Ontology (GO). We utilize a simple framework that identifies functional cross-communication lines in each of the three data types, in GO, and collectively in the integrated model of the three omics data types; we present each of them in our new Functional Organization Map (FOM) model. We compare the FOMs of the three omics datasets with the FOM of GO and find that GI is in best agreement with GO, followed COEX and PPI. We integrate the three FOMs into a unified FOM and find that it is in better agreement with the FOM of GO than those of any omics dataset alone, demonstrating functional complementarity of different omics data.

Type: Article
Title: Omics Data Complementarity Underlines Functional Cross-Communication in Yeast
Open access status: An open access version is available from UCL Discovery
DOI: 10.1515/jib-2017-0018
Publisher version: http://dx.doi.org/10.1515/jib-2017-0018
Language: English
Additional information: Copyright © 2017, Nataša Pržulj et al., published by De Gruyter, Berlin/Boston. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. BY-NC-ND 3.0. (http://creativecommons.org/licenses/by-nc-nd/3.0)
Keywords: Molecular omics data; cell’s functional organization; data-integration
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Computer Science
URI: http://discovery.ucl.ac.uk/id/eprint/1568251
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