Jump to main content
Jump to site search

Issue 12, 2013
Previous Article Next Article

Network-based analysis of omics with multi-objective optimization

Author affiliations


Nowadays, computational and statistical methods focusing on integrated analysis of omics data are necessary. A few approaches have been recently described in the literature and a small number of software packages are available. We have developed a new method to generate networks of biological components that incorporate multi-omics information. The novelty of this method relies on using a multi-objective (MO) optimization procedure in order to drive the identification of networks that are enriched according to several statistical estimators. The network-based analysis of omics with MO optimization described in this work can be applied to different types of omics and biological interactions. By using this approach we found protein networks that participate in the establishment of the increased basal differentiation observed in breast tumors of BRCA1-mutation carriers. Additionally, we showed how MO optimization can be used to carry out a network-based comparison among several omic data sets: using transcriptomic data from two types of breast tumors and the corresponding epithelial cells from which tumors were generated, we found a protein network that shows a strong and coherent (the same direction) differential expression when comparing each tumor with its respective epithelial tissue. We have also compared the transcriptional variation detected in three different types of tumors originated in breast, colon and pancreas with the corresponding healthy tissues. Despite the global low correlation observed in the three pairs of tumors, we found more similar networks regulated in the same direction in colon and pancreas tumor cells. In conclusion, we propose the network-based analysis of omics with MO optimization as a valid tool for integrated analysis of omics data.

Graphical abstract: Network-based analysis of omics with multi-objective optimization

Back to tab navigation

Supplementary files

Article information

02 Aug 2013
27 Sep 2013
First published
30 Sep 2013

Mol. BioSyst., 2013,9, 2971-2980
Article type

Network-based analysis of omics with multi-objective optimization

E. Mosca and L. Milanesi, Mol. BioSyst., 2013, 9, 2971
DOI: 10.1039/C3MB70327D

Search articles by author