PT  - JOURNAL ARTICLE
AU  - Jérôme Mariette
AU  - Nathalie Villa-Vialaneix
TI  - Unsupervised multiple kernel learning for heterogeneous data integration
AID  - 10.1101/139287
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 139287
4099  - http://biorxiv.org/content/early/2017/10/10/139287.short
4100  - http://biorxiv.org/content/early/2017/10/10/139287.full
AB  - Recent high-throughput sequencing advances have expanded the breadth of available omics datasets and the integrated analysis of multiple datasets obtained on the same samples has allowed to gain important insights in a wide range of applications. However, the integration of various sources of information remains a challenge for systems biology since produced datasets are often of heterogeneous types, with the need of developing generic methods to take their different specificities into account.We propose a multiple kernel framework that allows to integrate multiple datasets of various types into a single exploratory analysis. Several solutions are provided to learn either a consensus meta-kernel or a meta-kernel that preserves the original topology of the datasets. We applied our framework to analyse two public multi-omics datasets. First, the multiple metagenomic datasets, collected during the TARA Oceans expedition, was explored to demonstrate that our method is able to retrieve previous findings in a single KPCA as well as to provide a new image of the sample structures when a larger number of datasets are included in the analysis. To perform this analysis, a generic procedure is also proposed to improve the interpretability of the kernel PCA in regards with the original data. Second, the multi-omics breast cancer datasets, provided by The Cancer Genome Atlas, is analysed using a kernel Self-Organizing Maps with both single and multi-omics strategies. The comparison of this two approaches demonstrates the benefit of our integration method to improve the representation of the studied biological system.Proposed methods are available in the R package mixKernel, released on CRAN. It is fully compatible with the mixOmics package and a tutorial describing the approach can be found on mixOmics web site http://mixomics.org/mixkernel/.