Sparse group factor analysis for biclustering of multiple data sources

Kerstin Bunte*, Eemeli Leppäaho, Inka Saarinen, Samuel Kaski

*Corresponding author for this work

Research output: Contribution to journalArticleScientificpeer-review

15 Citations (Scopus)

Abstract

Motivation: Modelling methods that find structure in data are necessary with the current large volumes of genomic data, and there have been various efforts to find subsets of genes exhibiting consistent patterns over subsets of treatments. These biclustering techniques have focused on one data source, often gene expression data. We present a Bayesian approach for joint biclustering of multiple data sources, extending a recent method Group Factor Analysis to have a biclustering interpretation with additional sparsity assumptions. The resulting method enables data-driven detection of linear structure present in parts of the data sources. Results: Our simulation studies show that the proposed method reliably infers biclusters from heterogeneous data sources. We tested the method on data from the NCI-DREAM drug sensitivity prediction challenge, resulting in an excellent prediction accuracy. Moreover, the predictions are based on several biclusters which provide insight into the data sources, in this case on gene expression, DNA methylation, protein abundance, exome sequence, functional connectivity fingerprints and drug sensitivity.

Original languageEnglish
Pages (from-to)2457-2463
Number of pages7
JournalBioinformatics
Volume32
Issue number16
DOIs
Publication statusPublished - 15 Aug 2016
MoE publication typeA1 Journal article-refereed

Fingerprint Dive into the research topics of 'Sparse group factor analysis for biclustering of multiple data sources'. Together they form a unique fingerprint.

Cite this