Independent principal component analysis for biologically meaningful dimension reduction of large biological data sets

Yao, Fangzhou, Coquery, Jeff and Le Cao, Kim-Anh (2012) Independent principal component analysis for biologically meaningful dimension reduction of large biological data sets. BMC Bioinformatics, 13 Article 24: 1-15. doi:10.1186/1471-2105-13-24


Author Yao, Fangzhou
Coquery, Jeff
Le Cao, Kim-Anh
Title Independent principal component analysis for biologically meaningful dimension reduction of large biological data sets
Journal name BMC Bioinformatics   Check publisher's open access policy
ISSN 1471-2105
Publication date 2012-02-01
Sub-type Article (original research)
DOI 10.1186/1471-2105-13-24
Open Access Status DOI
Volume 13
Issue Article 24
Start page 1
End page 15
Total pages 15
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2013
Language eng
Formatted abstract
Background: A key question when analyzing high throughput data is whether the information provided by the measured biological entities (gene, metabolite expression for example) is related to the experimental conditions, or, rather, to some interfering signals, such as experimental bias or artefacts. Visualization tools are therefore useful to better understand the underlying structure of the data in a ‘blind’ (unsupervised) way. A well-established technique to do so is Principal Component Analysis (PCA). PCA is particularly powerful if the biological question is related to the highest variance. Independent Component Analysis (ICA) has been proposed as an alternative to PCA as it optimizes an independence condition to give more meaningful components. However, neither PCA nor ICA can overcome both the high dimensionality and noisy characteristics of biological data.

Results: We propose Independent Principal Component Analysis (IPCA) that combines the advantages of both PCA and ICA. It uses ICA as a denoising process of the loading vectors produced by PCA to better highlight the important biological entities and reveal insightful patterns in the data. The result is a better clustering of the biological samples on graphical representations. In addition, a sparse version is proposed that performs an internal variable selection to identify biologically relevant features (sIPCA).

Conclusions:
On simulation studies and real data sets, we showed that IPCA offers a better visualization of the data than ICA and with a smaller number of components than PCA. Furthermore, a preliminary investigation of the list of genes selected with sIPCA demonstrate that the approach is well able to highlight relevant genes in the data with respect to the biological experiment. IPCA and sIPCA are both implemented in the R package mixomics dedicated to the analysis and exploration of high dimensional biological data sets, and on mixomics’ web-interface.
Keyword Gene Expression Data
Microarray
Rat
Acetaminophen
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2013 Collection
Institute for Molecular Bioscience - Publications
 
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