Bioinformatics Advance Access originally published online on June 23, 2009
Bioinformatics 2009 25(17):2222-2228; doi:10.1093/bioinformatics/btp388
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Prestige centrality-based functional outlier detection in gene expression analysis
The Scripps Translational Science Institute and Scripps Genomic Medicine, Scripps Health and The Scripps Research Institute, 3344 North Torrey Pines Court, Room 306 La Jolla, CA 92037 USA
* To whom correspondence should be addressed.
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Abstract |
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Motivation: Traditional gene expression analysis techniques capture an average gene expression state across sample replicates. However, the average signal across replicates will not capture activated gene networks in different states across replicates. For example, if a particular gene expression network is activated within a subset or all sample replicates, yet the activation state across the sample replicates differs by the specific genes activated in each replicate, the activation of this network will be washed out by averaging across replicates. This situation is likely to occur in single cell gene expression experiments or in noisy experimental settings where a small sub-population of cells contributes to the gene expression signature of interest.
Results and Implementation: In this light, we developed a novel network-based approach which considers gene expression within each replicate across its entire gene expression profile, and identifies outliers across replicates. The power of this method is demonstrated by its ability to enrich for distant metastasis related genes derived from noisy expression data of CD44+CD24-/low tumor initiating cells.
Contact: atorkama{at}scripps.edu; atorkama{at}scrippshealth.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Received on March 13, 2009; revised on June 11, 2009; accepted on June 19, 2009
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