Journal
INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS
Volume 9, Issue 3, Pages 277-304Publisher
INDERSCIENCE ENTERPRISES LTD
DOI: 10.1504/IJDMB.2014.060052
Keywords
data mining; bioinformatics; statistical modelling; transcriptome; gene expression; microarray data analysis; GSEA; gene set enrichment analysis; ICA; independent component analysis; T lymphocyte; regulatory T cell; Treg; molecular signature; signature discovery
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Funding
- Universite Pierre et Marie Curie, Centre National de la Recherche Scientifique
- European Union [LSHB-CT-04-005246, LSBH-CT-06-018933]
- French Ministry of Research
- Universite Pierre et Marie Curie
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Microarray analysis often leads to either too large or too small numbers of gene candidates to allow meaningful identification of functional signatures. We aimed at overcoming this hurdle by combining two algorithms: i Independent Component Analysis to extract statistically-based potential signatures. ii Gene Set Enrichment Analysis to produce a score of enrichment with statistical significance of each potential signature. We have applied this strategy to identify regulatory T cell (Treg) molecular signatures from two experiments in mice, with cross-validation. These signatures can detect the similar to 1% Treg in whole spleen. These findings demonstrate the relevance of our approach as a signature discovery tool.
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