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Analyzing time-dependent microarray data using independent component analysis derived expression modes from human macrophages infected with F. tularensis holartica.

J. Biomed. Inform. 42, 605-611 (2009)
DOI
Open Access Green as soon as Postprint is submitted to ZB.
The analysis of large-scale gene expression profiles is still a demanding and extensive task. Modern machine learning and data mining techniques developed in linear algebra, like Independent Component Analysis (ICA), become increasingly popular as appropriate tools for analyzing microarray data. We applied ICA to analyze kinetic gene expression profiles of human monocyte derived macrophages (MDM) from three different donors infected with Francisella tularensis holartica and compared them to more classical methods like hierarchical clustering. Results were compared using a pathway analysis too[, based on the Gene Ontology and the MeSH database. We could show that both methods lead to time-dependent gene regulatory patterns which fit well to known TNF alpha induced immune responses. In comparison, the nonexclusive attribute of ICA results in a more detailed view and a higher resolution in time dependent behavior of the immune response genes. Additionally, we identified NF kappa B as one of the main regulatory genes during response to F. tularensis infection.
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Publication type Article: Journal article
Document type Scientific Article
Keywords Independent component analysis; Microarray; Gene chip; Infection; Time course; Clustering; Francisella tularensis; gene-expression; lvs; activation
Reviewing status