Analyzing time-dependent microarray data using independent component analysis derived expression modes from human macrophages infected with F. tularensis holartica.
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 tool, 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 TNFalpha 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 NFkappaB as one of the main regulatory genes during response to F. tularensis infection.
Lutter
D
D
Clinical Chemistry, University Clinic, 93053 Regensburg, Germany; CIML Group, Institute of Biophysics, University of Regensburg, 93040 Regensburg, Germany; Institute of Bioinformatics and Systems Biology, CMB, Helmholtz Zentrum Muenchen, Germany.
Langmann
Th
T
Ugocsai
P
P
Moehle
C
C
Seibold
E
E
Splettstoesser
W D
WD
Gruber
P
P
Lang
E W
EW
Schmitz
G
G
D000465:Algorithms; D002478:Cells, Cultured; D016000:Cluster Analysis; D005604:Francisella tularensis / Q000502:physiology*; D020869:Gene Expression Profiling / Q000379:methods*; D053263:Gene Regulatory Networks; D006801:Humans; D008264:Macrophages / Q000378:metabolism / Q000382:microbiology / Q000502:physiology*; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D025341:Principal Component Analysis; D014406:Tularemia / Q000235:genetics* / Q000378:metabolism