Data Center: Cancer

Partition clustering identifies four distinct patterns of gene expression in genome-wide analysis of Drosophila immune response

Microarray Platform:
Affymetrix® GeneChip® Drosophila Genome Array

Reference:
CEL files were obtained from http://www.fruitfly.org.
Data originally published in -
De Gregorio E, Spellman PT, Rubin GM, Lemaitre B. Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays. Proc Natl Acad Sci U S A. 2001 Oct 23;98(22):12590-5.

Abstract:
Gene expression profiles in adult fruit flies subjected to microbial infection were monitored using the Affymetrix® GeneChip® Drosophila Genome Array (De Gregario et al., 2001). CEL files were obtained from the authors' website and RMA was used to derive expression measurements from the probe level data. Of the more than 13,500 genes interrogated, 624 were differentially expressed (at least 1.5 fold-change and less than a 5% false discovery rate) following infection. Hierarchical clustering and PCA suggested that at least 4 distinct patterns of gene expression were present in this filtered dataset. PAM was used to partition the 624 genes into 4 discrete clusters. The biological process ontologies associated with the genes in each cluster were also analyzed using a z-score report. This analysis showed that distinct biological themes were associated with each of the 4 patterns of gene expression. One cluster showed dramatic (>8 fold) up-regulation immediately following septic injury. Of the 37 genes in this cluster, 17 were involved in the response to external stimulus and 11 were involved in antibacterial humoral response. 10 genes in this cluster had no known biological function. These 10 genes are potential new regulators of the innate defense response in Drosophila and specifically the antibacterial peptide response.

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