Cancer

Neuroscience

Cardiovascular

Immunology

Endocrinology

Oral Biology

Hematology

Using two-way ANOVA to dissect the immune response to hookworm infection in mouse lung

Microarray Platform: Affymetrix® GeneChip® Mouse Genome 430 2.0 array

Reference: Data available from Gene Expression Omnibus (GEO, GSE3414). GEO Summary: The goal of this experiment was to examine the innate immune response to helminth infection in the lung. Hookworms (like many other helminths) use an obligate migration pathway through the lung. Their infection has been characterized in the gut in detail, but early immune responses in the lung have not been fully characterized.

Analysis summary:
Gene expression was examined using the Affymetrix® GeneChip® Mouse Genome 430 2.0 array in mouse lung at days 2,3,4,8 and 12 following infection with the nematode Nippostrongylus brasiliensis in wild type and SCID mice. SCID mice have no functional B or T cells but do have a fully functional innate immune system. Using two-way ANOVA allowed for the isolation of genes showing a strain effect due to the SCID deficiency, genes showing a time effect due to the hookworm infection and genes showing interaction between the two effects. 1054 genes were identified with a strain effect p-value less than 0.001. 517 genes were identified with a time effect p-value less than 0.001. 54 genes were identified with an interaction p-value less than 0.001. Genes with a significant interaction p-value are those that show a time effect but only in one strain. Two prominent clusters of interaction genes were identified: one cluster showing decreased expression over time in the wild type but not SCID mice and one cluster showing increased expression in the wild type mice over time but no change in the SCID mice.

Scientific analysis of the dataset:
Archived Webinar:	[ view ]