Changes in colon gene expression associated with increased colon inflammation in interleukin-10 gene-deficient mice inoculated with Enterococcus species

Table 2 Number of differentially expressed genes in colon tissue of Il10^-/- mice compared to C57 mice

	Differentially expressed genes (q< 0.05)			Ingenuity Pathways Analysis
Comparison	Increase	Decrease	Total	Network eligible	Fold-change cut-off	Functions/pathways/lists eligible
Between strain comparisons(Il10 ^-/- vs. C57)
SPF	76	46	122	45	N/A	38
C	115	70	185	90	N/A	80
EF	2,258	2,565	4,823	2,494	\|1.70\|	740
CIF	1,630	1,845	3,475	1,136	\|1.42\|	736
EF·CIF	2,111	2,074	4,185	2,138	\|1.47\|	740
Within strain comparisons (Il10 ^-/- )
EF vs. C	1,602	2,028	3,630	1,085	\|1.36\|	746
CIF vs. C	756	734	1,490	463	N/A	421
EF·CIF vs. C	1,572	2,231	3,808	1,030	\|1.36\|	723

Data represent numbers of differentially expressed genes for each comparison, calculated using BioConductor 'limma analysis' package. False discovery rate control of q < 0.05 was used as a filtering criterion, and the fold-change cut-off listed applied to each group to reduce the Network Eligible genes for Ingenuity Pathways Analysis to 800 ± 1. The most significant functions were identified using Ingenuity Pathway Analysis Software. Total RNA from colon tissue was used for microarray hybridization to Agilent Technologies 44 k (G4122-60510) mouse 60 mer oligonucleotide arrays. Data represent mean values from two pools of RNA for each mouse strain, with RNA from either two or three mice in each pool.

ISSN: 1471-2172