TABLE 2.
Gene ontology terms that showed the most significant gene expression alterations in the enterocytes of IE-Cpr-null mice
Pathway analysis was performed using GenMAPP 2.1, MAPP Finder 2.0, and the Mm-std_20070817.gdb database (available at the GenMAPP Web site). The criteria for identification of genes with significantly increased or decreased expression were as follows: fold change ≥ 25% (≥1.25 or ≤0.80) and p ≤ 0.05. GO terms are sorted into three types: biological process, molecular function, and cellular component. For each GO term, the number of genes that meet the criteria for a significant increase or decrease was determined (No. changed). This number was compared with the number of genes in the GO term that are measured by the MOE 430A chip (No. of genes measured), for the calculation of the percentage of genes measured in the GO term that meet the criteria for a significant increase or decrease (% changed, in parentheses). z score, a standardized difference score for comparison of the relative extents of gene expression changes in various GO nodes, was also shown. The pathways shown were filtered using the following criteria: percent changed ≥ 10%, z score ≥ 4.0, and number changed ≥ 4. Redundant pathways were excluded. The specific genes meeting the criteria for changed expression in each GO term are shown in supplemental Tables 3 and 4.
| GO term | No. of genes in GO term | No. of genes measured | No. of genes changed (% changed) | z score |
|---|---|---|---|---|
| Significantly increased | ||||
| Biological process | ||||
| Antigen processing and presentation | 73 | 44 | 11 (25.0%) | 14.1 |
| Isoprenoid biosynthetic process | 18 | 10 | 6 (60/0%) | 16.6 |
| Negative regulation of transferase activity | 54 | 40 | 4 (10.0%) | 4.9 |
| Steroid metabolic process | 145 | 92 | 15 (16.3%) | 12.9 |
| Cellular component | ||||
| Multivesicular body | 10 | 7 | 4 (70.0%) | 13.2 |
| MHC protein complex | 47 | 24 | 8 (33.3%) | 14.0 |
| Significantly decreased | ||||
| Biological process | ||||
| Hormone metabolic process | 82 | 41 | 6 (14.6%) | 5.6 |
| Molecular function | ||||
| Serine esterase activity | 36 | 31 | 4 (12.9%) | 4.2 |
| Oxidoreductase activity, incorporation, or reduction of molecular oxygen | 143 | 84 | 9 (10.7%) | 5.5 |
| Cellular component | ||||
| Apical part of the cell | 69 | 50 | 6 (12%) | 4.8 |