Table 2.
Functional annotation analysis of differentially expressed genes
| Biological processes affected by over-expression of wild type and truncated HMGA2 | |
|---|---|
| Vascular development (4 of 66 up-regulated genes) | p = 0.039 |
| Response to wounding (17 of 139 down-regulated genes) | p < 0.001 |
| Signal transduction (40/139) | p < 0.001 |
| Chemotaxis (11/139) | p < 0.001 |
| Cytosolic calcium ion homeostasis (5/139) | p < 0.001 |
| Phosphate transport (5/139) | p = 0.0017 |
| Regulation of cell proliferation (11/139) | p = 0.0033 |
| Cell migration (8/139) | p = 0.0057 |
| Cell recognition (3/139) | p = 0.027 |
| Epithelial cell differentiation (3/139) | p = 0.026 |
| Wound healing (4/139) | p = 0.042 |
| Biological processes affected by over-expression of wild type HMGA2 | |
| Multi-cellular organismal development (20 of 84 up-regulated genes) | p = 0.0011 |
| Response to hormone stimulus (4/84) | p = 0.0034 |
| Regulation of signal transduction (7/84) | p = 0.022 |
| Pyridine nucleotide biosynthetic process (3 of 99 down-regulated genes) | p = 0.0017 |
| Steroid hormone receptor activity (3/99) | p = 0.0032 |
| Negative regulation of transcription factor activity (3/99) | p = 0.0034 |
| Positive regulation of transcription (7/99) | p = 0.0065 |
| Response to external stimulus (8/99) | p = 0.042 |
| Biological processes affected by over-expression of truncated HMGA2 | |
| Regulation of transcription (61 of 258 up-regulated genes) | p < 0.001 |
| Intracellular protein transport across a membrane (6/258) | p = 0.0032 |
| Membrane organization and biogenesis (11/258) | p = 0.011 |
| Ras protein signaling transduction (9/258) | p = 0.031 |
| Regulation of cytoskeleton organization and biogenesis (4/258) | p = 0.042 |
| Antigen processing and presentation (10 of 239 down-regulated genes) | p < 0.001 |
| Multi-cellular organismal development (41/239) | p = 0.0021 |
| Cell adhesion (16/239) | p = 0.019 |
| Eye morphogenesis (3/239) | p = 0.035 |
The genes were classified into biological processes using gene ontology terms. Each biological process was determined if it was significantly over- or underrepresented (p < 0.05) by comparing the observed frequency of genes to the expected frequency of genes on the Affymetrix GeneChip that cover 50 547 known genes. Significantly over- or under-represented processes were grouped and ranked according to the geometric mean of their p-values. A representative annotation term for each cluster, the number of genes associated with the term and its p-value was listed.