Table 2. Functional Classification of Differentially Expressed Genes in Colon Tumor versus Adjacent Normal Tissue.
| Differentially Expressed Genes in Tumor vs. Normal Colon Tissue (n=1573 genes) | Differentially Expressed Genes Located in Regions of Recurrent CNA (n=356 genes) | Differentially Expressed Genes Located in Regions of Recurrent CNAs in Adenomas* (n=248 genes) | Differentially Expressed Genes Located in Regions of Recurrent CNAs in Caricinomas** (n=108 genes) | |
|---|---|---|---|---|
|
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| Ingenuity Pathway Analysis | ||||
|
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| disease and disorder | Cancer | Cancer | Cancer | Developmental Disorder |
| disease and disorder | Gastrointestinal Disease | Gastrointestinal Disease | Gastrointestinal Disease | Genetic Disorder |
|
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| molecular and cellular functions | Cellular Growth and Proliferation | Cell Cycle | Cell Cycle | Cell Cycle |
| molecular and cellular functions | Cell Cycle | Cell Death | Cell Death | Cell-to-Cell Signaling and Interaction |
|
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| networks | DNA Replication Recombination, and Repair; RNA Post-Transcriptional Modification; Cell Cycle | DNA Replication, Recombination, and Repair; Cell Cycle; Gene Expression | Cell Cycle; Gene Expression; Amino Acid Metabolism | Cell-To-Cell Signaling and Interaction; Connective Tissue Dev and Func; Cardiovasular System Development and Function |
| networks | Cell Cycle; Cellular Assembly and Organization; DNA Replication, Recombination, and Repair | Molecular Transport; Small Molecule Biochemistry; Genetic Disorder | Cell Cycle; Cancer; DNA Replication, Recombination, and Repair | Cell Cycle; DNA Replication, Recombination, and Repair; Reproductive System Disease |
|
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| Gene Ontology Enrichment Analysis*** | ||||
|
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| biological processes | cellular process (ES=41) | cellular process (ES=29.8) | cellular process and growth functions (ES=23.9) | cellular process (ES=8.2) |
| cell proliferation (ES=18) | metabolic process (ES=8.3) | growth (ES=7.4) | metabolic process (ES=6.8) | |
| developmental process (ES=11) | cell proliferation (ES=6.8) | cellular proliferation (ES=6.9) | ||
| metabolic process (ES=9.2) | growth (ES=5.3) | metabololic process (ES=4.26) | ||
| biological adhesion (ES=8.5) | rhythmic process (ES=3.5) | rhythmic process (ES=3.1) | ||
| growth (ES=6.3) | ||||
| rhythmic process (ES=3.6) | ||||
|
| ||||
| molecular functions | catalytic activity (ES=41.6) | catalytic activity (ES=19.6) | catalytic activity and binding (ES=11.0) | catalytic activity (ES=10.7) |
| binding (ES=22.4) | binding (ES=11.4) | binding (ES=10.9) | ||
| antioxidant activity (ES=4.1) | translation regulatory activity (ES=3.3) | |||
| translation regulator activity (ES=3.0) | ||||
|
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| cellular components | extracellular region part (ES=26) | cell part (ES=6.0) | cell part (ES=11.8) | |
| extracellular region (ES=14) | ||||
| cell part (ES=4.8) | ||||
*
Genomic regions with frequent copy number alterations associated with adenomas.
**
Genomic regions with frequent copy number alteraions that were not observed in adenomas, but observed in carcinomas.
***
The Enrichment Score (ES) reflects the degree to which the set of differentially expressed genes is enriched for the ontologic term or phenotype.