Table 2.
The gene ontology terms overrepresented in the set of genes down-regulated by at least 2-fold in adenocarcinomas
| Annotation term | Total | Found | Expected | P-value |
|---|---|---|---|---|
| GeneOntology terms | ||||
| Globin | 17 | 12 | 0.0E+00 | 0.0E+00 |
| Rhodopsin-like receptor activity | 384 | 49 | 3.8E−04 | 1.0E−06 |
| G-protein chemoattractant receptor activity | 34 | 8 | 2.8E−02 | 8.4E−04 |
| Peptide receptor activity | 139 | 23 | 1.7E−03 | 1.2E−05 |
| G-protein-coupled receptor binding | 52 | 21 | 0.0E+00 | 0.0E+00 |
| Defense/immunity protein activity | 230 | 39 | 0.0E+00 | 0.0E+00 |
| Antimicrobial peptide activity | 32 | 8 | 1.7E−02 | 5.4E−04 |
| Complement activity | 32 | 8 | 1.7E−02 | 5.4E−04 |
| Signal transducer activity | 2558 | 253 | 0.0E+00 | 0.0E+00 |
| Receptor activity | 1542 | 162 | 0.0E+00 | 0.0E+00 |
| Transmembrane receptor activity | 1083 | 121 | 0.0E+00 | 0.0E+00 |
| G-protein coupled receptor activity | 467 | 61 | 0.0E+00 | 0.0E+00 |
| Chemokine receptor activity | 34 | 8 | 2.8E−02 | 8.4E−04 |
| Receptor binding | 592 | 72 | 0.0E+00 | 0.0E+00 |
| Cytokine activity | 253 | 39 | 0.0E+00 | 0.0E+00 |
| Heavy metal binding | 23 | 8 | 9.4E−04 | 4.1E−05 |
| Sugar binding | 132 | 28 | 0.0E+00 | 0.0E+00 |
| Extracellular | 1085 | 138 | 0.0E+00 | 0.0E+00 |
| Extracellular space | 457 | 72 | 0.0E+00 | 0.0E+00 |
| Hemoglobin complex | 18 | 12 | 0.0E+00 | 0.0E+00 |
| Plasma membrane | 2297 | 219 | 0.0E+00 | 0.0E+00 |
| Integral to plasma membrane | 1702 | 176 | 0.0E+00 | 0.0E+00 |
| Oxygen and reactive oxygen species metabolism | 65 | 15 | 4.6E−04 | 7.0E−06 |
| Calcium ion homeostasis | 26 | 8 | 2.9E−03 | 1.1E−04 |
| Cell motility | 414 | 50 | 1.2E−03 | 3.0E−06 |
| Chemotaxis | 133 | 39 | 0.0E+00 | 0.0E+00 |
| Muscle contraction | 202 | 25 | 1.3E−01 | 6.2E−04 |
| Response to stress | 1025 | 143 | 0.0E+00 | 0.0E+00 |
| Defense response | 1031 | 169 | 0.0E+00 | 0.0E+00 |
| Inflammatory response | 218 | 50 | 0.0E+00 | 0.0E+00 |
| Immune response | 950 | 153 | 0.0E+00 | 0.0E+00 |
| Humoral immune response | 235 | 38 | 0.0E+00 | 0.0E+00 |
| Antimicrobial humoral response (sensu Invertebrata) | 145 | 24 | 1.2E−03 | 8.0E−06 |
| Cellular defense response | 139 | 45 | 0.0E+00 | 0.0E+00 |
| Cell communication | 3667 | 326 | 0.0E+00 | 0.0E+00 |
| Cell adhesion | 658 | 84 | 0.0E+00 | 0.0E+00 |
| Heterophilic cell adhesion | 97 | 20 | 9.7E−05 | 1.0E−06 |
| Signal transduction | 2947 | 254 | 0.0E+00 | 0.0E+00 |
| Cell surface receptor linked signal transduction | 1124 | 117 | 0.0E+00 | 0.0E+00 |
| G-protein coupled receptor protein signaling pathway | 657 | 77 | 0.0E+00 | 0.0E+00 |
| Cytosolic calcium ion concentration elevation | 49 | 10 | 3.2E−02 | 6.5E−04 |
| Cell-cell signaling | 689 | 64 | 3.7E−01 | 5.4E−04 |
| Development | 1920 | 150 | 1.5E+00 | 8.1E−04 |
| Histogenesis and organogenesis | 125 | 18 | 7.5E−02 | 6.0E−04 |
| Muscle development | 167 | 27 | 5.0E−04 | 3.0E−06 |
| Respiratory gaseous exchange | 36 | 11 | 2.2E−04 | 6.0E−06 |
| Chemokine activity | 52 | 21 | 0.0E+00 | 0.0E+00 |
| Circulation | 142 | 22 | 7.2E−03 | 5.1E−05 |
| Peptide receptor activity/G-protein coupled | 139 | 23 | 1.7E−03 | 1.2E−05 |
| Response to external stimulus | 1591 | 210 | 0.0E+00 | 0.0E+00 |
| Response to biotic stimulus | 1126 | 179 | 0.0E+00 | 0.0E+00 |
| Response to wounding | 356 | 91 | 0.0E+00 | 0.0E+00 |
| Response to pest/pathogen/parasite | 596 | 123 | 0.0E+00 | 0.0E+00 |
| Response to bacteria | 19 | 6 | 1.3E−02 | 7.1E−04 |
| Response to abiotic stimulus | 577 | 71 | 0.0E+00 | 0.0E+00 |
| Morphogenesis | 1119 | 101 | 4.9E−02 | 4.4E−05 |
| Organogenesis | 1029 | 91 | 2.2E−01 | 2.2E−04 |
| Cellular process | 7140 | 534 | 0.0E+00 | 0.0E+00 |
| Membrane | 4225 | 356 | 0.0E+00 | 0.0E+00 |
| Integral to membrane | 3220 | 281 | 0.0E+00 | 0.0E+00 |
| Cell growth | 97 | 17 | 7.3E−03 | 7.5E−05 |
| Humoral defense mechanism (sensu Invertebrata) | 145 | 24 | 1.2E−03 | 8.0E−06 |
| Cell–cell adhesion | 220 | 30 | 6.8E−03 | 3.1E−05 |
| Antimicrobial humoral response | 145 | 24 | 1.2E−03 | 8.0E−06 |
| Cytolysis | 20 | 8 | 2.4E−04 | 1.2E−05 |
| Cytokine binding | 80 | 14 | 2.6E−02 | 3.2E−04 |
| Chemokine binding | 34 | 8 | 2.8E−02 | 8.4E−04 |
| Carbohydrate binding | 133 | 28 | 0.0E+00 | 0.0E+00 |
| Chemoattractant activity | 52 | 21 | 0.0E+00 | 0.0E+00 |
| Response to chemical substance | 206 | 48 | 0.0E+00 | 0.0E+00 |
| Peptide binding | 213 | 26 | 1.3E−01 | 6.1E−04 |
| Taxis | 133 | 39 | 0.0E+00 | 0.0E+00 |
| Chemokine receptor binding | 52 | 21 | 0.0E+00 | 0.0E+00 |
| Innate immune response | 220 | 50 | 0.0E+00 | 0.0E+00 |
| Eicosanoid biosynthesis | 25 | 7 | 1.4E−02 | 5.7E−04 |
| Protein domain | ||||
| Vertebrate metallothionein | 12 | 7 | 2.4E−05 | 2.0E−06 |
| Aspartic acid and asparagine hydroxylation site | 143 | 21 | 3.5E−02 | 2.5E−04 |
| Rhodopsin-like GPCR superfamily | 289 | 42 | 0.0E+00 | 0.0E+00 |
| Endothelin receptor | 6 | 4 | 1.3E−03 | 2.1E−04 |
| Small chemokine, C-C subfamily | 26 | 11 | 0.0E+00 | 0.0E+00 |
| Fos transforming protein | 13 | 6 | 9.5E−04 | 7.3E−05 |
| Thrombospondin, type I | 52 | 13 | 7.8E−04 | 1.5E−05 |
| Globin | 16 | 12 | 0.0E+00 | 0.0E+00 |
| Small chemokine, C-X-C subfamily | 18 | 6 | 1.1E−02 | 6.0E−04 |
| C-type lectin | 95 | 19 | 5.7E−04 | 6.0E−06 |
| Alpha crystallin | 8 | 4 | 7.2E−03 | 9.0E−04 |
| Myelin proteolipid protein (PLP) | 7 | 6 | 0.0E+00 | 0.0E+00 |
| Zn-binding protein, LIM | 95 | 18 | 2.2E−03 | 2.3E−05 |
| Small chemokine, interleukin-8 like | 48 | 20 | 0.0E+00 | 0.0E+00 |
| EGF-like calcium-binding | 147 | 21 | 5.3E−02 | 3.6E−04 |
| Heat shock protein Hsp20 | 8 | 4 | 7.2E−03 | 9.0E−04 |
| Fibrinogen, beta/gamma chain, C-terminal globular | 38 | 10 | 3.4E−03 | 8.9E−05 |
| P2 purinoceptor | 21 | 7 | 4.3E−03 | 2.1E−04 |
| Myoglobin | 9 | 6 | 3.6E−05 | 4.0E−06 |
| Beta haemoglobin | 8 | 7 | 0.0E+00 | 0.0E+00 |
| Alpha haemoglobin | 6 | 5 | 3.6E−05 | 6.0E−06 |
| Pi haemoglobin | 6 | 5 | 3.6E−05 | 6.0E−06 |
| Small chemokine, C-X-C/Interleukin 8 | 18 | 8 | 1.1E−04 | 6.0E−06 |
| Metallothionein superfamily | 12 | 7 | 2.4E−05 | 2.0E−06 |
| Orphan nuclear receptor | 9 | 5 | 9.1E−04 | 1.0E−04 |
| Immunoglobulin C-2 type | 223 | 31 | 6.2E−03 | 2.8E−05 |
| Immunoglobulin subtype | 368 | 48 | 3.7E−04 | 1.0E−06 |
| PMP-22/EMP/MP20 family | 8 | 4 | 7.2E−03 | 9.0E−04 |
| L1 transposable element | 8 | 4 | 7.2E−03 | 9.0E−04 |
| EGF-like domain | 431 | 46 | 1.4E−01 | 3.3E−04 |
| Type I EGF | 169 | 23 | 6.7E−02 | 4.0E−04 |
| AIG1 family | 6 | 4 | 1.3E−03 | 2.1E−04 |
| BRICHOS domain | 13 | 8 | 0.0E+00 | 0.0E+00 |
| Immunoglobulin-like | 678 | 75 | 6.8E−04 | 1.0E−06 |
| LST-1 | 6 | 6 | 0.0E+00 | 0.0E+00 |
| Thrombospondin, subtype 1 | 27 | 8 | 5.0E−03 | 1.8E−04 |
| Saposin-like type B, 2 | 7 | 5 | 1.3E−04 | 1.9E−05 |
| Saposin B | 12 | 5 | 6.5E−03 | 5.4E−04 |
| Pathway | ||||
| GPCRs_Class_A_Rhodopsin-like | 212 | 34 | 0.0E+00 | 0.0E+00 |
| Peptide_GPCRs | 88 | 20 | 0.0E+00 | 0.0E+00 |
| MAP00590//Prostaglandin and leukotriene metabolism | 41 | 9 | 3.2E−02 | 7.7E−04 |
| GPCRs_Class_B_Secretin-like | 34 | 10 | 9.2E−04 | 2.7E−05 |
| Chromosomal location | ||||
| 12p | 301 | 32 | 2.4E−01 | 8.1E−04 |
| 8p21 | 117 | 18 | 1.8E−02 | 1.5E−04 |
| 17q23 | 68 | 14 | 2.2E−03 | 3.2E−05 |
| 16q13 | 37 | 12 | 3.7E−05 | 1.0E−06 |
For each gene ontology term, the total number of genes with this term in the HG-U133A GeneChip, the total number of genes carrying that term in MAD, the P-value of this and the expected number of genes are tabulated. The member genes for each gene ontology term can be downloaded at http://bioinfo.hku.hk/~daniely/lung_microarray.