Table 3. Chi-square tests of the relationship between genes functions and phylogenetic hypotheses.
| GO/KEGG category | A+ | A− | O+ | O− | X2 | P |
| A. Test of the Archosaur Hypothesis [((Zebra Finch, Chicken), Chinese Pond Turtle)] | ||||||
| Biological Process | ||||||
| organophosphate metabolic process (GO:0019637) | 61 (49) | 1975 (1987) | 46 (58) | 2342 (2030) | 5.3 | 0.0210 |
| hormone metabolic process (GO:0042445) | 49 (39) | 1987 (1997) | 35 (45) | 2353 (2343) | 5.2 | 0.0223 |
| macromolecule metabolic process (GO:0043170) | 1180 (1148) | 856 (888) | 1314 (1346) | 1074 (1042) | 3.8 | 0.0500 |
| primary metabolic process (GO:0044238) | 1419 (1385) | 617 (651) | 1590 (1624) | 798 (764) | 4.9 | 0.0269 |
| Cellular Component | ||||||
| organelle lumen (GO:0043233) | 682 (648) | 1354 (1388) | 726 (760) | 1662 (1628) | 4.8 | 0.0276 |
| extracellular matrix (GO:0031012) | 77 (65) | 1959 (1971) | 64 (76) | 2324 (2312) | 4.3 | 0.0376 |
| extracellular matrix part (GO:0044420) | 37 (25) | 1999 (2011) | 18 (30) | 2370 (2358) | 10.1 | 0.0015 |
| Molecular Function | ||||||
| nucleotide binding (GO:0000166) | 409 (381) | 1627 (1655) | 419 (447) | 1969 (1941) | 4.7 | 0.0307 |
| hormone binding (GO:0042562) | 25 (18) | 2011 (2018) | 15 (22) | 2373 (2366) | 4.4 | 0.0357 |
| cofactor binding (GO:0048037) | 72 (60) | 1964 (1976) | 59 (71) | 2329 (2317) | 4.3 | 0.0372 |
| KEGG pathway | ||||||
| inositol phosphate metabolism (map00562) | 28 (18) | 318 (328) | 10 (20) | 375 (365) | 11.2 | 0.0008 |
| phosphatidylinositol signaling system (map04070) | 31 (22) | 315 (324) | 15 (24) | 370 (361) | 7.9 | 0.0049 |
| arginine and proline metabolism (map00330) | 24 (18) | 322 (328) | 14 (20) | 371 (365) | 4.0 | 0.0448 |
| B. Test of the Lepidosaur Hypothesis [(Pond Turtle, Green Anole)] | ||||||
| Biological Process | ||||||
| cell activation (GO:0001775) | 76 (61) | 701 (716) | 274 (289) | 3373 (3358) | 4.5 | 0.0334 |
| translational initiation (GO:0006413) | 17 (10) | 760 (767) | 40 (47) | 3607 (3600) | 6.0 | 0.0143 |
| cellular component disassembly (GO:0022411) | 45 (34) | 732 (743) | 149 (160) | 3498 (3487) | 4.4 | 0.0350 |
| fertilization (GO:0009566) | 14 (8) | 763 (769) | 33 (39) | 3614 (3608) | 4.9 | 0.0268 |
| pollination (GO:0009856) | 16 (10) | 761 (767) | 40 (46) | 3607 (3601) | 4.7 | 0.0293 |
| system process (GO:0003008) | 156 (135) | 621 (642) | 610 (631) | 3037 (3016) | 5.0 | 0.0250 |
| digestion (GO:0007586) | 13 (6) | 764 (771) | 23 (30) | 3624 (3617) | 8.6 | 0.0033 |
| stem cell maintenance (GO:0019827) | 14 (8) | 763 (769) | 34 (40) | 3613 (3607) | 4.5 | 0.0336 |
| regulation of multi-organism process (GO:0043900) | 15 (9) | 762 (768) | 34 (40) | 3613 (3607) | 5.8 | 0.0158 |
| Cellular Component | ||||||
| cell projection (GO:0042995) | 130 (110) | 647 (667) | 499 (519) | 3148 (3128) | 4.9 | 0.0271 |
| membrane part (GO:0044425) | 329 (296) | 448 (481) | 1355 (1388) | 2292 (2259) | 7.3 | 0.0068 |
| Molecular Function | ||||||
| protein complex scaffold (GO:0032947) | 12 (5.6) | 765 (771) | 20 (26) | 3627 (3621) | 8.8 | 0.0029 |
| KEGG pathway | ||||||
| glycerolipid metabolism (map00561) | 14 (7) | 119 (126) | 25 (32) | 573 (566) | 8.7 | 0.0032 |
| glycerophospholipid metabolism (map00564) | 13 (7) | 120 (126) | 28 (34) | 570 (564) | 5.3 | 0.0210 |
Only significant results are presented. A: the archosaur hypothesis; L: the lepidosaur hypothesis; O: other hypotheses. +: number of genes which have a particular GO category or KEGG pathway; −: number of genes which do not have the GO category or KEGG pathway. Numbers in parentheses are expected numbers of genes under random distribution. For example, of the 2117 genes that support the Archosaur hypothesis, 2036 genes have the GO category of “biological process”; among them, 61 have the GO category of “organophosphate metabolic process” and 1975 genes do not have the term.