Table 3 |
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|
Comparison of genome localization by retroelement lineage |
||||||||
| Hypotheses |
Test |
Group(s) tested |
p-values by chromosome |
Accept? |
||||
|
|
||||||||
| 1 |
2 |
3 |
4 |
5 |
||||
|
|
||||||||
| All families are randomly distributed according to a uniform distribution |
Uniform goodness of fit, 10,000 random permutations |
MV(F) |
0.0000 |
0.0000 |
0.0000 |
0.0000 |
0.0000 |
No |
| PV(F) |
0.0000 |
0.0007 |
0.0000 |
0.0022 |
0.0464 |
No |
||
| MV(S) |
0.0000 |
0.0000 |
0.0000 |
0.0000 |
0.0000 |
No |
||
| PV(S) |
0.0000 |
0.0000 |
0.0000 |
0.0000 |
0.0000 |
No |
||
| MV(R) |
0.0000 |
0.0000 |
0.0000 |
0.0000 |
0.0000 |
No |
||
| PV(R) |
0.0000 |
0.0007 |
0.0000 |
0.0097 |
0.0000 |
No |
||
| NL(R) |
0.0000 |
0.0000 |
0.0000 |
0.0002 |
0.0000 |
No |
||
| Retroelement family distributions are organized similarly in the genome |
MRPP, 10,000 random permutations |
MV(FSR), PV(FSR), NL(R) |
0.0000 |
0.0000 |
0.0000 |
0.0000 |
0.0000 |
No |
| MV(FSR), PV(FSR) |
0.0000 |
0.0000 |
0.0000 |
0.0000 |
0.0000 |
No |
||
| MV(FSR), NL(R) |
0.0000 |
0.0000 |
0.0000 |
0.0000 |
0.0000 |
No |
||
| PV(FSR), NL(R) |
0.3498 |
0.8326 |
0.0241 |
0.1468 |
0.1417 |
Yes |
||
| All Metaviridae sublineages have similar distributions |
MRPP, 10,000 random permutations |
MV Athila, Metavirus, Tat |
0.2200 |
0.1365 |
0.5676 |
0.4174 |
0.2788 |
Yes |
| MV Athila, Metavirus |
0.1057 |
0.3010 |
0.2657 |
0.4526 |
0.4453 |
Yes |
||
| MV Athila, Tat |
0.1687 |
0.0970 |
0.7116 |
0.3773 |
0.2781 |
Yes |
||
| MV Metavirus, Tat |
0.4903 |
0.1268 |
0.7341 |
0.5753 |
0.2361 |
Yes |
||
| Metaviridae subtypes have similar distributions |
MRPP, 10,000 random permutations |
MV(FSR) |
0.7742 |
0.1247 |
0.0000 |
0.7425 |
0.0659 |
Yes |
| MV(FS) |
0.4544 |
0.1357 |
0.0003 |
0.4435 |
0.7241 |
Yes |
||
| MV(FR) |
0.5184 |
0.9461 |
0.5750 |
0.5480 |
0.2135 |
Yes |
||
| MV(SR) |
0.9068 |
0.1339 |
0.0051 |
0.8194 |
0.0157 |
Yes |
||
| Pseudoviridae subtypes have similar distributions |
MRPP, 10,000 random permutations |
PV(FSR) |
0.0509 |
0.2039 |
0.2199 |
0.0953 |
0.0379 |
Yes |
| PV(FS) |
0.2732 |
0.0853 |
0.2665 |
0.6567 |
0.0453 |
Yes |
||
| PV(FR) |
0.0136 |
0.5055 |
0.1185 |
0.0521 |
0.0281 |
Yes |
||
| PV(SR) |
0.0743 |
0.5604 |
0.2513 |
0.0307 |
0.3476 |
Yes |
||
|
|
||||||||
|
MV, Metaviridae; PV, Pseudoviridae; NL, non-LTR retrotransposon; R, RT-only; S, solo LTR; F, full-length element. p-values < 0.05 are displayed in bold text. |
||||||||
|
Peterson-Burch et al. Genome Biology 2004 5:R78 doi:10.1186/gb-2004-5-10-r78 |
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