Table 5 |
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|
Motif similarity between neighboring unique promoters |
|||||||||||||||
|
Similara |
Intermediatea |
Differenta |
# of used pairs |
# of omitted pairs |
|||||||||||
|
|
|||||||||||||||
|
allb |
high qualityc |
capd |
all |
high quality |
cap |
all |
high quality |
cap |
all |
high quality |
cap |
all |
high quality |
cap |
|
|
|
|||||||||||||||
|
Observed value (shared motifs allowed) |
17.81 |
16.44 |
15.47 |
16.36 |
16.90 |
21.13 |
65.83 |
66.67 |
63.40 |
1516 |
1083 |
530 |
8224 |
4200 |
983 |
|
|
|||||||||||||||
|
Observed value (shared motifs not allowed) |
16.64 |
15.06 |
14.34 |
15.50 |
15.91 |
19.96 |
67.86 |
69.03 |
65.70 |
1484 |
1056 |
516 |
8256 |
4227 |
997 |
|
|
|||||||||||||||
|
Random meane |
8.48 |
8.25 |
7.60 |
10.45 |
10.96 |
11.96 |
81.07 |
80.79 |
80.44 |
1516 |
1083 |
530 |
8224 |
4200 |
983 |
|
|
|||||||||||||||
|
p-valuef (random >= observed value, shared motifs allowed) |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
-- |
-- |
-- |
-- |
-- |
-- |
|
|
|||||||||||||||
|
p-valuef (random <= observed value, shared motifs allowed) |
1 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
-- |
-- |
-- |
-- |
-- |
-- |
|
|
|||||||||||||||
|
p-valuef (random >= observed value, shared motifs not allowed) |
0 |
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
-- |
-- |
-- |
-- |
-- |
-- |
|
|
|||||||||||||||
|
p-valuef (random <= observed value, shared motifs not allowed) |
1 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
-- |
-- |
-- |
-- |
-- |
-- |
|
|
|||||||||||||||
|
apercentage of promoter pairs defined as similar, intermediate, and different (see Methods). bThe promoter set contains all promoters from Drosophila genome annotation release 5.5. cThe promoter set contains only high quality promoters in fly genome; see Methods. dThe promoter set contains only cap-supported promoters in fly genome; see Methods. emean of 10,000 randomizations. fempirical p-value calculated as the proportion of sampled randomizations where the percentage of the promoter pairs in each of the three similarity levels was no less than/no greater than the observed values. |
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|
Zhu and Halfon BMC Genomics 2009 10:9 doi:10.1186/1471-2164-10-9 |
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