Table 2 |
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|
Indel density for annotation features (across all 44 ENCODE regions) |
|||||||
|
Indels |
Rate (number per 100 kb) |
Rate (bp per 100 kb) |
|||||
|
|
|||||||
|
n |
bp |
n |
99% CI |
bp |
99% CI |
Feature length (kb) |
|
|
|
|||||||
|
Manual |
2,186 |
6,504 |
14.6 |
11.7 to 18.2 |
43.4 |
34.4 to 54.7 |
14,998 |
|
Random |
2,300 |
6,506 |
15.3 |
13.6 to 17.3 |
43.4 |
37.5 to 50.2 |
15,000 |
|
Overall |
4,486 |
13,010 |
15.0 |
13.4 to 16.7 |
43.4 |
38.3 to 49.1 |
29,998 |
|
RNA transcription |
|||||||
|
CDS |
5 |
5 |
0.7 |
0.1 to 8.6 |
0.7 |
0.1 to 8.6 |
675 |
|
TSS |
2 |
2 |
3.3 |
3.3 |
61 |
||
|
RACEfrags |
9 |
28 |
2.1 |
0.8 to 5.4 |
6.6 |
1.3 to 33.9 |
425 |
|
TARs/transfrags |
37 |
78 |
5.8 |
3.5 to 9.6 |
12.3 |
6.8 to 22.3 |
634 |
|
Pseudo-exons |
9 |
26 |
6.6 |
2.6 to 16.6 |
19.1 |
5.8 to 63.3 |
136 |
|
3' UTR |
48 |
103 |
11.0 |
7.2 to 16.7 |
23.6 |
13.5 to 41.3 |
436 |
|
5' UTR |
7 |
32 |
6.0 |
1.6 to 22.3 |
27.4 |
3.8 to 198.7 |
117 |
|
TUF |
53 |
160 |
12.2 |
7.8 to 19.2 |
36.9 |
20.2 to 67.6 |
433 |
|
Open chromatin |
|||||||
|
FAIRE-sites |
106 |
327 |
7.7 |
5.6 to 10.6 |
23.8 |
15.5 to 36.7 |
1,372 |
|
DHS (NHGRI) |
19 |
61 |
6.1 |
3.3 to 11.3 |
19.7 |
8.3 to 46.9 |
310 |
|
DHS (Regulome) |
43 |
135 |
8.6 |
5.3 to 14.0 |
27.0 |
13.4 to 54.4 |
499 |
|
DNA-protein intreraction/transcript regulation |
|||||||
|
HisPolTAF |
141 |
348 |
13.1 |
10.0 to 17.2 |
32.4 |
22.5 to 46.5 |
1,076 |
|
Seq_specific (all motifs) |
131 |
420 |
11.2 |
8.3 to 15.0 |
35.8 |
23.1 to 55.3 |
1,174 |
|
SeqSp (sequence specific factors) |
54 |
225 |
10.2 |
6.2 to 16.7 |
42.5 |
20.1 to 89.5 |
530 |
|
Ancestral repeats |
532 |
1,592 |
7.9 |
6.7 to 9.2 |
26.5 |
21.7 to 32.5 |
5,998 |
|
Evolutionary constraint |
|||||||
|
MCS strict |
19 |
31 |
2.5 |
1.3 to 5.1 |
4.1 |
1.6 to 10.4 |
748 |
|
MCS moderate |
78 |
170 |
5.1 |
3.5 to 7.6 |
11.2 |
6.8 to 18.5 |
1,515 |
|
MCS loose |
356 |
960 |
9.8 |
8.2 to 11.7 |
26.4 |
20.9 to 33.4 |
3,637 |
|
Cell cycle |
|||||||
|
EarlyRepSeg |
1,124 |
2,989 |
16.4 |
13.8 to 19.4 |
43.5 |
33.3 to 56.9 |
6,868 |
|
MidRepSeg |
1,190 |
3,352 |
15.4 |
13.5 to 17.5 |
43.2 |
35.3 to 53.0 |
7,751 |
|
LateRepSeg |
1,110 |
3,345 |
13.9 |
12.1 to 15.9 |
41.9 |
32.9 to 53.3 |
7,991 |
|
|
|||||||
|
bp, base pairs; CDS, coding sequence; CI, confidence interval; DHS, DNAse hypersensitive sites; ENCODE, Encyclopedia of DNA Elements; FAIRE, formaldehyde assisted isolation of regulatory elements; kb, kilobases; MCS, multi-species conserved sequence; NHGRI, National Human Genome Research Institute; transfrag, transcribed fragment; RACEfrag, rapid amplification of cDNA ends fragment; TAR, transcriptionally active region; TSS, transcription start site; TUF, transcripts of unknown function; UTR, untranslated region. |
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|
Clark et al. Genome Biology 2007 8:R180 doi:10.1186/gb-2007-8-9-r180 |
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