Table 5 |
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|
Comparison of ENCODE and Bhangale et al. (ten ENCODE regions) indel data |
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|
ENCODE (44 ENCODE regions/Baylor) |
Bhangale et al. (ten ENCODE regions/Baylor) |
|||||||
|
|
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|
Indels |
Rate (per 100 kb) |
Indels |
Rate (per 100 kb) |
|||||
|
|
||||||||
|
n |
bp |
n |
bp |
n |
bp |
n |
bp |
|
|
|
||||||||
|
Manual |
2,186 |
6,504 |
14.6 |
43.4 |
362 |
1,122 |
13.0 |
40.4 |
|
Random |
2,300 |
6,506 |
15.3 |
43.4 |
502 |
1,350 |
14.3 |
38.6 |
|
Overall |
4,486 |
13,010 |
15.0 |
43.4 |
864 |
2,472 |
13.8 |
39.4 |
|
RNA transcription |
||||||||
|
CDS |
5 |
5 |
0.7 |
0.7 |
1 |
1 |
1.2 |
1.2 |
|
TSS |
2 |
2 |
3.3 |
3.3 |
0 |
0 |
0.0 |
0.0 |
|
RACEfrags |
9 |
28 |
2.1 |
6.6 |
0 |
0 |
0.0 |
0.0 |
|
TARs/transfrags |
37 |
78 |
5.8 |
12.3 |
6 |
11 |
7.5 |
13.7 |
|
Pseudo-exons |
9 |
26 |
6.6 |
19.1 |
2 |
10 |
9.7 |
48.7 |
|
3' UTR |
48 |
103 |
11.0 |
23.6 |
11 |
29 |
18.7 |
49.2 |
|
5' UTR |
7 |
32 |
6.0 |
27.4 |
4 |
8 |
37.3 |
74.6 |
|
TUF |
53 |
160 |
12.2 |
36.9 |
4 |
18 |
8.1 |
36.4 |
|
Open chromatin |
||||||||
|
FAIRE sites |
106 |
327 |
7.7 |
23.8 |
17 |
72 |
5.6 |
23.6 |
|
DHS (NHGRI) |
19 |
61 |
6.1 |
19.7 |
1 |
1 |
2.8 |
2.8 |
|
DHS (Regulome) |
43 |
135 |
8.6 |
27.0 |
15 |
40 |
8.5 |
22.6 |
|
DNA-protein intreraction/transcript Regulation |
||||||||
|
HisPolTAF |
141 |
348 |
13.1 |
32.4 |
32 |
114 |
12.8 |
45.5 |
|
Seq_specific (all motifs) |
131 |
420 |
11.2 |
35.8 |
28 |
122 |
33.4 |
145.3 |
|
SeqSp (sequence specific factors) |
54 |
225 |
10.2 |
42.5 |
9 |
45 |
5.1 |
25.6 |
|
Ancestral repeats |
532 |
1,592 |
7.9 |
26.5 |
110 |
280 |
8.7 |
22.1 |
|
Evolutionary constraint |
||||||||
|
MCS strict |
19 |
31 |
2.5 |
4.1 |
5 |
9 |
3.3 |
5.9 |
|
MCS moderate |
78 |
170 |
5.1 |
11.2 |
17 |
36 |
5.4 |
11.4 |
|
MCS loose |
356 |
960 |
9.8 |
26.4 |
63 |
136 |
8.4 |
18.1 |
|
Cell cycle |
||||||||
|
EarlyRepSeg |
1,124 |
2,989 |
16.4 |
43.5 |
161 |
495 |
16.4 |
50.4 |
|
MidRepSeg |
1,190 |
3,352 |
15.4 |
43.2 |
270 |
797 |
16.4 |
48.3 |
|
LateRepSeg |
1,110 |
3,345 |
13.9 |
41.9 |
300 |
819 |
11.3 |
31.0 |
|
|
||||||||
|
Both datasets (Encyclopedia of DNA Elements [ENCODE] and that reported by Bhangale and coworkers [19]) are based on a subset of 8 African Americans (the Baylor samples). 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; SNP, single nucleotide polymorphism; 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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