Table 1.
Characterization of editing prediction pipeline
|
A | ||||
|---|---|---|---|---|
| # of all m.m. in Alu | # of A-to-I in Alu | A-to-I ration in all m.m. | ||
| STEP2: w/o PSS cutoff |
95,187 |
57,502 |
60.41% |
|
| STEP3: PSS cutoff |
8,721 |
7,266 |
83.32% |
|
| STEP4: in editing box |
1,995 |
1,995 |
100% |
|
|
B | ||||
| |
Alu |
Non-Alu repetitive |
Non-repetitive |
|
|
A-to-I |
Editing boxes (sites) |
238 (1995) |
7 (61) |
21 (189) |
| Ave. length (nt) |
~108 nt |
~86 nt |
~71 nt |
|
| |
Ave. conversion rate of As to Is |
~31% |
~40% |
~51% |
| A-to-C |
0 |
0 |
2 [14] |
|
| T-to-G |
0 |
0 |
1 [6] |
|
| A-to-T |
0 |
0 |
0 |
|
| T-to-A |
0 |
0 |
0 |
|
| C-to-A |
0 |
1 [6] |
1 [5]* |
|
| G-to-T |
0 |
0 |
1 [5] |
|
| C-to-G |
0 |
0 |
0 |
|
| G-to-C |
0 |
0 |
1 [5]* |
|
| C-to-T |
0 |
0 |
1 [5] |
|
| G-to-A |
0 |
0 |
1 [6]* |
|
|
C | ||||
| |
in IR AIu s |
within 1 kb to IR AIu s |
> 1 kb to IR AIu s |
|
| A-to-I editing boxes (sites) | 208 (1763) | 36 (310) | 24 (172) | |
(A) The enrichment of A-to-I conversion in Alu elements after each step of our computational flow. (B) Editing boxes/sites distribution in Alu, non-Alu repetitive and non-repetitive regions. Asterisk indicated non A-to-Gs (noncanonical editing) sites are validated to be false positives. (C) Editing boxes/sites distribution in IRAlus, within 1 kb to IRAlus and over 1 kb to IRAlus.