Table 5 |
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|
Pfam domains and the undergoing events – Gene & events distribution$ |
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|
Percent fraction of genes that show the following events with the domain. |
Percent fraction of events as per the following types with the domain |
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|
Pfam domain |
No. of Genes that encode the domain (in how many of these genes, the domain undergoes change) |
insertion/deletion Gene-% |
Truncation Gene-% |
insertion/deletion Event-% |
Truncation Event-% |
|
|
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|
Pkinase |
149 (139) |
29% |
77% |
27% |
72% |
|
48 (4) |
2% |
6% |
25% |
75% |
|
|
zf-C2H2 |
138 (106) |
75% |
1% |
98% |
1% |
|
127 (61) |
48% |
0% |
100% |
0% |
|
|
C1-set |
108 (86) |
37% |
43% |
46% |
53% |
|
2 (1) |
50% |
0% |
100% |
0% |
|
|
PH |
94 (73) |
62% |
25% |
71% |
28% |
|
50 (24) |
44% |
12% |
78% |
21% |
|
|
Ank |
67 (55) |
80% |
7% |
91% |
8% |
|
72 (25) |
34% |
5% |
86% |
13% |
|
|
ig |
62 (52) |
82% |
8% |
91% |
8% |
|
Not seen in ASD |
|||||
|
fn3 |
59 (49) |
77% |
30% |
71% |
28% |
|
21 (6) |
28% |
4% |
85% |
14% |
|
|
SPRY |
59 (48) |
77% |
5% |
93% |
6% |
|
4 (3) |
75% |
0% |
100% |
0% |
|
|
Trypsin |
47 (47) |
42% |
68% |
38% |
61% |
|
36 (29) |
30% |
55% |
35% |
64% |
|
|
PDZ |
65 (46) |
66% |
27% |
70% |
29% |
|
42 (20) |
42% |
11% |
78% |
21% |
|
|
zf-C3HC4 |
72 (46) |
61% |
4% |
93% |
6% |
|
14 (7) |
50% |
0% |
100% |
0% |
|
|
Collagen |
51 (45) |
88% |
37% |
70% |
29% |
|
12 (8) |
66% |
0% |
100% |
0% |
|
|
KRAB |
90 (43) |
46% |
2% |
95% |
4% |
|
69 (34) |
49% |
1% |
97% |
2% |
|
|
SH3_1 |
77 (43) |
51% |
9% |
85% |
14% |
|
45 (4) |
8% |
0% |
100% |
0% |
|
|
WD40 |
48 (43) |
83% |
18% |
81% |
18% |
|
90 (35) |
38% |
2% |
94% |
5% |
|
|
Sushi |
40 (40) |
97% |
27% |
78% |
22% |
|
23 (17) |
73% |
4% |
94% |
5% |
|
|
EGF |
48 (40) |
83% |
8% |
90% |
9% |
|
27 (5) |
18% |
0% |
100% |
0% |
|
|
Ras |
41 (39) |
4% |
92% |
5% |
95% |
|
Not present in ASD |
|||||
|
Helicase_C |
51 (38) |
62% |
35% |
64% |
36% |
|
27 (13) |
44% |
11% |
80% |
20% |
|
|
RRM_1 |
43 (38) |
72% |
46% |
60% |
39% |
|
45 (24) |
46% |
20% |
70% |
30% |
|
|
MHC_I |
50 (35) |
12% |
70% |
14% |
85% |
|
5 (3) |
0% |
60% |
0% |
100% |
|
|
ABC_tran |
36 (33) |
50% |
80% |
38% |
61% |
|
18 (13) |
38% |
61% |
38% |
61% |
|
|
zf-B_box |
47 (33) |
46% |
25% |
64% |
35% |
|
14 (3) |
21% |
0% |
100% |
0% |
|
|
C2 |
44 (32) |
61% |
36% |
62% |
37% |
|
30 (17) |
53% |
10% |
84% |
15% |
|
|
LIM |
23 (22) |
82% |
39% |
67% |
32% |
|
27 (20) |
74% |
14% |
83% |
16% |
|
|
Mito_carr |
23 (22) |
91% |
73% |
55% |
44% |
|
22 (19) |
86% |
59% |
59% |
40% |
|
|
|
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|
$, Line 1 gives the values from Vega data set and Line 2 gives the values from ASD data set. Domains that particularly undergo insertion/deletion events in a higher fraction of genes (containing the specific domain) as compared to truncation events are: zf-C2H2, PH, Ank, SPRY, KRAB, WD40, Sushi, and EGF. Domains that undergo truncation events in higher fraction of genes (containing the specific domain) as compared to insertion/deletion events: Trypsin, Ras, MHC_1, and ABC_trans. Since Swap events were seen in few instances, they are not considered in deriving this table |
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|
Floris et al. BMC Genomics 2008 9:453 doi:10.1186/1471-2164-9-453 |
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