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BIOINF 08-002: SynBlast: Assisting the Analysis of Conserved Synteny Information
Example application 1: Vertebrate Hox clusters
reference cluster |
SynBlast alignment results |
|
human HoxA |
HOXA9_ENSG00000078399_5e5 |
|
human HoxB |
HOXB9_ENSG00000170689_2e5 |
|
human HoxC |
HOXC9_ENSG00000180806_3e5 |
|
human HoxD |
HOXD9_ENSG00000128709_5e5 |
Example application 2: Zebrafish ParaHox clusters
reference cluster |
SynBlast alignment results |
human ParaHoxA (cdx2) |
C1_CDX2_ENSG00000165556_2e6
|
human ParaHoxB (cdx4) |
C2_CDX4_ENSG00000131264_15e5
|
human ParaHoxC (gsh2) |
C3_GSH2_HUMAN_ENSG00000180613_2e6
|
human ParaHoxD (cdx1) |
C4_CDX1_ENSG00000113722_1e6
|
ParaHox results for Danio rerio (Table 3 as online version)
| Reference | DrA1 chr.24 20M pdx1 |
DrA2 chr.5 60M gsh1 |
DrB chr.7 50M |
DrB1 chr.14 37M cdx4 |
DrC1 chr.20 20M gsh2 |
DrC2 chr.1 10M |
DrD1? chr.14 53M |
DrD1? chr.14 22M |
DrD1 chr.14 25M cdx1a |
DrD2 chr.21 43M CDX1 |
DrD2? chr.21 36M |
|---|---|---|---|---|---|---|---|---|---|---|---|
| HsA/C1 CDX2 chr.13 |
2.49 8343 2/1 |
0.25 2291 7/2 |
0.52 1605 5/5 |
0.05 1537 9/6 |
-0.65 1922 40/3 |
- - - |
- - - |
- - - |
1.3 1757 3/4 |
- - - |
(0.13) (1112) (8/8) |
| HsB/C2 CDX4 chr.X |
(-0.41) (237) (19/25) |
(-0.7) (139) (31/38) |
2.53 2934 1/1 |
0.47 1192 3/2 |
(-0.04) (114) (7/41) |
-0.02 669 5/7 |
- - - |
- - - |
-0.75 543 34/10 |
-0.14 183 12/32 |
- - - |
| HsC/C3 GSH2 chr.4 |
-1.47 1478 54/4 |
-1.56 507 55/7 |
-0.33 1424 19/5 |
-2.52 1595 56/3 |
3.23 4756 1/1 |
0.91 1880 3/2 |
- - - |
- - - |
-0.46 469 26/9 |
- - - |
(-0.37) (488) (23/8) |
| HsD/C4 CDX1 chr.5 |
-0.6 439 13/41 |
(-2.77) (254) (24/57) |
(-3.57) (2238) (42/2) |
-3.44 953 41/12 |
-3.31 940 37/13 |
(-0.06) (991) (7/11) |
0.79 1796 2/4 |
0.03 1514 6/5 |
-0.41 846 11/16 |
0.18 1107 4/9 |
5.27 2550 1/1 |
Hox results for Danio rerio (Table 1 as online version)
| Reference | DrAa chr.19 10.5M |
DrAb chr.16 16M |
DrBa chr.3 23M |
DrBb chr.12 26.5M |
DrCa1 chr.23 33.7M |
DrCa2 chr.23 35.2M |
DrCb chr.11 0.6M |
DrDa chr.9 2M |
|---|---|---|---|---|---|---|---|---|
| HsA HOXA9 chr.7 |
2.58 5581 2/1 |
3.29 4073 1/3 |
-0.76 4690 7/2 |
-0.39 2119 3/7 |
-1.98 3322 9/4 |
-1.98 3318 10/5 |
-0.4 1490 4/8 |
-0.74 3269 6/6 |
| HsB HOXB9 chr.17 |
-1.14 2702 6/4 |
-0.01 1342 3/7 |
3.13 6201 1/1 |
0.42 1647 2/6 |
-1.66 3008 7/2 |
-1.69 2982 8/3 |
-0.64 1003 5/8 |
-0.48 1678 4/5 |
| HsC HOXC9 chr.12 |
-0.89 2361 7/6 |
-1.51 2323 8/7 |
-0.26 3108 5/5 |
-0.34 1346 6/8 |
6.44 8687 2/1 |
7.58 6537 1/2 |
0.22 4150 3/3 |
-2.51 3798 9/4 |
| HsD HOXD9 chr.2 |
-0.92 2799 8/4 |
-0.63 1811 5/6 |
-0.85 2660 7/5 |
-0.6 871 4/8 |
-0.41 3017 3/2 |
-0.41 3013 2/3 |
-0.71 1303 6/7 |
1.76 4326 1/1 |
Further Examples
human reference cluster |
SynBlast alignment results (Ensembl rel42 versions of Canis, Macaca, Gallus, Gasterosteus) |
Notes |
DHX15_2e6 |
hits for query ENSP00000308272 score below threshold | |
OLIG2_ENSG00000205927_5e5 |
hits for query p9 score below threshold; focal gene not contained in best syntenic hit for Cfa, Gga. | |
PBX2_ENSG00000204304_2e5 |
score-threshold here often excludes hits in syntenic blocks | |
SREBF2_ENSG00000198911_2e5 |
||
TP53_ENSG00000141510_1e5 |
region 1 and 4 are overlapping (by default up to 25 percent of regions' range may initially overlap) | |
human reference cluster |
SynBlast alignment results (Ensembl rel49 version of platypus) |
Notes |
DHX15_2e6 |
DHX15-hit for platypus (region3) comprises both separated fragments annotated in Compara |