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BIOINF 08-002: SynBlast: Assisting the analysis of conserved synteny information

Jörg Lehmann, Peter F. Stadler, Sonja J. Prohaska

SynBlast tool (SynBlast-0.03c.tar.gz)

SynBlast tutorial

Example application 1: Vertebrate Hox clusters

reference cluster

SynBlast alignment results

human HoxA
[info-file]

HOXA9_ENSG00000078399_5e5
HOXA9_ENSG00000078399_5e5 logRatioSum-ranked

human HoxB
[info-file]

HOXB9_ENSG00000170689_2e5
HOXB9_ENSG00000170689_2e5 logRatioSum-ranked

human HoxC
[info-file]

HOXC9_ENSG00000180806_3e5
HOXC9_ENSG00000180806_3e5 logRatioSum-ranked

human HoxD
[info-file]

HOXD9_ENSG00000128709_5e5
HOXD9_ENSG00000128709_5e5 logRatioSum-ranked

Example application 2: Zebrafish ParaHox clusters

reference cluster

SynBlast alignment results

human ParaHoxA (cdx2)
[info-file]

C1_CDX2_ENSG00000165556_2e6
C1_CDX2_ENSG00000165556_2e6 logRatioSum-ranked

human ParaHoxB (cdx4)
[info-file]

C2_CDX4_ENSG00000131264_15e5
C2_CDX4_ENSG00000131264_15e5 logRatioSum-ranked

human ParaHoxC (gsh2)
[info-file]

C3_GSH2_HUMAN_ENSG00000180613_2e6
C3_GSH2_HUMAN_ENSG00000180613_2e6 logRatioSum-ranked

human ParaHoxD (cdx1)
[info-file]

C4_CDX1_ENSG00000113722_1e6
C4_CDX1_ENSG00000113722_1e6 logRatioSum-ranked

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
[info-file]

DHX15_ENSG00000109606_2e6 alnScore-ranked

hits for query ENSP00000308272 score below threshold

OLIG2_ENSG00000205927_5e5
[info-file]

OLIG2_ENSG00000205927_5e5 alnScore-ranked

hits for query p9 score below threshold; focal gene not contained in best syntenic hit for Cfa, Gga.

PBX2_ENSG00000204304_2e5
[info-file]

PBX2_ENSG00000204304_2e5 alnScore-ranked

score-threshold here often excludes hits in syntenic blocks

SREBF2_ENSG00000198911_2e5
[info-file]

SREBF2_ENSG00000198911_2e5 alnScore-ranked

TP53_ENSG00000141510_1e5
[info-file]

TP53_ENSG00000141510_1e5 alnScore-ranked

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
[info-file]

DHX15_ENSG00000109606_2e6 alnScore-ranked

DHX15-hit for platypus (region3) comprises both separated fragments annotated in Compara