COMPUTER SYSTEM BDNA VIDEO

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COMPUTER SYSTEM B-DNA VIDEO
http//wwwmgs.bionet.nsc.ru/systems/BDNAVideo/
Bioinformatics 1999, vol. 15(7), pp.
654-668. Conformational and physicochemical DNA
features specific for transcription factor
binding sites. Ponomarenko J.V., Ponomarenko
M.P., Frolov A.S., Vorobyev D.G., Overton G.C.,
Kolchanov N.A.
Fig. 1.
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Fig. 1a. Internet Interface of the BDNA Video
System
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Fig. 2. Local conformational parameters of
DNA double helix.
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Fig.3. Description of the Helical twist angle in
the computer system B-DNA-VIDEO
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Fig. 4. Conformational DNA properties
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Fig.5. Physicochemical DNA properties
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Random Sequences R
Fig. 6. Selection of significant conformational
and physicochemical characteristics of sites
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Fig. 7. Estimation of discriminating ability
of the characteristic Xk,a,b within the
framework of the Fishburn's Theory of Utility
for Decision Making
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ER (region -6 17)
Fig. 8. Comparison of distributions of
significant conformational and physicochemical
parameters of transcription factor binding sites
(black columns) with random sequences (white
columns)
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Fig. 8A Significant conformational and physicalal
and chemicalfeatures of the DNA transcription
factor binding sites
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Fig. 8b Classification tree of transcription
factor binding sites constructed on the basis of
significant conformational and physico-chemical
features
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Fig.9. Histograms of significant B-DNA features
for eukaryotic TATA box (open columns) and the
random sequences (black columns) (a) "Mobility
bend towards Minor groove" averaged on the region
-8 6 relative to the TATA box start (b) "Bend
angle" averaged on the region -8 4 (c) "Tip
angle " averaged on the region -10 7 (d)
"Melting temperature" averaged on the region
-10 6
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Fig. 9a The profile of bending stiffness for
TATA-containing promoters of verterbrates
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Fig.9b. The histograms of the mean value twist
angle for invertebrate TATA-boxes, the random
sequences and the nucleosome binding sites
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Fig. 10. An entry of B-DNA-FEATURES database
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Figure 10A The gallery for significant B-DNA
features for site HNF1 (free energy change is
the best).
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Fig 10B The gallery for TF sites for property
free energy change
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Fig. 13. The scenario of B-DNA-VIDEO system
simultaneous usage in both "searching for static
data" and "active computation" modes, for the
HNF1 transcription factor binding site taken as
an example. By SRS user's interface, the search
is possible for (A) database SAMPLES entry
describing the HNF1 site sequence. By clicking
the field "DR FEATURES HNF1" of the SAMPLE entry
above, (B) B-DNA-FEATURES entry containing the
HNF1-spesific conformational and physico-chemical
B-DNA features can be loaded. Whence the field
"WW PROGRAMS" is chosen, (C) the Web-based tools
recognising the potential HNF1 sites within an
arbitrary DNA sequence starts to work. The
results of HNF1 recognition tools constructing
the profiles of the significant conformational
and physico-chemical features along the human
apolipoprotein AII gene sequence (EMBL X04898
HSAPOA2 (181360) with experimentally determined
HNF1 binding site (TRASFAC R03260 (270294) are
presented as follows. (D) The averaged values of
the parameter "Melting temperature" on the
sliding interval i-21 i4 relative to the
sequence point. (E) Averaged values of the
parameter "Roll in DNA-protein complex" on the
sliding interval i-21 i3 relative to the
sequence point. (F) Mean B-DNA-FEATURE ScoreF
profile recognising the HNF1 transcription
factor-binding site. Horizontal arrow, the
experimentally known HNF1 site (TRANSFAC R03260
(270294) solid arrows, pathway "data
processing" broken arrows, pathway "result
interpretation" dot arrows, contribution of
"Melting temperature" and "Roll in DNA-protein
complex" properties into B-DNA-FEATURE Score
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Fig. 14. The B-DNA-VIDEO recognition profiles
along the sequence from the human alpha-globin
gene cluster (EMBL S49899 fragment 1356) with
two experimentally determined AP-1 binding sites,
TRANSFAC R03439 (119137) and TRANSFAC R03440
(155175). Solid arrow denotes the known AP-1
site dotted line denotes the known GATA site
"false positively" recognised as "potential AP-1
site" broken arrows are non-interpretable "false
positives".
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Fig. 15. The B-DNA-VIDEO recognition profiles
along the sequence from the yeast CYC1 gene
5'-terminus for iso-1-cytochrome C (EMBL X03472
M11345) with experimentally determined TATA box
(bold-faced arrow) and four "TATA-like" regions
(solid arrows). Four "false positives" (broken
arrows) are not interpreted yet