CE
V$E2F_Q6 PWM cut-offs
%
FP
FN
human TNFα promoter
mast cells
T-cells + ?
dendritic cells
T-cells
-107
-74
NFAT
NFAT
AP-1
NF-kB
C/EBP
AP-1
VDR
TRANSFAC – experimentally proven TF binding sites
organ,
tissue,
cell
stage of
development
cell cycle
phase
extracellular
signals
TF combinations encode gene expression pattern
Composite elements (CE)
Minimal functional units where both protein-DNA and protein-protein
interactions contribute to a highly specific pattern of gene expression
and provide cross-coupling of different signal transduction pathways.
tgccacacaggtagactcttTTGAAAATAtgTGTAATAtgtaaaa catcgtgaca cccccatatt… …
. . . . . . .
-96
-79
ST
COMPEL:C00050
NF-ATp
AP-1
Mouse Interleukin-2
gene promoter
TGAGTCA
AP-1 consensus
V$<cluster4>
Studied tissue: liver
Nrf2
NFe2l1
Bach1
Bach2
NF-E2p45
Nrf3
49.3
18.4
17.6
5.8
2.6
2.3
Expression values
V$<cluster4>
Studied tissue: liver
Nrf2
Nrf3
16.6
-3.5
-4.4
-2.0
3.8
0.1
Bach1
Bach2
NF-E2p45
NFe2l1
Expression diff from average
0,01418
0,07975
0,03902
0,10333
0,36808
0,13904
Tissue specificity
Tissue preference
≤0.014
≤0.019
≤0.025
≤0.031
≤0.045
≤0.07
≤0.13
≤0.23
≤0.4
≤1.0
V$<cluster22>
Studied tissue: liver
SREBP1
USF2
SREBP2
USF1
TFEA
TFEB
TFEC
MITF
49.9
47.9
20.4
19.1
14.1
5.0
2.8
1.8
Expression values
V$<cluster22>
Studied tissue: liver
SREBP1
USF2
USF1
TFEA
33.2
13.3
-3.6
-6.2
-7.9
2.8
-2.2
-2.4
TFEC
TFEB
SREBP2
MITF
Tissue preference
Expression diff from average
≤0.014
≤0.019
≤0.025
≤0.031
≤0.045
≤0.07
≤0.13
≤0.23
≤0.4
≤1.0
V$<cluster16>
Studied tissue: liver
HAND2
Dermo-1
EC2
TWIST
FIGLA
Scx
EHAND
PTF1
8.2
0
0.3
0.3
0.3
0.1
0.1
0.1
Expression values
V$<cluster16>
Studied tissue: pancreas
PTF1
HAND2
FIGLA
Scx
Dermo-1
TWIST
EC2
EHAND
129.8
3.8
2.8
0.1
2.8
0.7
0.4
0.1
Expression values
V$<cluster16>
Studied tissue: liver
FIGLA
HAND2
EC2
PTF1
-2.4
-4.6
-4.9
-1.3
-2.2
-2.3
EHAND
Dermo-1
Scx
TWIST
Tissue preference
-1.1
-0.3
Expression diff from average
≤0.014
≤0.019
≤0.025
≤0.031
≤0.045
≤0.07
≤0.13
≤0.23
≤0.4
≤1.0
V$<cluster16>
Studied tissue: pancreas
-4.5
-4.5
-5.5
0.3
-1.5
-2.3
≤0.014
≤0.019
≤0.025
≤0.031
≤0.045
≤0.07
≤0.13
≤0.23
≤0.4
≤1.0
Tissue preference
2.4
127.6
PTF1
FIGLA
Scx
EC2
EHAND
TWIST
Dermo-1
HAND2
Expression diff from average
Phylogenetic footprint
(human/mouse)
Spec1
Spec2
The result of applying of the “Phylogenetic Footprint” tool to the proximal part of the human/mouse PTH CNS3. The beginning of the fist exon in both sequences is marked by a shadow. Two sites are marked (CREB and VDRE) that have been described previously for this region in human PTH gene. Conservative sites found by this analysis are shown by the arrows above each sequence. A number of new potential sites is revealed: CREB site, OCT site near start of transcription, a couple of NF-AT sites, SP-1 sites, GATA sites and some others
Alignment of c-fos promoters
Spec1
Spec2
Phylogenetic anti-footprint
(human/chimp)
Examples of anti-footprint (human/chimp) (minimized FP)