A basic example shown with
button .
To clear changes and return to the default state use
.
The example is taken from Schwartz et al. 2017 and shows EBF1 (COE1) TF binding site present in SLAMF1 human promoter but absent in the respective orthologous mouse promoter. The demo visualization can be reproduced by with the step-by-step guide.
First, add binding models from HOCOMOCO to the models list.
To perform this step, start browsing models by typing TF
name or family
in the search field
().
Click on a
Motif ID
(
)
in the drop-down list and a new motif will appear below.
Note that chosen Motif ID COE1_HUMAN.H11MO.0.A contains a Hyperlink to the HOCOMOCO database.
Click the
button or type/paste sequences manually. FASTA format is supported. The allowed alphabet is -
{A, a, T, t, G, g, C, c, N, n}.
Note that PWM
score = 0 is assigned to {N, n} letters.
Click
to parse the sequences. Separated
Tabs
will be created
for each sequence in the list.
Switch the
button to
“Yes”,
if you want to clear all previously parsed sequences on submit.
If there are no parsing errors, multiple (one-per-sequence) new
Tabs
()
will be created in the field below. To see the
name
of a particular sequence click
.
As long as the list of chosen binding modes is not empty, the predicted binding sites will be visually
marked in the sequences.
To copy the markup click the
Copy icon
().
Font size
(
) and
Color
can be adjusted if necessary.
To compare several sequences at once, switch mode to
Multiple
with the
button. Use
Lock
(
,
)
to prevent a particular tab from horizontal scrolling.
An important note. In this mode the table with the TFBS predictions
at the bottom of the page includes
predictions for ALL sequences.
To visualize binding sites for a single sequence switch mode to
Single
().
An important note. In this mode the table will contain sites only
for the ACTIVE, currently visible sequence.
Set desired motif P-value precisely or by dragging the slider. The value is shown in both linear and logarithmic scale and restricted to the [ 1.00e-6, 5.00e-2 ] interval. You may experience a minor slowdown when visualizing TFBS for long sequences (100bp+).
The recommended permissive P-value = 0.0005 (approximately 1 expected prediction in a stretch of random 1000 nucleotides of double-stranded DNA). Check [HOCOMOCO v9] for details.
Detailed data on detected binding sites are provided in the table at the bottom of the page.
The population of the complete table is the most
time-consuming
operation. To maintain overall page responsiveness while tweaking settings the table can be switched off
using the
button.
The table has additional controls.
can be used to show additional data on predicted TFBS.
Info button
(
)
unfolds additional information directly within the table.
The table contents can be saved using
Export buttons
().
The results can be filtered with the
Search field
(
).
An important note.
According to the chosen
Mode
( - Single,
- Multiple)
the table will contain different sites. They are either from all sequences or from the single active sequence
visualized. Details are given above in the
Add sequences
part of the guide.