CNVinspector
Documentation |
This software is being further developed. You
might occasionally discover new features that haven't yet made it
into the manual. We apologise in advance if this causes confusion,
but we want to make new features available as soon as possible.
|
|
|
Create your profile in order to set access
restrictions (only you, everyone, selected co-operation partners)
at any time.
It is not possible to choose a user name that is already in use,
CNVinspector will raise an error in such cases. You should always
enter a valid e-mail address because we will inform you in advance
when major changes to the website are planned.
If you
forgot your password, please send us an e-mail. Lost passwords will
only be sent to the email address entered here.
After you have created an account, you will be automatically logged
in. If you return to CNVinspector, please click on the login link on the homepage
and enter your credentials.
|
|
|
|
|
import format
CNVinspector needs positional information and the number of
deletetions / duplications for each CNV. We offer two methods to
enter CNV data:
| 1) a tab-delimited
file with the following columns |
|
| content |
column heading |
| chromosome |
must start with 'chr' |
| start of CNV |
must start with 'start', 'begin', or
'from' |
| end of CNV |
must start with 'end', or 'to' |
| number of duplications |
must contain 'dup' |
| number of deletions |
must contain 'del' |
| frequency of duplications * |
must contain 'freq' and 'dup' |
| frequency of deletions * |
must contain 'freq' and 'del' |
| * this column is optional;
if it is not present, the frequency is calculated from the
number of duplications/deletions and the sample size |
Example: Chromosome Start End Deletions Duplications
2 126475608 127637960 0 1
2 167702243 168013155 1 0
3 1749945 1842229 1 0
3 19076081 20243011 1 0
4 30654062 32070748 0 1 A sample file for cohorts can
be found here, one for single
patients here. If you
have a different format, please send us an e-mail. We'll gladly
add it to our import routine.
|
| 2) an input field |
|
If you want to enter only a few CNVs, the direct (manual)
input might be faster. The format is the same as above, but
please be aware that web browsers will not let you enter tabs
directly. You can either copy and paste them from the example
input (which can be inserted by clicking the hyperlink on top of
the text field) or switch to spaces instead. Consecutive
spaces/tabs are treated as a single delimiter, it is hence
mandatory to specify non-existing deletions as 0 instead of just
leaving them blank. |
To import the CNVs, please fill out all fields:
| logged in as user |
this is automatically filled in by the
database (you do not have to be logged in to upload data) |
| description |
a short description of your study (e.g.
'125 sporadic cases of epilepsy') |
| access restriction |
uncheck this if you want to make your data
public |
| method (brief) |
select the method that best suits your
method - this is helpful if you want to group similar methods
when querying the data |
| method |
the method you used (e.g. Array CGH) |
| sample size |
the number of samples included in your
study |
| genome build |
36 / 37 |
| CNVs file |
your CNV file (see
above for format)
|
You can decide whether or not you want to make the project public
(checkbox access restriction).
If you are logged in with a personal account, this setting can be
changed at any time and you can also share your data with selected
collaborators (via the grant access to your data link on the
homepage). If you upload your data as guest, you will receive
special URLs for access-restricted data; the data will be invisible
to anyone else. Without the URL, you will not be able to access
your data again.
Please note that public data created as
guest can be accessed (i.e. viewed and also deleted) by
anyone.
When the upload has been finished, you can analyse
your data.
|
|
|
After the CNVs were imported, you are ready to analyse the data.
The interface shows all studies uploaded for the selected build that are accessible to you. You
can sort the data by clicking on the column heading; another click
will reverse the sorting order. Sorted project are grouped if they
share the same value in the column they are sorted by with a grey
bar above the group. The two checkboxes in the grey bars can be
used to check or uncheck all boxes within the group.
| |
1 |
select the genome build of your study
|
| |
2 |
select one analysis as 'cases' |
| |
3 |
select one or more analyses as control
experiment(s) you want to see by clicking the display as controls checkbox
|
| |
4 |
select one or more analyses as control
experiment(s) you want to use to filter the data against by
clicking the filter against
checkbox
|
| |
5 |
select one or more analyses as control
experiment(s) you want to use to filter the data for by clicking
the positive controls checkbox
This option is only available upon selection of the show filtering options checkbox on
the upper left side (below the CNVinspector logo)
.
|
| |
| find all interesting
CNVs |
| |
4 |
enter the criteria you search for |
| |
|
| frequency
in cases [%] |
finds regions in which the percentage
of case samples withs CNVs is higher than this value |
|
number of cases [n] |
finds regions in which the number of
case samples withs CNVs is higher than this value |
| frequency
in controls [%] |
excludes regions in which the
percentage of control samples with the same CNVs (dup/del) as
the cases is higher than this value |
| number
in controls [n] |
excludes regions in which the number of
control samples with the same CNVs (dup/del) as the cases is
higher than this value |
|
| |
5 |
click on find
CNVs
|
| |
|
You will now get a list of all matching
CNVs. The output is described here.
|
| |
|
|
| show all CNVs within
a region or a gene |
| |
4 |
specify a region |
| |
|
| A |
enter chromosome, start, end
of the region of interest into the respective fields
|
| B |
enter the Region as
chr:start-end
e.g. 1:120000000-122000000 for
the region between 120 and 120.2 Mbp on chromosome 1 |
| C |
enter a gene symbol
Please note that
only HGNC gene symbols may be used.
|
|
| |
5 |
click on display
region |
| |
|
You will see all genes and CNVs your
region contains. The output is described here.
|
|
|
|
Check the show filtering options
checkbox on the upper left side (below the CNVinspector logo) to
see filtering options and make your choice. The output is a simple
list of your 'cases' CNVs that match the filtering criteria
(number, frequency) you specified. Whenever one of your control
studies contains the same CNV (dup/del) in these regions and the
frequency / number exceeds the threshold you entered for filtering,
this region of this CNV is excluded from the cases' CNVs.
The remaining 'validated' CNVs in your cases are sorted by
chromosome, start, end. Below each CNV, the CNVs in controls and
the genes contained in the region are printed. Clicking on the
hyperlink right of 'CNVs in case samples' will display the region (see below). Clicking on a gene symbol
will open the GeneDistiller page for this gene to provide some
information about the gene.
Below the figure, the actual data is printed. The genes offer
hyperlinks to GeneDistiller for further information and a hyperlink
below the genes will show information about all genes at once. |
|
|
This page shows the genes and the CNVs (from the projects you
selected) contained within your region. On top, the locations of
genes and CNVs are plotted. In the plot, genes are indicated as
green bars, duplications in blue, and deletions in red. Control
CNVs are displayed in light colours.
Genes are clickable
and open the respective gene's page in GeneDistiller.
Below the plot, the database lists the single CNVs and genes
with the actual positions in the genome build you have selected.
For each gene, a hyperlink to GeneDistiller is offered. You can
hence easily find out more about the gene. Below the genes, a
hyperlink will show information about all genes at once. |
|
|
You can use this interface to fine-tune access to
your data. It will display a table with all of your projects as
rows and all user logins as columns. For each user and project, you
can select whether he or she shall be allowed to query your data.
At the begin of each row, you have the option to grant (or revoke)
query permissions to the public.
Click on SetPermissions when
you're done.
|
|
|
Use this interface to delete one or more of your
projects.
All of your projects will be listed. Checking a project will
mark it for deletion.
Please note that deleted data will be lost forever. |
| implementation / technical details |
|
|
CNVinspector is based on a PostgreSQL database, all
interfaces were written in Perl.
The application was developed using various flavours of
Mozilla Firefox (versions 2-9 on Linux, Mac, Windows). It was
further tested with Microsoft Internet Explorer 8 and should work
all other current browsers as well. |
|
| Ellen Knierim |
Dept.
of Neuropaediatrics, Charité, Berlin, FRG |
| Jana Marie Schwarz |
NeuroCure
Clinical Research Centre, Charité, Berlin, FRG |
| Markus Schuelke |
NeuroCure
Clinical Research Centre, Charité, Berlin, FRG |
| Dominik Seelow |
NeuroCure
Clinical Research Centre, Charité, Berlin, FRG |
| |
|
|
|
snail
mail
Dominik Seelow
NeuroCure Clinical
Research Centre
Charité -
Universitätsmedizin Berlin
Charitéplatz 1
D-10117 Berlin
Federal Republic of Germany
|
e-mail |
dominik.seelow(at)charite.de |
| phone |
+49 30 450539096 |
| fax |
+49 30 450566920 |
| |
|
If you are unsure which medium best suits your contact needs:
E-Mails are preferred. :-) |