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 a profile

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.

upload CNVs 

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.

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.
find / filter CNVs  

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.

display region

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.

grant access to your data

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.

delete your data

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.

team
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
   
contact
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. :-)