Tag Archives: STRING

Resource: Cytoscape App for STRING

The STRING database of known and predicted protein–protein interactions is a heavily used resource by bioinformaticians and non-bioinformaticians alike. The former generally use STRING via its web interface, whereas the latter typically download the complete network and analyze it locally. However, we lacked a good way for non-bioinformaticians to work with networks that are just too large for the web interface. A typical example of this would be users, who wish to visualize the results of a proteomics or transcriptomics study as a STRING network.

To address this, I have worked with John “Scooter” Morris to develop a new Cytoscape app for STRING. The app allows you to quickly retrieve much larger networks than is possible via the web interface and gives you the powerful layout and analysis features of Cytoscape. At the same time, it retains the “glass ball” look that many people associate with a STRING network (shown here with a small example network):

cytoscape1

When retrieving network, the app also includes node attributes from the COMPARTMENTS and TISSUES databases. This allows users to easily, for example, color the nodes based on the confidence with which each protein is localized to a certain cellular compartment or expressed in a certain tissue. The app also includes node attributes for drug targets classification of human proteins, which are obtained from the Pharos web resource. Finally, since it is Cytoscape, you can obviously import your own attributes table.

cytoscape2

Although it is not yet feature complete, version 0.9 of the app is already available from the Cytoscape App Store under the name stringApp. Please note that it requires Cytoscape 3.3 to work.

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Resource: Antibodypedia bulk download file and STRING payload

Antibodypedia is a very useful resource for finding commercially available antibodies against human proteins developed by Antibodypedia AB and Nature Publishing Group.

The resource is made available under the Creative Commons Attribution-NonCommercial 3.0 license, which allows for reuse and redistribution of the data for non-commercial purposes. However, the data are purely available for browsing through a web interface, which greatly limits systems biology uses of the resource. I thus wrote a robot to scrape all information from the web resource and convert it into a convenient tab-delimited file, which I have made available for download under the same license. This dataset covers a total of 579,038 antibodies against 16,827 human proteins.

To be able to use the dataset in conjunction with STRING and related resources, I next mapped the proteins to STRING protein identifiers. I was able to map 92% of all proteins in Antibodypedia. Having done this, I created the necessary files for the STRING payload mechanism to be able to show the information from Antibodypedia directly within STRING.

The end result looks like this when searching for the WNT7A protein:

Antibodypedia STRING network

The halos around the proteins encode the type and number of antibodies available. Red rings imply that at least one monoclonal antibody exists whereas gray rings imply that only polyclonal antibodies exist. The darker the ring (be it red or gray), the more different antibodies are available.

They STRING payload mechanism also extends the popups with additional information, here shown for LRP6:

Antibodypedia STRING popup

The popup shows the total number of antibodies available and how many of them are monoclonal. It also provides a direct linkout to the relevant protein page on Antibodypedia.

Please, feel free to use this Antibodypedia-STRING mashup.