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Frequently Asked Questions

What is Tabloid Proteome?

Tabloid Proteome is a database of protein association network generated using publically available mass spectrometry based experiments in PRIDE. These associations includes; protein-protein interaction, complex formation, or different role in single pathway.

How are all these associations calculated?

The association between two proteins are calculated using our method (Gupta et al. 2017) which uses Jaccard Similarity score to calculate the value for association. Our method is based on the assumption that consistent protein co-occurrence across a large collection of different, unrelated MS experiments is not merely due to chance, but that this instead reveals an underlying biological association between these co-occurring proteins. We have also included the biological relation between the protein pairs using existing knowledgebases; IntAct and BioGRID for interaction, CORUM for complex, Ensembl for paralogs, Reactome for pathways, DisGeNet for diseases.

Is it free to use?

Yes, Tabloid Proteome data are available for free.

How can I download data and in which formats?

You can download your search result in tab delimited and CSV format, from Data Table view. You can also download the image of the Graph provided in graph view. You can change nodes/edges position and download as image., in .png format.

Does it provide all interacting partners of protein from IntAct and BioGRID?

Tabloid proteome include protein-protein interaction only for the protein pairs determined using our association study using public proteomics MS data (Gupta et al. 2017). It does not include protein-protein interaction which are not found in our study.

Documentation

You can find documentation (pdf) link here .

API

Tabloid Proteome provides REST (Representational State Transfer) API which enables you to get the data without using the graphical user interface of the web page. This can be used to programmatically access some information without downloading entire dataset.


Please click here for api information.

Here you can see an example of using RESTful web services for Python and Java.

Developer Guide

Source code is available on GitHub.

For any further questions, feedback or suggestions, you can send mail to one of the following persons:

Surya Gupta surya.gupta@vib-ugent.be

Demet Turan demet.turan@vib-ugent.be

Lennart Martens lennart.martens@vib-ugent.be