The PINOT server help page

Description

Given a list of genes (input seeds’ list), the PINOT pipeline retrieves protein protein interactions (PPI) collected in databases within the IMEx consortium. PINOT’s output is a PPI network built with all the direct interactors of the seeds in the input list. Every interaction in the network is weighted based on number of different “interaction detection methods” and “publications” reporting the interaction. [PMID:32527260] [PMID:28004582] [PMID:29898659]

Guidelines for using the server

• Prepare a list of genes (input seeds’ list) for the network. The seed’s list should be a .txt file with all seeds in column. Seeds should be identified by the HUGO approved gene.name (UniProt IDs may also be used and these will be converted to gene names). [DOWNLOAD EXAMPLE OF SEED LIST INPUT TXT FILE HERE]. PINOT checks the format of the seed’s list reporting an error for incorrect uploads. Similarly, if some of the gene.name is not recognized, that will be flagged. You can download the dictionary and check that the gene.name you are using is the HUGO approved gene.name – chances are you are using a synonym. However, not all the genes are present in the PINOT dictionary.
• The online PINOT pipeline is -at the moment- limited to 1,000 seeds. If you need to run a bigger network, you can download the scripts and run them on your terminal.
• The PINOT output will be emailed to the address you have submitted with your query. The main output is made of a network.txt file and a log.txt file. The log.txt file reports all the seeds that have been dropped during the generation of the network. There is also a list of all the providers that were available online at the moment of the analysis. [VIEW EXAMPLE OF OUTPUT HERE].
• For additional information on the PINOT pipeline please refer to the following papers: [PMID:32527260] [PMID:28004582]

How long will it take?

Length of query list	Approx. runtime in min
10	4.13
100	9.10
250	17.39
500	31.20
1000	58.81

Run it yourself!

You can download the R scripts and run them on your local computer and modify them under the GNU licence they are provided with. Instructions on how to run the PINOT scripts are in the comments of the Network_GUIDE_Script.R file.
Download PINOT scripts

How to reference the PINOT algorithm

If you use PINOT in your work, please help us by referencing our papers:

Tomkins, J.E., Ferrari, R., Vavouraki, N., Hardy, J., Lovering, R.C., Lewis, P.A., McGuffin, L.J. and Manzoni, C. (2020) PINOT: an intuitive resource for integrating protein-protein interactions. Cell Communication and Signaling. 18, 92. DOI PubMed

Ferrari, R., Lovering, R.C., Hardy, J., Lewis, P.A., Manzoni, C. J. (2017) Weighted Protein Interaction Network Analysis of Frontotemporal Dementia. Proteome Res. 16(2), 999-1013. DOI PubMed

PINOT score

The PINOT score is straightforward and based on “Method Score” and “Publication Score”

“Method Score” – The number of different interaction detection methods are counted after they have been grouped by similarity (the conversion method table is available here). The reasons for grouping singular interaction detection methods are:
1. Control for annotation bias – the same interaction, from the same publication, can be annotated in 2 different databases with a different, but synonymous, interaction detection method.
2. Stringent control for reproducibility. Interaction detection methods that are very similar are not considered counting toward replication i.e. Two Hybrid MI:0018; Two Hybrid Array MI:0397; Two Hybrid Pooling Approach MI:0398; Two Hybrid Fragment pooling approach MI:0399 etc …. are all combined in a single category called Two Hybrid.

“Publication Score” – The number of different publications – identified by different PMIDs – are counted.

Interactions with a final score >2 have been replicated with at least 2 different methods and/or at least 2 different publications.
Interactions with a final score of 2 have been reported with 1 method only and in 1 publication only. This happens if the interaction is not extensively studied (i.e. a recently discovered gene, a result of an highthroughput put approach that hasn’t yet reached validation) or because the interaction is a false positive.

Log of version updates

Download version 1.1 update notes here.

Disclaimer

The PINOT tool and the PINOT scripts are offered for free and only for private, non-commercial use. The authors do not guarantee or warrant that the information and material on this webportal (Information) is up-to-date, complete, accurate, free of defects, errors and/or viruses. If you choose to rely on any of the Information, you do so at your own risk. We reserve the right to interrupt the availability of and/or cease to publish the webportal for any reason and without notice. To the extent permitted by law, the authors and the University of Reading do not accept any liability for any damage or loss arising in relation to your use of the webportal and/or the Information. PINOT links to external websites and resources that are independent and not under the control of the authors. The authors have no control over and are not liable for the nature, content and availability of those sites.

Fair usage policy

You are only permitted to have 1 job running at a time for each IP address, so please wait until your previous job completes before submitting further data. If you already have a job running then you will be notified and your uploaded files will be deleted. Once your job has completed your IP address will be unlocked and you will be able to submit new data.

If you wish to submit numerous sequences or batch jobs then please contact l.j.mcguffin@reading.ac.uk, with a short description of your project.