No results found when searching Uni-Prot ID's with STRING protein search

[Vaishali]

Hi Team,

Is it possible to do any analysis with String when I have only the Uni-Prot IDs. From an Agilent Proteomics experiment, I found 15 proteins of my interest having only one annotation column i.e., UniProt ID. When I tried searching String using these protein ID's it gave me no result.

However, when I just search the same protein ID's in the string website it does give me a network automatically with just the Swiss-Prot ID's but when I search it in String within cytoscape 3.6.0, it gives me no results.

Here is the link to network created in String: https://string-db.org/cgi/network.pl?taskId=AzOv77YEbkWh

Organism is Saccharomyces cerevisiae (Yeast)

Also, the below is the list of protein ID's

P15274
P15454
P36010
P36973
P38625
P38697
P47143
P47165
P49435
P50094
P50095
P53909
Q04178
Q05788
Q07729

Let me know if you need any further information and look forward to hearing from you.

Best regards,
Vaishali

[Scooter Morris]

Hi Vaishali,
    I get a network with 15 proteins and 84 interactions when I set the species to Saccharomyces cerevisiae and a cutoff of 0.4.  How are you entering the protein IDs and species?

-- scooter

[vais...@strandls.com]

Thank you Scooter!

Sorry I was on sick leave so was unable to check this before, I am sure I might be doing something silly. At the moment, I am just selecting on the left side panel of Cytoscape 3.6 - 'STRING protein query' and then pasting the 15 Swiss Prot ID's --> enter to search then it gives me the message that no results found.

Here is a link to the image: https://drive.google.com/file/d/15Ie_lYpp2fDmjk_RSi-gNYv3VIMDEzTF/view?usp=sharing

It will be great in future if you guys can add the ability to attach files/images in the post :)

Let me know if you need any further info.

[Scooter Morris]

Hi Vaishali,

    OK, so what we probably need to do is to run Cytoscape on the
command line so we can see the messages STRING outputs.  What platform
OS are you running?

-- scooter

[vais...@strandls.com]

It's windows 7, 64 bit and 8 GB RAM machine

[Scooter Morris]

On 12/18/2017 08:13 PM, vaishali via cytoscape-helpdesk wrote:
> It's windows 7, 64 bit and 8 GB RAM machine
>

OK, fine.  So bring up the CMD window and then run cytoscape.bat (it
will be in the directory that you used to install Cytoscape). That will
echo various log messages to the window.   Then try to do the query
again.  That should print a number of things to the log window that will
help me figure out what's going on.

-- scooter

[vais...@strandls.com]

Hi Scooter,

I was able to get the same results i.e., 84 interactions. I was able to do this by going to File --> Import Network --> From Public Databases, a window comes up. In this window when I choose the Data Source as 'STRING: protein query', set the species to yeast and enter the 15 protein ID's then it gives me a network with 84 interactions.

Maybe when directly searching from the search bar, setting of the organism is not present so that I guess might be causing an issue. Anyhow, its working now and I'll try out more things and let you know if I face any difficulties.

Thank you,
Vaishali

[Scooter Morris]

Ah, right.  The settings bar to the right allows you to set the
organism.  In the latest version, there's even a little message with an
arrow pointing at it.

-- scooter