Cytoscape cannot load interactions from STITCH for certain compounds

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veni...@connect.hku.hk

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Nov 14, 2018, 2:52:47 PM11/14/18
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Dear Sir/ Madam,

I have encountered problem using your STRING APP on cytoscape.
I am using the STITCH compound query function and I realized that for a few of the compounds which I enquired, the network could not load. I have tried trouble shooting including checking cytoscape memory and double checking that I am already using Java 8. Could you please help me?

Yours
Venice

Alex Pico

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Nov 15, 2018, 3:07:28 PM11/15/18
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Hi Venice,

Can you provide a query that doesn't work? Can you describe the steps and symptoms in more detail, for example:

1. Enter "Glucose" into STITCH compound search
2. Click search icon
3. Confirm identity of "glucose" in pop up dialog
4. Set "Maximum additional interactors" to 20
5. Click OK
Outcome: a network is generated!

These steps, for example, work fine for me. Do they work for you? What exactly does not work for you?
 - Alex

HO, Wing Tung Venice

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Nov 15, 2018, 9:35:04 PM11/15/18
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Hi Alex,

These are the three compound queries which I have trouble with:
1. 5-Methylcoumarin-4-Gentiobioside
2. Gerberinol I
3. 5-Methylcoumarin-4-Cellobioside

These are the steps I have done:
1. Enter "Gerberinol I" into STITCH compound search
2. Click search icon

A pop-up bubble says getting annotations, and then the following pop-up says:
Screen Shot 2018-11-14 at 10.54.52 AM.png

Thank you so much for your help
Venice

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Nadezhda Doncheva

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Nov 16, 2018, 4:17:09 AM11/16/18
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Hi Venice,

I just checked in the STITCH database (stitch.embl.de) and it appears these compounds are not found in the database. I think that this the reason why you don't get a network, but I will double check and make sure the message about not found compounds is a bit more informative in the next version of the stringApp.

Do you maybe have some synonyms of theses compounds that you can search for?

Best wishes,
Nadya

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Nadezhda Doncheva

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Nov 16, 2018, 4:21:06 AM11/16/18
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On Fri, 16 Nov 2018 at 10:16, Nadezhda Doncheva <ndon...@gmail.com> wrote:
Hi Venice,

I just checked in the STITCH database (stitch.embl.de) and it appears these compounds are not found in the database.
Ok, the identifiers are actually found in the database, but they don't have any interactions as indicated by this message from STITCH: "This chemical does not have an interaction in any species."

Best wishes,
Nadya

veni...@connect.hku.hk

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Nov 16, 2018, 5:27:41 AM11/16/18
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Dear Nadya,

Thank you for your reply. I thought there were problems with loading the interactions as with other query compounds, I received another message saying there are no results for that query compound. 
And also, is the STITCH compound query on cytoscape 100% based on the STITCH database (stitch.embl.de)? As it happens that for many compounds which I found no interactions on the STITCH online database has interaction network when searched in cytoscape.

Best,
Venice

Von meinem iPhone gesendet

Nadezhda Doncheva

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Nov 19, 2018, 4:56:03 PM11/19/18
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On Fri, 16 Nov 2018 at 11:27, <veni...@connect.hku.hk> wrote:
Dear Nadya,

Thank you for your reply. I thought there were problems with loading the interactions as with other query compounds, I received another message saying there are no results for that query compound. 
And also, is the STITCH compound query on cytoscape 100% based on the STITCH database (stitch.embl.de)? As it happens that for many compounds which I found no interactions on the STITCH online database has interaction network when searched in cytoscape.

Hi Venice,

Can you please give me an example for a few of these compounds, where you get different results in the app and on the website. I would like to check them.

Thanks,
Nadya

HO, Wing Tung Venice

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Nov 20, 2018, 12:53:33 AM11/20/18
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Yep
eg. 
Swertiamarin
Sweroside
Gentiopicrin
Loganic acid
Secoxyloganin
Mangiferin
Neomangiferin
Vanilloloside
etc

Is it because of the search settings or something?

Venice

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Scooter Morris

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Nov 29, 2018, 10:51:30 AM11/29/18
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Hi Venice,
   I'm getting results for at least some of these.  What species are you using?

-- scooter
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HO, Wing Tung Venice

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Dec 10, 2018, 2:52:06 AM12/10/18
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Hi scooter,

sorry for the late reply. I have been using homo sapiens as species.
eg. for Mangiferin, the results shown in cytoscape stitch compound query and on stitch online db are different. 
for Cytoscape compound query, I have chosen confidence score 0.4 and maximum interacters 0.
For stitch online database, I have also chosen confidence score 0.4

Thank you for your help

Yours
Venice

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HO, Wing Tung Venice

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Dec 10, 2018, 3:13:41 AM12/10/18
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Hi Scooter,

Sorry, I think I figured... I should have increased the number of maximum interacters for stitch online database as well.
Though I got a question, what happens if the number of interactors is larger than the maximum number of interactors allowed (ie 100) in cytoscape stitch compound query?

Best regards,
Venice

HO, Wing Tung Venice

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Dec 10, 2018, 5:49:55 AM12/10/18
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Hi scooter,

I have a similar enquiry regarding the online stitch database. Take succinate as an example. I have put in confidence score cutoff as 0.4 and maximum interactors as 500.
But at the bottom of the list generated, the compounds are still with confidence score 0.521 and funny enough the list of results includes only 479 protein targets. Yet, when I tried further increasing the number of maximum interactors, results could not be loaded.

Yours sincerely,
Venice

Scooter Morris

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Dec 13, 2018, 10:36:28 AM12/13/18
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Hi Venice,

In that case, you will only get the top 100 and it will be somewhat random which of the bottom scoring ones you actually wind up getting.

-- scooter
Venice

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Scooter Morris

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Dec 13, 2018, 10:38:00 AM12/13/18
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Hi Venice,
   Do you have any evidence that there are more than 479 protein targets for succinate in STITCH?  If that's all there is, then it seems like regardless of the "maximum interactors" setting, you only get 479.

-- scooter
Venice

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