Re: [cytoscape-helpdesk] Help with String via Psicquic

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Rafael Jimenez

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Jul 26, 2013, 9:41:17 AM7/26/13
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The String PSICQUIC service seems to have interactions for these proteins ...

Interactions between RARA and NCOR1

Interactions for RARA or NCOR1


I have not tried in cytoscape, but some reasons why it din't work could be ... 
 - The String PSICQUIC service was down at that moment
 - The Cytoscape PSICQUIC plugin has a bug (which cytoscape version are you using?), 
 - Maybe the cytoscape plugin is just looking at the identifiers columns and not the aliases. Try to query uising the uniprot accs (Q5BLJ8 AND Q9CUV3 ) 

Regards,
Rafael


On 26 July 2013 14:07, Massimo Acquaviva <massimo.ac...@gmail.com> wrote:
Hallo to everyone...

During the retrieval of a network from String using query by ID I noticed that some of the resulting interactions do not overlap with results from String website. I.e. RARA and NCOR1  have no interaction retrieved  but they have a lot on the website.

Any suggestion will be highly appreciated

Thank you in advance


Massimo Acquaviva


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Massimo Acquaviva

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Jul 26, 2013, 10:15:25 AM7/26/13
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Dear Rafael, thank you very much for your reply. I have tried both Cytoscape 2.8.3 and 3.0.1 and the same situation occured

Now I'm trying your suggestions ....I will let you know....

Thank you again

Massimo


Il giorno venerdì 26 luglio 2013 15:41:17 UTC+2, Rafael ha scritto:
The String PSICQUIC service seems to have interactions for these proteins ...

Interactions between RARA and NCOR1

Interactions for RARA or NCOR1


I have not tried in cytoscape, but some reasons why it din't work could be ... 
 - The String PSICQUIC service was down at that moment
 - The Cytoscape PSICQUIC plugin has a bug (which cytoscape version are you using?), 
 - Maybe the cytoscape plugin is just looking at the identifiers columns and not the aliases. Try to query uising the uniprot accs (Q5BLJ8 AND Q9CUV3 ) 

Regards,
Rafael
On 26 July 2013 14:07, Massimo Acquaviva <massimo.ac...@gmail.com> wrote:
Hallo to everyone...

During the retrieval of a network from String using query by ID I noticed that some of the resulting interactions do not overlap with results from String website. I.e. RARA and NCOR1  have no interaction retrieved  but they have a lot on the website.

Any suggestion will be highly appreciated

Thank you in advance


Massimo Acquaviva


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Massimo Acquaviva

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Jul 26, 2013, 10:50:04 AM7/26/13
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Ok , I have tried the accessions you passed me  (Q5BLJ8 AND Q9CUV3 )  and actually it gives me interactions, but only for mouse.

When I try with the human accessions O75376 P10276 it returns no results

Best 

Massimo



Il giorno venerdì 26 luglio 2013 15:41:17 UTC+2, Rafael ha scritto:
The String PSICQUIC service seems to have interactions for these proteins ...

Interactions between RARA and NCOR1

Interactions for RARA or NCOR1


I have not tried in cytoscape, but some reasons why it din't work could be ... 
 - The String PSICQUIC service was down at that moment
 - The Cytoscape PSICQUIC plugin has a bug (which cytoscape version are you using?), 
 - Maybe the cytoscape plugin is just looking at the identifiers columns and not the aliases. Try to query uising the uniprot accs (Q5BLJ8 AND Q9CUV3 ) 

Regards,
Rafael
On 26 July 2013 14:07, Massimo Acquaviva <massimo.ac...@gmail.com> wrote:
Hallo to everyone...

During the retrieval of a network from String using query by ID I noticed that some of the resulting interactions do not overlap with results from String website. I.e. RARA and NCOR1  have no interaction retrieved  but they have a lot on the website.

Any suggestion will be highly appreciated

Thank you in advance


Massimo Acquaviva


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Rafael Jimenez

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Jul 29, 2013, 8:24:18 AM7/29/13
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Unfortunately this is because String is not using the latest human UniProt Accs for these two proteins. Secondary accession for ... O75376 and  P10276 ... are ... Q9NQS0 and Q9UQ18

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