Import PPI from databases with scores.

[Hamza Umut Karakurt]

Hello everyone,

I need to download the whole PPI network of Mus musculus and I also need the scores of each interaction. I can download this network but it does not include any scores.

Is there any apps to do it?

Also, I tried to use PE Measure app but I am not sure it really gives results close to confidence scores of STRING data base?

[Scooter Morris]

The latest version of the stringApp will allow you to download the entire PPI for a species.  To do so, you need to go to File->Import->Network->Public databases... and then in the Data Source: pull-down select STRING: protein query.  You should now see a field you can use to enter (or pull down) the species and a check box for "All proteins of this species". 

-- scooter

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[Hamza Umut Karakurt]

I tried bu there is not a box. I have the most recent version.

3 Nisan 2018 Salı 18:54:41 UTC+3 tarihinde Scooter Morris yazdı:

The latest version of the stringApp will allow you to download the entire PPI for a species.  To do so, you need to go to File->Import->Network->Public databases... and then in the Data Source: pull-down select STRING: protein query.  You should now see a field you can use to enter (or pull down) the species and a check box for "All proteins of this species". 

-- scooter

On 04/03/2018 08:43 AM, Hamza Umut Karakurt wrote:

Hello everyone,

I need to download the whole PPI network of Mus musculus and I also need the scores of each interaction. I can download this network but it does not include any scores.

Is there any apps to do it?

Also, I tried to use PE Measure app but I am not sure it really gives results close to confidence scores of STRING data base?

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[Scooter Morris]

On 04/03/2018 09:34 AM, Hamza Umut Karakurt wrote:

I tried bu there is not a box. I have the most recent version.

Can you check and see what version of Cytoscape and stringApp you have?  The latest version does require Cytoscape 3.6, so you if you haven't updated Cytoscape, you won't be offered the latest stringApp.

-- scooter

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[Hamza Umut Karakurt]

Now I see. Thank you so much for your help.

3 Nisan 2018 Salı 19:35:50 UTC+3 tarihinde Scooter Morris yazdı:

On 04/03/2018 09:34 AM, Hamza Umut Karakurt wrote:

I tried bu there is not a box. I have the most recent version.

Can you check and see what version of Cytoscape and stringApp you have?  The latest version does require Cytoscape 3.6, so you if you haven't updated Cytoscape, you won't be offered the latest stringApp.

-- scooter

3 Nisan 2018 Salı 18:54:41 UTC+3 tarihinde Scooter Morris yazdı:

The latest version of the stringApp will allow you to download the entire PPI for a species.  To do so, you need to go to File->Import->Network->Public databases... and then in the Data Source: pull-down select STRING: protein query.  You should now see a field you can use to enter (or pull down) the species and a check box for "All proteins of this species". 

-- scooter

On 04/03/2018 08:43 AM, Hamza Umut Karakurt wrote:

Hello everyone,

I need to download the whole PPI network of Mus musculus and I also need the scores of each interaction. I can download this network but it does not include any scores.

Is there any apps to do it?

Also, I tried to use PE Measure app but I am not sure it really gives results close to confidence scores of STRING data base?

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