interactions on the website and downloaded version don't match

[Tamara]

Hi everyone,

I am encountering a problem and maybe it's a simple issue since I'm a
beginner still, but there is something I don't understand.

for example, when I search the interactions for entry EBI-1778843 I
get 12 hits on the IntAct website:

EBI-1778943
EBI-1778933
EBI-1778938
EBI-1779038
EBI-1779063
EBI-1778850
EBI-1778887
EBI-1778998
EBI-1779197
EBI-1779237
EBI-1779103
EBI-1778983

However, when I search for the same entry in intact.txt that I
downloaded from ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.zip
I get 12 different interactions (none overlaps with the above ones):

EBI-1778690
EBI-1538385
EBI-1779073
EBI-1778690
EBI-1538109
EBI-1237867
EBI-1779008
EBI-1538385
EBI-1778843 (2 times same protein!)
EBI-1778812
EBI-1778821
EBI-622057

Notice, there is also 1 interaction reported where both proteins are
the same.

I don't know what I'm doing wrong , please help.

This also happened with other entries I tried out, I just don't want
to paste the results now, it would be too long.

Thanks in advance,

Tamara Bobic

[Samuel Kerrien]

Dear Tamara,

First of all, thanks you very much for your interest in IntAct !

As for your questions, I have just looked into the data you pointed out and the explanation is (fortunately) very simple.

The PSIMITAB format you looking at on our web site, of which the IntAct web site is only a representation are essentially the same. The order of the interaction present in the file and on the web site is not the same though. Now down to the interacting molecules, the format accomodate 2 interacting molecules referred to as A and B. I have a feeling you have only looked at one of them (most likely A). When we export the data, we cannot really make a "clever" choice as to where put a given molecule under A or B, this is why as a user you will always have to check both molecule A and B in order to find you molecule. The screen capture below illustrate the position of EBI-1778843 in intact.zip:

As for this molecule showing interaction with itself, this is perfectly possible. If you have any specific reason to believe that Ninja proteins cannot interact together, I am sure our curators will be happy to discuss this further with you. You can view the details of that interactions here: http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=EBI-1778933

I hope this short explanation clarifies the matter.

Should you have any more questions, please do get in touch with us again.

Cheers

Samuel