Re: [intact-developers] IntAct db File discordances

[Marine]

Hello Rossella,

Thanks for your interest in IntAct!

I think you are not looking at the species organism but at the experiment host organism (cell line used in the experiment for detecting the interaction).
The species for interactor A and interactor B are at the column 10 (interactor A) and column 11 (interactor B) in MITAB 2.6 and 2.7 (see http://code.google.com/p/psicquic/wiki/MITAB27Format). In the MITAB file, you will see that column 10 and 11 are mouse because it is the species of the interactors and the column 29 is taxid:9606(Homo sapiens 293 cells transformed with SV40 large T antigen) because the experiment was done in human 293 cells.

In our website, the columns 'Species A' and 'Species B' are mouse because are showing the content of columns 10 and 11 and the column 'Host Organism' is human-293t because it shows the content of column 29.

In the cytoscape graph, you only see mouse because it is the species of the interactors but you don't see the host organism/cell line used in the experiment. If you export your results in XGMML and then import in cytoscape, you will find an attribute host attached to the edge not the node and this host attribute should show human-293t.

Don't hesitate to contact us again if you find other results that are confusing,

Regards,

Marine

Hi to everyone,

I'm quite new to use IntAct but I would be very happy to integrate intAct data in my analysis.

I downloaded the DB intact.zip in the repository, and I try to use it... but I see any differences between the interface and the file content, can some one tell me if I'm doing something wrong or why there are this differences?

As follows some examples:

From the Search box in the interface page if you search interaction for the gene TGFBR1 and visualise the cytoscape graph the genes DACT1 and DACT2 are tagged in the mouse network (as the interaction is demonstrated in a  mouse experiment) instead of querying the text file for all the interaction with the TGFBR1 the same two gene are tagged as human genes.

$VAR27 = 'Dact2';

$VAR28 = {

           'taxid:9606(human-293t)|taxid:9606(Homo sapiens 293 cells transformed with SV40 large T antigen)' => '0.40'

         };

$VAR11 = 'Dact1';

$VAR12 = {

           'taxid:9606(human-293t)|taxid:9606(Homo sapiens 293 cells transformed with SV40 large T antigen)' => '0.40'

         };

And this is not just one case that I verified.

Thanks in advances,

Rossella

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