I am getting interaction data from Arabidopsis interaction viewer database, maintained by toronto. I am trying to separate out protein-protein interaction and protein-DNA interaction. The data which belongs to the database has separate options for separating PPIs and PDIs. But they have other options to extract information from Inact and biogrid database. It looks like biogrid has only PPIs (my predictions based on MI terms appeared). But it looks like Inact has both PPIs and PDIs (my predictions based on MI terms appeared). So I tried to filter out PPIs and PDIs based on MI terms. The problem is that all the interactions were turned out to be PPIs and some of them were PDIs but none of the interactions were only PDIs. Am I doing something wrong or the Arabidopsis Interaction viewer database is showing only PPIs from Inact database. Any comment or thought about this problem is highly appreciated. Thank you
I went to the Inact database and queried indiviual genes. There I could get only PPIs but no PDIs. But the paper which explains about the Inact database says that it has protein-nucleic acid interactions as well. But I could not find for any Transcription factor having PDI.
Paper reference: Article The IntAct molecular interaction database in 2012
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