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closeComment on paper
Posted by davet on 30 Mar 2010 at 16:59 GMT
I was surprised that the only interaction data used in this study was from a predicted protein interaction dataset, (Geisler-Lee (2007)). In fact there is a large dataset of experimentally detected PPis within the IntAct database (http://www.ebi.ac.uk/inta...). Recent studies have shown that the link between gene expression and protein interaction in Arabidopsis is far less reliable than assumed by many in the systems biology field (Lysenko., et al (2009).Plant Physiology). The total omission of incorporating other metrics into the study and ignoring experimentally demonstrated PPi's undermines the conclusions of this study. The application of complex mathematical analysis to data which is of arguable relevance to real biological systems is all too common in this field and produces swathes of data of questionable usefulness.
RE: Comment on paper
JoelBader replied to davet on 01 Apr 2010 at 03:57 GMT
Hi,
Thanks for your comment. I agree that predicted interactions are often low quality, and that it would have been better to include experimental interactions. Unfortunately, we were pressed for time, and when we submitted this manuscript we (and our collaborators who are Arabidopsis experts) weren't aware of any large-scale experimental screens. We are planning follow-up work and will definitely use experimental interaction data at that point.
Our point here wasn't to investigate the quality of interaction data, but rather to show how gene expression data and interaction data can be combined. Our main conclusions have to do with the context of differentially expressed genes: whether they generate new protein complexes, or whether they merge into core complexes (which was our conclusion). I am interested to hear whether any of these dynamic co-complex predictions appear incorrect.
Best,
Joel