Blogging the biotechnology revolution

Systems Biology is changing the way biology is done. Is it a fad or is it effective? This blog tracks current happenings and helps you stay on top of the field. You can find a list of relevant papers at systems biology paper watch Have you heard a talk or read a paper in bioinformatics / systems biology you would like to tell other people about? Email: and get the word out!

Friday, June 15, 2007

Confirmation of Organized Modularity in the Yeast Interactome. From Vidal, Roth and colleagues is a rebuttal to a recent paper that there isn't dynamic modularity in the yeast (and other) interactomes which was a rebuttal of a Vidal Nature paper on date and party hubs and a Fraser Science paper on Evolutionary rate and Hubs. Basically the debate is that one group accused the other of using an interaction dataset that was skewed to show what the authors wanted, then the original authors tested a few more yeast datasets to show that the effect was ubiquitous. However how come the authors don't present any data on other organisms? They make an argument about the need for high quality data, but there is such information for human (published by the same authors no less), which support from different species I think we could lay this argument to rest.

But I think the argument gets at something deeper, is it worth publishing global trends in data? So what if there are some hubs whose partners are temporally versus constituitively expressed? I fail to see how this reveals anything there are plenty of exceptions to this rule. In my opinion the most over-use of trends in the name of network science was the early paper on Evolutionary rate and hubs in the interactome network. I have posted Figure 1 from this Science paper, which is the apparent motivation for the whole work. They draw a trendline, but im sorry this isnt much of a correlation (r=-0.24 !!!). All i see is a few points that follow this trend and many that dont. I fail to see how saying that hubs have a lower evolutionary rate is a definite conclusion given the data, enough to warrant a Science paper