Are there errors in "Relating 3D structures to protein networks provides evolutionary insights"?

After reading your paper "Relating 3D structures to protein networks provides evolutionary insights" which was published at SCIENCE in 2006, I have some questions about some details. In the third paragraph you said "proteins connected by simultaneously possible interactions are more likely to share the same function than are those connected by mutually exclusive ones", but the result which was shown in Table 1 looks like conversed. I also want to know the computing method of coexpression correlation and expression correlation, because I found their respective results which occur in Table1 and Table2 are also conversed.

You're right, also refer to our website sin.gersteinlab.org, where we list this typo.

Non-PDF format for 1136174s_TableS6 in Paper

In the paper relating three dimensional structures to protein networks provides evolutionary insights, the file (1136174s_TableS6) that could be obtained on line is only in PDF format. I wonder whether you have other format file (like .txt)?

We have put up Table S6 (and other supplementary data) as .xls and .tab format on our website:
http://sin.gersteinlab.org

Table 1 Discrepancy

Regarding the Science paper titled Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights the numbers in the Table 1 tell something different. According to Table 1, Simultaneously possible interactions have less fraction of same functions, as well as less fraction in co-expression correlation. Can you please clarify?

The table headings unfortunately got switched at some unknown point during copy editing. We have posted a note to that point on our site. Do let me know if you need more help on this!

Atomic Structure

Regarding the paper, "Relating Three-Dimensional, Structures to Protein Networks Provides Evolutionary Insights", how do I obtain the the atomic information about your structural network, namely PDB files containing your interacting interfaces?

I think this is possible. I think we can put this on our data download page on
sin.gersteinlab.org . We'll follow up shortly on this.

Clarification for table 1 of "Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights"

I have been reading your paper titled "Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights" with great interest. Specifically, there is one section that I am confused about that I would like to ask for clarification of: page 1939, column three, paragraph 1, description of table 1. In comparing hubs with simultaneously possible interaction partners to those with mutually exclusive interaction partners, table 1 seems to indicate that the fraction of protein partners with same biological process, molecular function, cellular component and coexpression correlation is higher in hubs with mutually exclusive interactions with partners, however, the text seems to indicate the reverse. I feel that I must be misinterpreting something, so any clarification would be greatly appreciated.

Yes, you're right, unfortunately the column headings of table 1 got switched at a late stage of editing. Since we've been getting a fair share of email about this, there is a note regarding this on the paper website http://sin.gersteinlab.org