Video Tip of the Week: Phosida, a post-translational modification database

Over 2 years ago I did a tip of the week on Phosida (links to Phosida). Phosida is a database of phosphorylation, acetylation, and N-glycosylation data. Since the last tip, Phosida has undergone significant growth and some changes, including the addition of much more data (80,000 phosphorylation, acetylation and N-glycosylated sites from 9 different species) and tools (prediction and motif analysis). You can read more about those changes in this year’s NAR database issue article.

Today’s tip will revisit the database and redo a search that was done in the tip from 2009, this time using a protein search instead of a category search.
Gnad, F., Gunawardena, J., & Mann, M. (2010). PHOSIDA 2011: the posttranslational modification database Nucleic Acids Research, 39 (Database) DOI: 10.1093/nar/gkq1159

Quick link to Phosida

Below the fold you’ll find the text of the last tip of the week more information:

I recently read an article in Science entitled “Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions” written by Choudhary et al. The research uses “high-resolutionmass spectrometry to identify 3600 lysine acetylation siteson 1750 proteins” and “demonstrate[s] that the regulatory scopeof lysine acetylation is broad and comparable with that of othermajor posttranslational modifications.”

I’m going to admit, I know little of acetylation as a regulatory mechanism, though after reading through the paper, I found this quite and interesting find and it suggests to me that genomics has a lot to offer in the advance in our understanding of regulation and evolution.

Three things jumped out at me though.

The first is minor. The authors use the term Acytelome. You can now add that to the huge list of -omics termsto keep straight :D.

acetalnetworkThe second is that they use STRING to complete an analysis of networked interactions of the proteins discovered in their study and the processes where they are found, as you can see in their figure.

I did my postdoc and some later research in the lab (Peer Bork, EMBL) that developed STRING, and I’ve created a tutorial on it, so any time it’s used, I’m interested :D. So, I went to Methods and Materials to see how the analysis was done. Though there was a decent explanation of the process, it was not enough for me to recreate the analysis. This is not a criticism of the paper or the authors, but of how papers are being published. More and more, papers include genomics analysis, but rarely are these reported in the research paper in the detail needed to easily reproduce the analysis. Projects like Galaxy (publicly available tutorial) and Taverna are filling that void, so I’d like to see more Methods and Materials sections include analysis histories and workflows. It definitely would help in the advancement of science.

And now to the tip of the week. The paper also refers to a new database (at least new to me, it’s at least two years old and was reported in “Phosida: management, structural and evolutionary investigation and prediction of phosphosites.“) called Phosida. The database “allows retrieval of phosphorylation and acetylation data of any protein of interest.” The Tip-of-the-Week today is a quick introduction to that database.

Choudhary, C., Kumar, C., Gnad, F., Nielsen, M., Rehman, M., Walther, T., Olsen, J., & Mann, M. (2009). Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions Science, 325(5942), 834-840 DOI: 10.1126/science.1175371

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  1. Pingback: Video Tips of the Week: Annual Review IV, 2nd half | The OpenHelix Blog

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