So far at OpenHelix we’ve generally been focusing on the more broad tools that are of use to the largest cross-section of biomedical researchers. Everybody needs genome browsers pretty much at some point in their research. However, I’ve always had a soft spot for tissue-specific resources. Since my PhD project was on muscle, I have a lot of thoughts on tissue-specific regulation, expression, and splicing that I think are going to be just fascinating as we build on the whole genome sequencing base projects. A lot of the “hypothetical” and “unknown” predicted sequences are going to fall out of spatial-and temporal-specific expression projects as we move forward.
That appears to be the case in liver according to a new proteomics paper. There’s a commentary in the Journal of Proteome Research that speaks to this:
Mammoth data set from human liver reported by Quinn Martin Eastman
A total of 6788 proteins were identified, though that number excludes >6000 proteins that had only one peptide match and were eliminated from the final count. The researchers identified proteins corresponding to 60% of all of the protein-encoding genes expressed in liver, which were identified by RNA analysis from the same samples….
Some 3721 of the identified proteins had not been seen in human liver before, though they had been detected in other human organs. Almost 1000 were “hypothetical”—their existence previously inferred from DNA sequence information only.
Emphasis mine. That’s very cool stuff.
The commentary refers to a paper in the same issue from a consortium of researchers, and links to the resulting database for the project. The database has about the most complicated name I’ve ever seen, visible in the paper title here:
First Insight into the Human Liver Proteome from PROTEOMESKY-LIVERHu 1.0, a Publicly Available Database
Hyphens and superscripts–oh my!
You can check out the corresponding databases associated with this project at 2 URLs:
dbLEP for Liver Expression Profile: http://dblep.hupo.org.cn
and Liverbase: http://liverbase.hupo.org.cn
I’m looking forward to other tissue collections as well.