linkstream2 microblog

#SingleCell Coexpression…Reveals Distinct Func. Modules [v clustering bulk RNAseq]… & Clinical Outcomes [in GBM]
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004892

QT:{{”
We found that the co-expressed genes observed in single cells and bulk tumors have little overlap and show distinct characteristics. The co-expressed genes identified in bulk tumors tend to have similar biological functions, and are enriched for intrachromosomal
interactions with synchronized promoter activity. In contrast, single-cell co-expressed genes are enriched for known protein-protein interactions, and are regulated through interchromosomal interactions. “}}

Nat. Methods. 2011 Aug; vol. 8(8) pp. 677-83
A large-scale method to measure absolute protein phosphorylation stoichiometries.
Wu R, Haas W, Dephoure N, Huttlin EL, Zhai B, Sowa ME, Gygi SP URL – http://www.ncbi.nlm.nih.gov/pubmed/21725298?dopt=Citation
Q: how does phosphorylation stoichiometry relate to the phosphorylome ? how many of the things are fully phosphorylated ?

http://www.ncbi.nlm.nih.gov/pubmed/21183079
A tissue-specific atlas of mouse protein phosphorylation and expression
interesting to intersect with mouse encode in relation to TFs & gene expression – how does it relate to cell lines ?

http://www.sciencemag.org/content/325/5948/1682.abstract

Relates to the lab’s rewiring paper (Shou et al.) and should have been cited as it has the same conclusion

http://www.ncbi.nlm.nih.gov/pubmed/18668037

few genes go down substantially in prot. abundance with a fall in RNA abundance from miRNA

http://www.cell.com/developmental-cell/retrieve/pii/S1534580711001213

Expression time course comparison of orthologs, which are closer than random. Uses sigmoid approximations for gene expression levels — on & off. Discussion on purifying selection related to expression.

Some interesting terms :
http://en.wikipedia.org/wiki/Heterochrony
http://medical-dictionary.thefreedictionary.com/heterometric