Posts Tagged ‘i0hsb’

Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes

Saturday, July 2nd, 2016

#SingleCell Coexpression…Reveals Distinct Func. Modules [v clustering bulk RNAseq]… & Clinical Outcomes [in GBM]

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. “}}

Reference “A large-scale method to measure absolute protein p…”

Sunday, June 10th, 2012

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 –
Q: how does phosphorylation stoichiometry relate to the phosphorylome ? how many of the things are fully phosphorylated ?

A tissue-specific atlas of mouse protein phosphorylatio… Cell. 2010 – PubMed – NCBI

Sunday, June 10th, 2012
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 ?

Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution

Sunday, June 10th, 2012

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

The impact of microRNAs on protein output. Nature. 2008 – PubMed – NCBI

Sunday, June 10th, 2012

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

Developmental Cell – Mapping Gene Expression in Two Xenopus Species: Evolutionary Constraints and Developmental Flexibility

Sunday, June 10th, 2012

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 :