PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-3 (3)
 

Clipboard (0)
None
Journals
Authors
more »
Year of Publication
Document Types
1.  A map of human protein interactions derived from co-expression of human mRNAs and their orthologs 
The human protein interaction network will offer global insights into the molecular organization of cells and provide a framework for modeling human disease, but the network's large scale demands new approaches. We report a set of 7000 physical associations among human proteins inferred from indirect evidence: the comparison of human mRNA co-expression patterns with those of orthologous genes in five other eukaryotes, which we demonstrate identifies proteins in the same physical complexes. To evaluate the accuracy of the predicted physical associations, we apply quantitative mass spectrometry shotgun proteomics to measure elution profiles of 3013 human proteins during native biochemical fractionation, demonstrating systematically that putative interaction partners tend to co-sediment. We further validate uncharacterized proteins implicated by the associations in ribosome biogenesis, including WBSCR20C, associated with Williams–Beuren syndrome. This meta-analysis therefore exploits non-protein-based data, but successfully predicts associations, including 5589 novel human physical protein associations, with measured accuracies of 54±10%, comparable to direct large-scale interaction assays. The new associations' derivation from conserved in vivo phenomena argues strongly for their biological relevance.
doi:10.1038/msb.2008.19
PMCID: PMC2387231  PMID: 18414481
interactions; mass spectrometry; networks; proteomics; systems biology
2.  How complete are current yeast and human protein-interaction networks? 
Genome Biology  2006;7(11):120.
How can protein-interaction networks can be made more complete?
We estimate the full yeast protein-protein interaction network to contain 37,800-75,500 interactions and the human network 154,000-369,000, but owing to a high false-positive rate, current maps are roughly only 50% and 10% complete, respectively. Paradoxically, releasing raw, unfiltered assay data might help separate true from false interactions.
doi:10.1186/gb-2006-7-11-120
PMCID: PMC1794583  PMID: 17147767
3.  Systematic profiling of cellular phenotypes with spotted cell microarrays reveals mating-pheromone response genes 
Genome Biology  2006;7(1):R6.
Spotted cell microarrays were developed for measuring cellular phenotypes on a large scale and used to identify genes involved in the response of yeast to mating pheromone.
We have developed spotted cell microarrays for measuring cellular phenotypes on a large scale. Collections of cells are printed, stained for subcellular features, then imaged via automated, high-throughput microscopy, allowing systematic phenotypic characterization. We used this technology to identify genes involved in the response of yeast to mating pheromone. Besides morphology assays, cell microarrays should be valuable for high-throughput in situ hybridization and immunoassays, enabling new classes of genetic assays based on cell imaging.
doi:10.1186/gb-2006-7-1-r6
PMCID: PMC1431703  PMID: 16507139

Results 1-3 (3)