+ Resolve Article
+ Follow Us
Follow on FacebookFollow on Facebook
Follow on TwitterFollow on Twitter

+ Translate
+ Subscribe to Site Feed
GeoScience Most Shared ContentMost Shared Content

Computational framework for analysis of prey-prey associations in interaction proteomics identifies novel human protein-protein interactions and networks

, : Computational framework for analysis of prey-prey associations in interaction proteomics identifies novel human protein-protein interactions and networks. Journal of Proteome Research 11(9): 4476-4487

Large-scale protein-protein interaction data sets have been generated for several species including yeast and human and have enabled the identification, quantification, and prediction of cellular molecular networks. Affinity purification-mass spectrometry (AP-MS) is the preeminent methodology for large-scale analysis of protein complexes, performed by immunopurifying a specific "bait" protein and its associated "prey" proteins. The analysis and interpretation of AP-MS data sets is, however, not straightforward. In addition, although yeast AP-MS data sets are relatively comprehensive, current human AP-MS data sets only sparsely cover the human interactome. Here we develop a framework for analysis of AP-MS data sets that addresses the issues of noise, missing data, and sparsity of coverage in the context of a current, real world human AP-MS data set. Our goal is to extend and increase the density of the known human interactome by integrating bait-prey and cocomplexed preys (prey-prey associations) into networks. Our framework incorporates a score for each identified protein, as well as elements of signal processing to improve the confidence of identified protein-protein interactions. We identify many protein networks enriched in known biological processes and functions. In addition, we show that integrated bait-prey and prey-prey interactions can be used to refine network topology and extend known protein networks.


PMID: 22845868

DOI: 10.1021/pr300227y

Other references

de la Rue, Sarah R., 2008: Integrated quantitative palynology and chemostratigraphy of Upper Devonian black shales; implications for anoxia-related controls on green algal distributions. AAPG Bulletin 92.11

Kenny, P.J.; Boutrel, B.; Gasparini, F.; Koob, G.F.; Markou, A., 2004: Metabotropic glutamate 5 receptor blockade may attenuate cocaine self-administration by decreasing brain reward function in rats. Rationale: Evidence is accumulating that metabotropic glutamate 5 (mGlu5) receptors play an important role in regulating the reinforcing actions of drugs of abuse. Objectives: We examined the effects of the mGlu5 receptor antagonist MPEP on cocain...

Colinas Leon, M.T.; Lozoya Saldana, H.; Raya Rivera, M.Y., 1997: Isozyme patterns on cellulose acetate gel electrophoresis (CAGE) differentiate Mexican potato cultivars. Tubers and leaves of 16 potato (Solanum tuberosum) genotypes grown in vivo and in vitro, were evaluated for polymorphism of 9 isoenzymes by CAGE. For most of the enzymatic systems tested, bands from tubers were more evident than those from leaves....

Zhang, S.; Liang, F.; Zhu, J.; Chen, Q., 2017: Risk of Pneumonitis Associated with Programmed Cell Death 1 Inhibitors in Cancer Patients: A Meta-analysis. Pneumonitis, a rare but potentially life-threatening adverse event in cancer patients receiving programmed death 1 (PD-1) or programmed death ligand 1 (PD-L1) inhibitors, has been reported in case reports, clinical trials, and retrospective studie...

Ferri S.; Arrigo Reina R.; Candeletti S.; Costa G.; Murari G.; Speroni E.; Scoto G., 1983: Central and peripheral sites of action for the protective effect of opioids of the rat stomach. Rats exposed to combined cold and restraint exhibited a reduced intensity of gastric damage when pre-treated i.p. with morphine hydrochloride or with the synthetic enkephalin analog [D-Ala2,MePhe4,Met(O)5ol]enkephalin (FK 33-824). Morphine hydroch...

Booyse, F.M.; Hoveke, T.P.; Rafelson, M.E., 1968: Studies on human platelets. II. Protein synthetic activity of various platelet populations. Biochimica et Biophysica Acta 157(3): 660-663

Scholbach, T.; Girelli, E.; Scholbach, J., 2006: Tissue pulsatility index: A never parameter to evaluate renal transplant perfusion. Background. Chronic allograft nephropathy (CAN) is characterized by loss of parenchymal perfusion. We applied therefore the novel parameter Tissue Pulsatility Index (TPI) to quantify transplant perfusion in the long-term Surveillance of renal tran...

Spasski, A.A.; Ivashkin, V.M.; Bogoyavlenski, Y.K., 1959: The work of the 3o6th All-Union helminthological expedition in 1956 to the Tuva Autonomous Region. (Preliminary communication).. Spasski et al. give a preliminary report on the helminthological expedition to the Tuva region in 1956. Biological and veterinary sections examined a total of over 1, 650 fishes, amphibians, reptiles, birds and mammals, including domestic animals....

Saver, J.L.; Kidwell, C., 2004: Neuroimaging in TIAs. Neurology 62(8 Suppl 6): S22-S25

Amsterdam, J., D.; Brunswick, D., J., 2002: Site variability in treatment outcome in antidepressant trials. Objective: Site-specific differences in treatment outcome during multisite antidepressant drug trials may contribute to a negative or failed clinical trial. As part of a five-site, long-term, double-blind, placebo-controlled, relapse prevention tr...