PMC:4129400 / 50048-51781
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4129400","sourcedb":"PMC","sourceid":"4129400","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4129400","text":"To assess pQTL reproducibility, we compared our results with those from a recent pQTL study that consistently quantified 2,279 proteins by isobaric tandem mass tag-based quantitative mass spectrometry across LCLs derived from 74 unrelated individuals from four populations in the HapMap Consortium.14 None of the 13 pQTLs identified in the YRI population from the Wu et al.14 study overlapped proteins quantified in our study, and two of the four pQTLs identified in our study at an FDR \u003c 0.05 for proteins overlapping between both studies were in a concordant effect direction in the Wu et al. study. However, because of the small overlap of proteins (n = 61) and samples (n = 22) between studies, we do not feel that these conclusions are sufficient to make any larger inferences about pQTL reproducibility between studies. The fundamental differences between our approach and that of Wu et al.14 are in the methodology (mass spectrometry versus targeted antibody-based methods); the proteins chosen for measurement (highly abundant proteins detected by the mass spectrometer versus a smaller subset of targeted transcription factors and disease-related signaling molecules for which we had high-quality antibodies); and the population (68 YRI individuals versus a collection of four different ethnic panels with 1–53 individuals in each). However, 12% of cis and trans pQTLs identified in LCLs in this study at p \u003c 10−6 replicate (here defined as concordant effect direction and nominal significance) in an unrelated cohort of 129 human cerebellum samples of European ancestry (data not shown), suggesting that many of these pQTLs are indeed real, tissue-independent associations (versus the null expectation of 2.5% replication).","tracks":[{"project":"2_test","denotations":[{"id":"25087611-23676674-2046368","span":{"begin":298,"end":300},"obj":"23676674"},{"id":"25087611-23676674-2046369","span":{"begin":373,"end":375},"obj":"23676674"},{"id":"25087611-23676674-2046370","span":{"begin":896,"end":898},"obj":"23676674"}],"attributes":[{"subj":"25087611-23676674-2046368","pred":"source","obj":"2_test"},{"subj":"25087611-23676674-2046369","pred":"source","obj":"2_test"},{"subj":"25087611-23676674-2046370","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ac93ec","default":true}]}]}}