FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2953031504> ?p ?o ?g. }

• W2953031504 endingPage "794" @default.
• W2953031504 startingPage "787" @default.
• W2953031504 abstract "The majority of the human genome is composed of non-coding regions containing regulatory elements such as enhancers, which are crucial for controlling gene expression. Many variants associated with complex traits are in these regions, and may disrupt gene regulatory sequences. Consequently, it is important to not only identify true enhancers but also to test if a variant within an enhancer affects gene regulation. Recently, allele-specific analysis in high-throughput reporter assays, such as massively parallel reporter assays (MPRAs), have been used to functionally validate non-coding variants. However, we are still missing high-quality and robust data analysis tools for these datasets.We have further developed our method for allele-specific analysis QuASAR (quantitative allele-specific analysis of reads) to analyze allele-specific signals in barcoded read counts data from MPRA. Using this approach, we can take into account the uncertainty on the original plasmid proportions, over-dispersion, and sequencing errors. The provided allelic skew estimate and its standard error also simplifies meta-analysis of replicate experiments. Additionally, we show that a beta-binomial distribution better models the variability present in the allelic imbalance of these synthetic reporters and results in a test that is statistically well calibrated under the null. Applying this approach to the MPRA data, we found 602 SNPs with significant (false discovery rate 10%) allele-specific regulatory function in LCLs. We also show that we can combine MPRA with QuASAR estimates to validate existing experimental and computational annotations of regulatory variants. Our study shows that with appropriate data analysis tools, we can improve the power to detect allelic effects in high-throughput reporter assays.http://github.com/piquelab/QuASAR/tree/master/mpra.fluca@wayne.edu or rpique@wayne.edu.Supplementary data are available online at Bioinformatics." @default.
• W2953031504 created "2019-06-27" @default.
• W2953031504 creator A5024383046 @default.
• W2953031504 creator A5025934105 @default.
• W2953031504 creator A5035820223 @default.
• W2953031504 creator A5045777431 @default.
• W2953031504 creator A5053586170 @default.
• W2953031504 creator A5089187929 @default.
• W2953031504 date "2017-09-22" @default.
• W2953031504 modified "2023-10-10" @default.
• W2953031504 title "QuASAR-MPRA: accurate allele-specific analysis for massively parallel reporter assays" @default.
• W2953031504 cites W1533942137 @default.
• W2953031504 cites W1970326092 @default.
• W2953031504 cites W1972029972 @default.
• W2953031504 cites W1989004527 @default.
• W2953031504 cites W2007694108 @default.
• W2953031504 cites W2014347464 @default.
• W2953031504 cites W2023386301 @default.
• W2953031504 cites W2025943989 @default.
• W2953031504 cites W2027368464 @default.
• W2953031504 cites W2029892338 @default.
• W2953031504 cites W2033202128 @default.
• W2953031504 cites W2065020285 @default.
• W2953031504 cites W2066293229 @default.
• W2953031504 cites W2067673709 @default.
• W2953031504 cites W2070015764 @default.
• W2953031504 cites W2077874719 @default.
• W2953031504 cites W2094248448 @default.
• W2953031504 cites W2100640908 @default.
• W2953031504 cites W2101505979 @default.
• W2953031504 cites W2104116111 @default.
• W2953031504 cites W2107596936 @default.
• W2953031504 cites W2112087830 @default.
• W2953031504 cites W2120029762 @default.
• W2953031504 cites W2135993011 @default.
• W2953031504 cites W2136091734 @default.
• W2953031504 cites W2138253007 @default.
• W2953031504 cites W2142410561 @default.
• W2953031504 cites W2142933606 @default.
• W2953031504 cites W2145674897 @default.
• W2953031504 cites W2152239989 @default.
• W2953031504 cites W2152325859 @default.
• W2953031504 cites W2185560378 @default.
• W2953031504 cites W2196135315 @default.
• W2953031504 cites W2198606573 @default.
• W2953031504 cites W2212528563 @default.
• W2953031504 cites W2221356560 @default.
• W2953031504 cites W2259938310 @default.
• W2953031504 cites W2278401009 @default.
• W2953031504 cites W2412481123 @default.
• W2953031504 cites W2413629639 @default.
• W2953031504 cites W2532473654 @default.
• W2953031504 cites W2949145039 @default.
• W2953031504 cites W2951370351 @default.
• W2953031504 cites W2952255603 @default.
• W2953031504 doi "https://doi.org/10.1093/bioinformatics/btx598" @default.
• W2953031504 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/6049023" @default.
• W2953031504 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/29028988" @default.
• W2953031504 hasPublicationYear "2017" @default.
• W2953031504 type Work @default.
• W2953031504 sameAs 2953031504 @default.
• W2953031504 citedByCount "21" @default.
• W2953031504 countsByYear W29530315042018 @default.
• W2953031504 countsByYear W29530315042019 @default.
• W2953031504 countsByYear W29530315042020 @default.
• W2953031504 countsByYear W29530315042021 @default.
• W2953031504 countsByYear W29530315042022 @default.
• W2953031504 countsByYear W29530315042023 @default.
• W2953031504 crossrefType "journal-article" @default.
• W2953031504 hasAuthorship W2953031504A5024383046 @default.
• W2953031504 hasAuthorship W2953031504A5025934105 @default.
• W2953031504 hasAuthorship W2953031504A5035820223 @default.
• W2953031504 hasAuthorship W2953031504A5045777431 @default.
• W2953031504 hasAuthorship W2953031504A5053586170 @default.
• W2953031504 hasAuthorship W2953031504A5089187929 @default.
• W2953031504 hasBestOaLocation W29530315041 @default.
• W2953031504 hasConcept C104317684 @default.
• W2953031504 hasConcept C105795698 @default.
• W2953031504 hasConcept C111936080 @default.
• W2953031504 hasConcept C141231307 @default.
• W2953031504 hasConcept C150194340 @default.
• W2953031504 hasConcept C180754005 @default.
• W2953031504 hasConcept C2781162219 @default.
• W2953031504 hasConcept C33923547 @default.
• W2953031504 hasConcept C41008148 @default.
• W2953031504 hasConcept C54355233 @default.
• W2953031504 hasConcept C70721500 @default.
• W2953031504 hasConcept C86803240 @default.
• W2953031504 hasConceptScore W2953031504C104317684 @default.
• W2953031504 hasConceptScore W2953031504C105795698 @default.
• W2953031504 hasConceptScore W2953031504C111936080 @default.
• W2953031504 hasConceptScore W2953031504C141231307 @default.
• W2953031504 hasConceptScore W2953031504C150194340 @default.
• W2953031504 hasConceptScore W2953031504C180754005 @default.
• W2953031504 hasConceptScore W2953031504C2781162219 @default.
• W2953031504 hasConceptScore W2953031504C33923547 @default.
• W2953031504 hasConceptScore W2953031504C41008148 @default.
• W2953031504 hasConceptScore W2953031504C54355233 @default.

• next