FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2151513786> ?p ?o ?g. }

• W2151513786 abstract "Abstract Background Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3' targeted microarrays. Here, we use the well studied Microarray Quality Control (MAQC) dataset to benchmark the Affymetrix Exon Array, and compare it to two other popular platforms: Illumina, and Affymetrix U133. Results We show that at the gene expression level, the Exon Array performs comparably with the two 3' targeted platforms. However, the interplatform correlation of the results is slightly lower than between the two 3' arrays. We show that some of the discrepancies stem from the RNA amplification protocols, e.g. the Exon Array is able to detect expression of non-polyadenylated transcripts. More importantly, we show that many other differences result from the ability of the Exon Array to monitor more detailed isoform-level changes; several examples illustrate that changes detected by the 3' platforms are actually isoform variations, and that the nature of these variations can be resolved using Exon Array data. Finally, we show how the Exon Array can be used to detect alternative isoform differences, such as alternative splicing, transcript termination, and alternative promoter usage. We discuss the possible pitfalls and false positives resulting from isoform-level analysis. Conclusion The Exon Array is a valuable tool that can be used to profile gene expression while providing important additional information regarding the types of gene isoforms that are expressed and variable. However, analysis of alternative splicing requires much more hands on effort and visualization of results in order to correctly interpret the data, and generally results in considerably higher false positive rates than expression analysis. One of the main sources of error in the MAQC dataset is variation in amplification efficiency across transcripts, most likely caused by joint effects of elevated GC content in the 5' ends of genes and reduced likelihood of random-primed first strand synthesis in the 3' ends of genes. These effects are currently not adequately corrected using existing statistical methods. We outline approaches to reduce such errors by filtering out potentially problematic data." @default.
• W2151513786 created "2016-06-24" @default.
• W2151513786 creator A5015683073 @default.
• W2151513786 creator A5021951229 @default.
• W2151513786 creator A5028257685 @default.
• W2151513786 creator A5037048441 @default.
• W2151513786 creator A5040878528 @default.
• W2151513786 creator A5046125890 @default.
• W2151513786 date "2008-11-07" @default.
• W2151513786 modified "2023-10-10" @default.
• W2151513786 title "Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays" @default.
• W2151513786 cites W1506013368 @default.
• W2151513786 cites W1560913816 @default.
• W2151513786 cites W1971278266 @default.
• W2151513786 cites W1978826084 @default.
• W2151513786 cites W1983555686 @default.
• W2151513786 cites W2006425206 @default.
• W2151513786 cites W2010637767 @default.
• W2151513786 cites W2011682793 @default.
• W2151513786 cites W2028599385 @default.
• W2151513786 cites W2028998497 @default.
• W2151513786 cites W2063948613 @default.
• W2151513786 cites W2081410039 @default.
• W2151513786 cites W2091765691 @default.
• W2151513786 cites W2092645079 @default.
• W2151513786 cites W2098603697 @default.
• W2151513786 cites W2110304444 @default.
• W2151513786 cites W2111788381 @default.
• W2151513786 cites W2117259632 @default.
• W2151513786 cites W2117949279 @default.
• W2151513786 cites W2118028633 @default.
• W2151513786 cites W2122105991 @default.
• W2151513786 cites W2135827569 @default.
• W2151513786 cites W2136746865 @default.
• W2151513786 cites W2145025818 @default.
• W2151513786 cites W2152129478 @default.
• W2151513786 cites W2154487835 @default.
• W2151513786 cites W2154628824 @default.
• W2151513786 cites W2157221164 @default.
• W2151513786 cites W2160697089 @default.
• W2151513786 cites W2161926708 @default.
• W2151513786 cites W2170989872 @default.
• W2151513786 cites W2740984310 @default.
• W2151513786 doi "https://doi.org/10.1186/1471-2164-9-529" @default.
• W2151513786 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2666767" @default.
• W2151513786 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/18990248" @default.
• W2151513786 hasPublicationYear "2008" @default.
• W2151513786 type Work @default.
• W2151513786 sameAs 2151513786 @default.
• W2151513786 citedByCount "67" @default.
• W2151513786 countsByYear W21515137862012 @default.
• W2151513786 countsByYear W21515137862013 @default.
• W2151513786 countsByYear W21515137862014 @default.
• W2151513786 countsByYear W21515137862015 @default.
• W2151513786 countsByYear W21515137862016 @default.
• W2151513786 countsByYear W21515137862017 @default.
• W2151513786 countsByYear W21515137862018 @default.
• W2151513786 crossrefType "journal-article" @default.
• W2151513786 hasAuthorship W2151513786A5015683073 @default.
• W2151513786 hasAuthorship W2151513786A5021951229 @default.
• W2151513786 hasAuthorship W2151513786A5028257685 @default.
• W2151513786 hasAuthorship W2151513786A5037048441 @default.
• W2151513786 hasAuthorship W2151513786A5040878528 @default.
• W2151513786 hasAuthorship W2151513786A5046125890 @default.
• W2151513786 hasBestOaLocation W21515137861 @default.
• W2151513786 hasConcept C104317684 @default.
• W2151513786 hasConcept C142575336 @default.
• W2151513786 hasConcept C150194340 @default.
• W2151513786 hasConcept C18431079 @default.
• W2151513786 hasConcept C194583182 @default.
• W2151513786 hasConcept C36823959 @default.
• W2151513786 hasConcept C39917842 @default.
• W2151513786 hasConcept C53345823 @default.
• W2151513786 hasConcept C54355233 @default.
• W2151513786 hasConcept C54458228 @default.
• W2151513786 hasConcept C67705224 @default.
• W2151513786 hasConcept C70721500 @default.
• W2151513786 hasConcept C86803240 @default.
• W2151513786 hasConcept C95371953 @default.
• W2151513786 hasConceptScore W2151513786C104317684 @default.
• W2151513786 hasConceptScore W2151513786C142575336 @default.
• W2151513786 hasConceptScore W2151513786C150194340 @default.
• W2151513786 hasConceptScore W2151513786C18431079 @default.
• W2151513786 hasConceptScore W2151513786C194583182 @default.
• W2151513786 hasConceptScore W2151513786C36823959 @default.
• W2151513786 hasConceptScore W2151513786C39917842 @default.
• W2151513786 hasConceptScore W2151513786C53345823 @default.
• W2151513786 hasConceptScore W2151513786C54355233 @default.
• W2151513786 hasConceptScore W2151513786C54458228 @default.
• W2151513786 hasConceptScore W2151513786C67705224 @default.
• W2151513786 hasConceptScore W2151513786C70721500 @default.
• W2151513786 hasConceptScore W2151513786C86803240 @default.
• W2151513786 hasConceptScore W2151513786C95371953 @default.
• W2151513786 hasIssue "1" @default.
• W2151513786 hasLocation W21515137861 @default.
• W2151513786 hasLocation W21515137862 @default.
• W2151513786 hasLocation W21515137863 @default.
• W2151513786 hasLocation W21515137864 @default.
• W2151513786 hasLocation W21515137865 @default.
• W2151513786 hasLocation W21515137866 @default.

• next