FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2125847752> ?p ?o ?g. }

• W2125847752 endingPage "e1003598" @default.
• W2125847752 startingPage "e1003598" @default.
• W2125847752 abstract "Gene transcription mediated by RNA polymerase II (pol-II) is a key step in gene expression. The dynamics of pol-II moving along the transcribed region influence the rate and timing of gene expression. In this work, we present a probabilistic model of transcription dynamics which is fitted to pol-II occupancy time course data measured using ChIP-Seq. The model can be used to estimate transcription speed and to infer the temporal pol-II activity profile at the gene promoter. Model parameters are estimated using either maximum likelihood estimation or via Bayesian inference using Markov chain Monte Carlo sampling. The Bayesian approach provides confidence intervals for parameter estimates and allows the use of priors that capture domain knowledge, e.g. the expected range of transcription speeds, based on previous experiments. The model describes the movement of pol-II down the gene body and can be used to identify the time of induction for transcriptionally engaged genes. By clustering the inferred promoter activity time profiles, we are able to determine which genes respond quickly to stimuli and group genes that share activity profiles and may therefore be co-regulated. We apply our methodology to biological data obtained using ChIP-seq to measure pol-II occupancy genome-wide when MCF-7 human breast cancer cells are treated with estradiol (E2). The transcription speeds we obtain agree with those obtained previously for smaller numbers of genes with the advantage that our approach can be applied genome-wide. We validate the biological significance of the pol-II promoter activity clusters by investigating cluster-specific transcription factor binding patterns and determining canonical pathway enrichment. We find that rapidly induced genes are enriched for both estrogen receptor alpha (ERα) and FOXA1 binding in their proximal promoter regions." @default.
• W2125847752 created "2016-06-24" @default.
• W2125847752 creator A5020626165 @default.
• W2125847752 creator A5023995814 @default.
• W2125847752 creator A5036095832 @default.
• W2125847752 creator A5047230260 @default.
• W2125847752 creator A5071329195 @default.
• W2125847752 creator A5075254197 @default.
• W2125847752 creator A5079581490 @default.
• W2125847752 creator A5088432815 @default.
• W2125847752 date "2014-05-15" @default.
• W2125847752 modified "2023-10-18" @default.
• W2125847752 title "Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data" @default.
• W2125847752 cites W1520585082 @default.
• W2125847752 cites W1534349507 @default.
• W2125847752 cites W1964259728 @default.
• W2125847752 cites W1968343445 @default.
• W2125847752 cites W1968475238 @default.
• W2125847752 cites W1985621639 @default.
• W2125847752 cites W2002262418 @default.
• W2125847752 cites W2012284471 @default.
• W2125847752 cites W2016028169 @default.
• W2125847752 cites W2017297735 @default.
• W2125847752 cites W2023878500 @default.
• W2125847752 cites W2028748300 @default.
• W2125847752 cites W2033220168 @default.
• W2125847752 cites W2034071085 @default.
• W2125847752 cites W2040627562 @default.
• W2125847752 cites W2046317813 @default.
• W2125847752 cites W2074097219 @default.
• W2125847752 cites W2080683349 @default.
• W2125847752 cites W2083735573 @default.
• W2125847752 cites W2092992881 @default.
• W2125847752 cites W2102619694 @default.
• W2125847752 cites W2103248242 @default.
• W2125847752 cites W2105380177 @default.
• W2125847752 cites W2117089877 @default.
• W2125847752 cites W2118532317 @default.
• W2125847752 cites W2125373697 @default.
• W2125847752 cites W2132241624 @default.
• W2125847752 cites W2133465414 @default.
• W2125847752 cites W2144561939 @default.
• W2125847752 cites W2154968323 @default.
• W2125847752 cites W2156936974 @default.
• W2125847752 cites W2158217645 @default.
• W2125847752 cites W2166037178 @default.
• W2125847752 cites W2954040150 @default.
• W2125847752 cites W4206212643 @default.
• W2125847752 cites W4211018930 @default.
• W2125847752 cites W4211049957 @default.
• W2125847752 doi "https://doi.org/10.1371/journal.pcbi.1003598" @default.
• W2125847752 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/4022483" @default.
• W2125847752 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/24830797" @default.
• W2125847752 hasPublicationYear "2014" @default.
• W2125847752 type Work @default.
• W2125847752 sameAs 2125847752 @default.
• W2125847752 citedByCount "24" @default.
• W2125847752 countsByYear W21258477522015 @default.
• W2125847752 countsByYear W21258477522016 @default.
• W2125847752 countsByYear W21258477522017 @default.
• W2125847752 countsByYear W21258477522018 @default.
• W2125847752 countsByYear W21258477522020 @default.
• W2125847752 countsByYear W21258477522021 @default.
• W2125847752 countsByYear W21258477522022 @default.
• W2125847752 countsByYear W21258477522023 @default.
• W2125847752 crossrefType "journal-article" @default.
• W2125847752 hasAuthorship W2125847752A5020626165 @default.
• W2125847752 hasAuthorship W2125847752A5023995814 @default.
• W2125847752 hasAuthorship W2125847752A5036095832 @default.
• W2125847752 hasAuthorship W2125847752A5047230260 @default.
• W2125847752 hasAuthorship W2125847752A5071329195 @default.
• W2125847752 hasAuthorship W2125847752A5075254197 @default.
• W2125847752 hasAuthorship W2125847752A5079581490 @default.
• W2125847752 hasAuthorship W2125847752A5088432815 @default.
• W2125847752 hasBestOaLocation W21258477521 @default.
• W2125847752 hasConcept C101762097 @default.
• W2125847752 hasConcept C104317684 @default.
• W2125847752 hasConcept C107673813 @default.
• W2125847752 hasConcept C111350023 @default.
• W2125847752 hasConcept C134320426 @default.
• W2125847752 hasConcept C138885662 @default.
• W2125847752 hasConcept C150194340 @default.
• W2125847752 hasConcept C154945302 @default.
• W2125847752 hasConcept C160234255 @default.
• W2125847752 hasConcept C179926584 @default.
• W2125847752 hasConcept C41008148 @default.
• W2125847752 hasConcept C41895202 @default.
• W2125847752 hasConcept C54355233 @default.
• W2125847752 hasConcept C64350747 @default.
• W2125847752 hasConcept C70721500 @default.
• W2125847752 hasConcept C86803240 @default.
• W2125847752 hasConceptScore W2125847752C101762097 @default.
• W2125847752 hasConceptScore W2125847752C104317684 @default.
• W2125847752 hasConceptScore W2125847752C107673813 @default.
• W2125847752 hasConceptScore W2125847752C111350023 @default.
• W2125847752 hasConceptScore W2125847752C134320426 @default.
• W2125847752 hasConceptScore W2125847752C138885662 @default.
• W2125847752 hasConceptScore W2125847752C150194340 @default.

• next