FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W1591970889> ?p ?o ?g. }

• W1591970889 abstract "As sequencing costs are being lowered continuously, RNA-seq has gradually been adopted as the first choice for comparative transcriptome studies with bacteria. Unlike microarrays, RNA-seq can directly detect cDNA derived from mRNA transcripts at a single nucleotide resolution. Not only does this allow researchers to determine the absolute expression level of genes, but it also conveys information about transcript structure. Few automatic software tools have yet been established to investigate large-scale RNA-seq data for bacterial transcript structure analysis.In this study, 54 directional RNA-seq libraries from Salmonella serovar Typhimurium (S. Typhimurium) 14028s were examined for potential relationships between read mapping patterns and transcript structure. We developed an empirical method, combined with statistical tests, to automatically detect key transcript features, including transcriptional start sites (TSSs), transcriptional termination sites (TTSs) and operon organization. Using our method, we obtained 2,764 TSSs and 1,467 TTSs for 1331 and 844 different genes, respectively. Identification of TSSs facilitated further discrimination of 215 putative sigma 38 regulons and 863 potential sigma 70 regulons. Combining the TSSs and TTSs with intergenic distance and co-expression information, we comprehensively annotated the operon organization in S. Typhimurium 14028s.Our results show that directional RNA-seq can be used to detect transcriptional borders at an acceptable resolution of ±10-20 nucleotides. Technical limitations of the RNA-seq procedure may prevent single nucleotide resolution. The automatic transcript border detection methods, statistical models and operon organization pipeline that we have described could be widely applied to RNA-seq studies in other bacteria. Furthermore, the TSSs, TTSs, operons, promoters and unstranslated regions that we have defined for S. Typhimurium 14028s may constitute valuable resources that can be used for comparative analyses with other Salmonella serotypes." @default.
• W1591970889 created "2016-06-24" @default.
• W1591970889 creator A5005849751 @default.
• W1591970889 creator A5058160944 @default.
• W1591970889 creator A5063360595 @default.
• W1591970889 date "2015-05-07" @default.
• W1591970889 modified "2023-10-09" @default.
• W1591970889 title "An empirical strategy to detect bacterial transcript structure from directional RNA-seq transcriptome data" @default.
• W1591970889 cites W1597938147 @default.
• W1591970889 cites W1968698890 @default.
• W1591970889 cites W1970558305 @default.
• W1591970889 cites W1973404157 @default.
• W1591970889 cites W1977384011 @default.
• W1591970889 cites W1981342084 @default.
• W1591970889 cites W1984628925 @default.
• W1591970889 cites W1994170056 @default.
• W1591970889 cites W2016170819 @default.
• W1591970889 cites W2023401038 @default.
• W1591970889 cites W2023621259 @default.
• W1591970889 cites W2025853251 @default.
• W1591970889 cites W2044589156 @default.
• W1591970889 cites W2054073262 @default.
• W1591970889 cites W2056253073 @default.
• W1591970889 cites W2060095084 @default.
• W1591970889 cites W2062896692 @default.
• W1591970889 cites W2065637677 @default.
• W1591970889 cites W2086884639 @default.
• W1591970889 cites W2096959582 @default.
• W1591970889 cites W2101292724 @default.
• W1591970889 cites W2103441770 @default.
• W1591970889 cites W2105784079 @default.
• W1591970889 cites W2108388593 @default.
• W1591970889 cites W2112194896 @default.
• W1591970889 cites W2114104545 @default.
• W1591970889 cites W2116373379 @default.
• W1591970889 cites W2121365413 @default.
• W1591970889 cites W2124985265 @default.
• W1591970889 cites W2125069014 @default.
• W1591970889 cites W2127865724 @default.
• W1591970889 cites W2131417813 @default.
• W1591970889 cites W2138439355 @default.
• W1591970889 cites W2153992812 @default.
• W1591970889 cites W2154454968 @default.
• W1591970889 cites W2156274103 @default.
• W1591970889 cites W2158266834 @default.
• W1591970889 cites W2160165249 @default.
• W1591970889 cites W2162402851 @default.
• W1591970889 cites W2165202736 @default.
• W1591970889 doi "https://doi.org/10.1186/s12864-015-1555-8" @default.
• W1591970889 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/4422608" @default.
• W1591970889 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/25947005" @default.
• W1591970889 hasPublicationYear "2015" @default.
• W1591970889 type Work @default.
• W1591970889 sameAs 1591970889 @default.
• W1591970889 citedByCount "10" @default.
• W1591970889 countsByYear W15919708892015 @default.
• W1591970889 countsByYear W15919708892016 @default.
• W1591970889 countsByYear W15919708892017 @default.
• W1591970889 countsByYear W15919708892018 @default.
• W1591970889 countsByYear W15919708892019 @default.
• W1591970889 countsByYear W15919708892020 @default.
• W1591970889 crossrefType "journal-article" @default.
• W1591970889 hasAuthorship W1591970889A5005849751 @default.
• W1591970889 hasAuthorship W1591970889A5058160944 @default.
• W1591970889 hasAuthorship W1591970889A5063360595 @default.
• W1591970889 hasBestOaLocation W15919708891 @default.
• W1591970889 hasConcept C104317684 @default.
• W1591970889 hasConcept C107397762 @default.
• W1591970889 hasConcept C150194340 @default.
• W1591970889 hasConcept C162317418 @default.
• W1591970889 hasConcept C165864922 @default.
• W1591970889 hasConcept C203075996 @default.
• W1591970889 hasConcept C54355233 @default.
• W1591970889 hasConcept C547475151 @default.
• W1591970889 hasConcept C62361671 @default.
• W1591970889 hasConcept C67705224 @default.
• W1591970889 hasConcept C70721500 @default.
• W1591970889 hasConcept C86803240 @default.
• W1591970889 hasConcept C95371953 @default.
• W1591970889 hasConceptScore W1591970889C104317684 @default.
• W1591970889 hasConceptScore W1591970889C107397762 @default.
• W1591970889 hasConceptScore W1591970889C150194340 @default.
• W1591970889 hasConceptScore W1591970889C162317418 @default.
• W1591970889 hasConceptScore W1591970889C165864922 @default.
• W1591970889 hasConceptScore W1591970889C203075996 @default.
• W1591970889 hasConceptScore W1591970889C54355233 @default.
• W1591970889 hasConceptScore W1591970889C547475151 @default.
• W1591970889 hasConceptScore W1591970889C62361671 @default.
• W1591970889 hasConceptScore W1591970889C67705224 @default.
• W1591970889 hasConceptScore W1591970889C70721500 @default.
• W1591970889 hasConceptScore W1591970889C86803240 @default.
• W1591970889 hasConceptScore W1591970889C95371953 @default.
• W1591970889 hasIssue "1" @default.
• W1591970889 hasLocation W15919708891 @default.
• W1591970889 hasLocation W15919708892 @default.
• W1591970889 hasLocation W15919708893 @default.
• W1591970889 hasLocation W15919708894 @default.
• W1591970889 hasOpenAccess W1591970889 @default.
• W1591970889 hasPrimaryLocation W15919708891 @default.
• W1591970889 hasRelatedWork W1930517486 @default.

• next