FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2951837503> ?p ?o ?g. }

• W2951837503 abstract "The quantitative prediction of transcriptional activity of genes using promoter sequence is fundamental to the engineering of biological systems for industrial purposes and understanding the natural variation in gene expression. To catalyze the development of new algorithms for this purpose, the Dialogue on Reverse Engineering Assessment and Methods (DREAM) organized a community challenge seeking predictive models of promoter activity given normalized promoter activity data for 90 ribosomal protein promoters driving expression of a fluorescent reporter gene. By developing an unbiased modeling approach that performs an iterative search for predictive DNA sequence features using the frequencies of various k-mers, inferred DNA mechanical properties and spatial positions of promoter sequences, we achieved the best performer status in this challenge. The specific predictive features used in the model included the frequency of the nucleotide G, the length of polymeric tracts of T and TA, the frequencies of 6 distinct trinucleotides and 12 tetranucleotides, and the predicted protein deformability of the DNA sequence. Our method accurately predicted the activity of 20 natural variants of ribosomal protein promoters (Spearman correlation r = 0.73) as compared to 33 laboratory-mutated variants of the promoters (r = 0.57) in a test set that was hidden from participants. Notably, our model differed substantially from the rest in 2 main ways: i) it did not explicitly utilize transcription factor binding information implying that subtle DNA sequence features are highly associated with gene expression, and ii) it was entirely based on features extracted exclusively from the 100 bp region upstream from the translational start site demonstrating that this region encodes much of the overall promoter activity. The findings from this study have important implications for the engineering of predictable gene expression systems and the evolution of gene expression in naturally occurring biological systems." @default.
• W2951837503 created "2019-06-27" @default.
• W2951837503 creator A5012502919 @default.
• W2951837503 creator A5019857186 @default.
• W2951837503 creator A5059033429 @default.
• W2951837503 creator A5072425194 @default.
• W2951837503 creator A5080523815 @default.
• W2951837503 creator A5081185204 @default.
• W2951837503 creator A5086304683 @default.
• W2951837503 date "2015-10-27" @default.
• W2951837503 modified "2023-09-24" @default.
• W2951837503 title "Prediction of Fine-tuned Promoter Activity from DNA Sequence" @default.
• W2951837503 cites W1502406759 @default.
• W2951837503 cites W1968916935 @default.
• W2951837503 cites W1969230749 @default.
• W2951837503 cites W1970019286 @default.
• W2951837503 cites W1973850164 @default.
• W2951837503 cites W1979870939 @default.
• W2951837503 cites W1981779495 @default.
• W2951837503 cites W1982197590 @default.
• W2951837503 cites W1996065618 @default.
• W2951837503 cites W1996270170 @default.
• W2951837503 cites W1996852546 @default.
• W2951837503 cites W2004912100 @default.
• W2951837503 cites W2006228189 @default.
• W2951837503 cites W2014119967 @default.
• W2951837503 cites W2033072260 @default.
• W2951837503 cites W2038540528 @default.
• W2951837503 cites W2043481575 @default.
• W2951837503 cites W2049883153 @default.
• W2951837503 cites W2060789589 @default.
• W2951837503 cites W2061851611 @default.
• W2951837503 cites W2070340804 @default.
• W2951837503 cites W2072875800 @default.
• W2951837503 cites W2087177706 @default.
• W2951837503 cites W2090803844 @default.
• W2951837503 cites W2092044900 @default.
• W2951837503 cites W2095994064 @default.
• W2951837503 cites W2100668965 @default.
• W2951837503 cites W2108551329 @default.
• W2951837503 cites W2111846924 @default.
• W2951837503 cites W2114161957 @default.
• W2951837503 cites W2114504176 @default.
• W2951837503 cites W2118308505 @default.
• W2951837503 cites W2121761522 @default.
• W2951837503 cites W2121763778 @default.
• W2951837503 cites W2123868608 @default.
• W2951837503 cites W2125987139 @default.
• W2951837503 cites W2127754721 @default.
• W2951837503 cites W2130912501 @default.
• W2951837503 cites W2133990480 @default.
• W2951837503 cites W2135072516 @default.
• W2951837503 cites W2137794200 @default.
• W2951837503 cites W2142260323 @default.
• W2951837503 cites W2143855992 @default.
• W2951837503 cites W2149641002 @default.
• W2951837503 cites W2150236135 @default.
• W2951837503 cites W2151029800 @default.
• W2951837503 cites W2152223521 @default.
• W2951837503 cites W2153143918 @default.
• W2951837503 cites W2154109129 @default.
• W2951837503 cites W2155718935 @default.
• W2951837503 cites W2159420567 @default.
• W2951837503 cites W2160381044 @default.
• W2951837503 cites W2162066191 @default.
• W2951837503 cites W2166223559 @default.
• W2951837503 cites W2168103533 @default.
• W2951837503 cites W2170604299 @default.
• W2951837503 doi "https://doi.org/10.1101/030049" @default.
• W2951837503 hasPublicationYear "2015" @default.
• W2951837503 type Work @default.
• W2951837503 sameAs 2951837503 @default.
• W2951837503 citedByCount "0" @default.
• W2951837503 crossrefType "posted-content" @default.
• W2951837503 hasAuthorship W2951837503A5012502919 @default.
• W2951837503 hasAuthorship W2951837503A5019857186 @default.
• W2951837503 hasAuthorship W2951837503A5059033429 @default.
• W2951837503 hasAuthorship W2951837503A5072425194 @default.
• W2951837503 hasAuthorship W2951837503A5080523815 @default.
• W2951837503 hasAuthorship W2951837503A5081185204 @default.
• W2951837503 hasAuthorship W2951837503A5086304683 @default.
• W2951837503 hasBestOaLocation W29518375031 @default.
• W2951837503 hasConcept C101762097 @default.
• W2951837503 hasConcept C104317684 @default.
• W2951837503 hasConcept C150194340 @default.
• W2951837503 hasConcept C2778112365 @default.
• W2951837503 hasConcept C3662595 @default.
• W2951837503 hasConcept C38062823 @default.
• W2951837503 hasConcept C51679486 @default.
• W2951837503 hasConcept C54355233 @default.
• W2951837503 hasConcept C552990157 @default.
• W2951837503 hasConcept C67705224 @default.
• W2951837503 hasConcept C70721500 @default.
• W2951837503 hasConcept C86803240 @default.
• W2951837503 hasConcept C88478588 @default.
• W2951837503 hasConceptScore W2951837503C101762097 @default.
• W2951837503 hasConceptScore W2951837503C104317684 @default.
• W2951837503 hasConceptScore W2951837503C150194340 @default.
• W2951837503 hasConceptScore W2951837503C2778112365 @default.
• W2951837503 hasConceptScore W2951837503C3662595 @default.

• next