FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2893945166> ?p ?o ?g. }

• W2893945166 abstract "Microarray and DNA-sequencing based technologies continue to produce enormous amounts of data on gene expression. This data has great potential to illuminate our understanding of biology and medicine, but the data alone is of limited value without computational tools to allow human investigators to visualize and interpret it in the context of their problem of interest.We created a web server called SHOE that provides an interactive, visual presentation of the available evidence of transcriptional regulation and gene co-expression to facilitate its exploration and interpretation. SHOE predicts the likely transcription factor binding sites in orthologous promoters of humans, mice, and rats using the combined information of 1) transcription factor binding preferences (position-specific scoring matrix (PSSM) libraries such as Transfac32, Jaspar, HOCOMOCO, ChIP-seq, SELEX, PBM, and iPS-reprogramming factor), 2) evolutionary conservation of putative binding sites in orthologous promoters, and 3) co-expression tendencies of gene pairs based on 1,714 normal human cells selected from the Gene Expression Omnibus Database.SHOE enables users to explore potential interactions between transcription factors and target genes via multiple data views, discover transcription factor binding motifs on top of gene co-expression, and visualize genes as a network of gene and transcription factors on its native gadget GeneViz, the CellDesigner pathway analyzer, and the Reactome database to search the pathways involved. As we demonstrate here when using the CREB1 and Nf-κB datasets, SHOE can reliably identify experimentally verified interactions and predict plausible novel ones, yielding new biological insights into the gene regulatory mechanisms involved. SHOE comes with a manual describing how to run it on a local PC or via the Garuda platform ( www.garuda-alliance.org ), where it joins other popular gadgets such as the CellDesigner pathway analyzer and the Reactome database, as part of analysis workflows to meet the growing needs of molecular biologists and medical researchers. SHOE is available from the following URL http://ec2-54-150-223-65.ap-northeast-1.compute.amazonaws.com A video demonstration of SHOE can be found here: https://www.youtube.com/watch?v=qARinNb9NtE." @default.
• W2893945166 created "2018-10-05" @default.
• W2893945166 creator A5003706120 @default.
• W2893945166 creator A5014180691 @default.
• W2893945166 creator A5030301728 @default.
• W2893945166 creator A5051194003 @default.
• W2893945166 creator A5083894809 @default.
• W2893945166 creator A5086835862 @default.
• W2893945166 creator A5088005667 @default.
• W2893945166 date "2018-09-27" @default.
• W2893945166 modified "2023-10-08" @default.
• W2893945166 title "Sequence homology in eukaryotes (SHOE): interactive visual tool for promoter analysis" @default.
• W2893945166 cites W1499095623 @default.
• W2893945166 cites W1500600592 @default.
• W2893945166 cites W1515226261 @default.
• W2893945166 cites W1543392005 @default.
• W2893945166 cites W1606150020 @default.
• W2893945166 cites W1633265983 @default.
• W2893945166 cites W1868478050 @default.
• W2893945166 cites W1903553665 @default.
• W2893945166 cites W1937488454 @default.
• W2893945166 cites W1970635846 @default.
• W2893945166 cites W1985124929 @default.
• W2893945166 cites W1986931816 @default.
• W2893945166 cites W1987412804 @default.
• W2893945166 cites W1988393300 @default.
• W2893945166 cites W1993987848 @default.
• W2893945166 cites W1994634559 @default.
• W2893945166 cites W1998300401 @default.
• W2893945166 cites W1999547015 @default.
• W2893945166 cites W2000432226 @default.
• W2893945166 cites W2003967338 @default.
• W2893945166 cites W2005953884 @default.
• W2893945166 cites W2006735433 @default.
• W2893945166 cites W2007105300 @default.
• W2893945166 cites W2010173918 @default.
• W2893945166 cites W2016323400 @default.
• W2893945166 cites W2019784830 @default.
• W2893945166 cites W2029726120 @default.
• W2893945166 cites W2039747213 @default.
• W2893945166 cites W2041282741 @default.
• W2893945166 cites W2053035414 @default.
• W2893945166 cites W2053852189 @default.
• W2893945166 cites W2058539819 @default.
• W2893945166 cites W2065674437 @default.
• W2893945166 cites W2068448872 @default.
• W2893945166 cites W2069565384 @default.
• W2893945166 cites W2073850887 @default.
• W2893945166 cites W2079674166 @default.
• W2893945166 cites W2081375228 @default.
• W2893945166 cites W2084620487 @default.
• W2893945166 cites W2085442947 @default.
• W2893945166 cites W2091942844 @default.
• W2893945166 cites W2095020383 @default.
• W2893945166 cites W2096940705 @default.
• W2893945166 cites W2101004371 @default.
• W2893945166 cites W2110692190 @default.
• W2893945166 cites W2116467413 @default.
• W2893945166 cites W2117197721 @default.
• W2893945166 cites W2120125642 @default.
• W2893945166 cites W2124649441 @default.
• W2893945166 cites W2126993840 @default.
• W2893945166 cites W2128916701 @default.
• W2893945166 cites W2135722286 @default.
• W2893945166 cites W2141408320 @default.
• W2893945166 cites W2143129697 @default.
• W2893945166 cites W2143257167 @default.
• W2893945166 cites W2143314089 @default.
• W2893945166 cites W2144894706 @default.
• W2893945166 cites W2146280873 @default.
• W2893945166 cites W2146539504 @default.
• W2893945166 cites W2146994504 @default.
• W2893945166 cites W2153921000 @default.
• W2893945166 cites W2157009395 @default.
• W2893945166 cites W2160659225 @default.
• W2893945166 cites W2167980479 @default.
• W2893945166 cites W2170677539 @default.
• W2893945166 cites W2176034226 @default.
• W2893945166 cites W2177905053 @default.
• W2893945166 cites W93066617 @default.
• W2893945166 doi "https://doi.org/10.1186/s12864-018-5101-3" @default.
• W2893945166 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/6161448" @default.
• W2893945166 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/30261835" @default.
• W2893945166 hasPublicationYear "2018" @default.
• W2893945166 type Work @default.
• W2893945166 sameAs 2893945166 @default.
• W2893945166 citedByCount "2" @default.
• W2893945166 countsByYear W28939451662020 @default.
• W2893945166 countsByYear W28939451662022 @default.
• W2893945166 crossrefType "journal-article" @default.
• W2893945166 hasAuthorship W2893945166A5003706120 @default.
• W2893945166 hasAuthorship W2893945166A5014180691 @default.
• W2893945166 hasAuthorship W2893945166A5030301728 @default.
• W2893945166 hasAuthorship W2893945166A5051194003 @default.
• W2893945166 hasAuthorship W2893945166A5083894809 @default.
• W2893945166 hasAuthorship W2893945166A5086835862 @default.
• W2893945166 hasAuthorship W2893945166A5088005667 @default.
• W2893945166 hasBestOaLocation W28939451661 @default.
• W2893945166 hasConcept C101762097 @default.
• W2893945166 hasConcept C104317684 @default.

• next