FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4205134693> ?p ?o ?g. }

• W4205134693 abstract "Open chromatin regions (OCRs) allow direct interaction between cis-regulatory elements and trans-acting factors. Therefore, predicting all potential OCR-mediated loops is essential for deciphering the regulation mechanism of gene expression. However, existing loop prediction tools are restricted to specific anchor types. Here, we present CharID (Chromatin Accessible Region Interaction Detector), a two-step model that combines neural network and ensemble learning to predict OCR-mediated loops. In the first step, CharID-Anchor, an attention-based hybrid CNN-BiGRU network is constructed to discriminate between the anchor and nonanchor OCRs. In the second step, CharID-Loop uses gradient boosting decision tree with chromosome-split strategy to predict the interactions between anchor OCRs. The performance was assessed in three human cell lines, and CharID showed superior prediction performance compared with other algorithms. In contrast to the methods designed to predict a particular type of loops, CharID can detect varieties of chromatin loops not limited to enhancer-promoter loops or architectural protein-mediated loops. We constructed the OCR-mediated interaction network using the predicted loops and identified hub anchors, which are highlighted by their proximity to housekeeping genes. By analyzing loops containing SNPs associated with cardiovascular disease, we identified an SNP-gene loop indicating the regulation mechanism of the GFOD1. Taken together, CharID universally predicts diverse chromatin loops beyond other state-of-the-art methods, which are limited by anchor types, and experimental techniques, which are limited by sensitivities drastically decaying with the genomic distance of anchors. Finally, we hosted Peaksniffer, a user-friendly web server that provides online prediction, query and visualization of OCRs and associated loops." @default.
• W4205134693 created "2022-01-25" @default.
• W4205134693 creator A5000444357 @default.
• W4205134693 creator A5024537538 @default.
• W4205134693 creator A5075372002 @default.
• W4205134693 creator A5081156337 @default.
• W4205134693 creator A5085706122 @default.
• W4205134693 creator A5088654871 @default.
• W4205134693 date "2022-01-25" @default.
• W4205134693 modified "2023-10-18" @default.
• W4205134693 title "CharID: a two-step model for universal prediction of interactions between chromatin accessible regions" @default.
• W4205134693 cites W1019830208 @default.
• W4205134693 cites W1900337607 @default.
• W4205134693 cites W1964963969 @default.
• W4205134693 cites W1973062929 @default.
• W4205134693 cites W1996202672 @default.
• W4205134693 cites W1997271589 @default.
• W4205134693 cites W2018363492 @default.
• W4205134693 cites W2053234324 @default.
• W4205134693 cites W2056198580 @default.
• W4205134693 cites W2061412286 @default.
• W4205134693 cites W2078059415 @default.
• W4205134693 cites W2110417468 @default.
• W4205134693 cites W2131186458 @default.
• W4205134693 cites W2133557974 @default.
• W4205134693 cites W2140952049 @default.
• W4205134693 cites W2149454526 @default.
• W4205134693 cites W2157009395 @default.
• W4205134693 cites W2169710039 @default.
• W4205134693 cites W2170830174 @default.
• W4205134693 cites W2195190137 @default.
• W4205134693 cites W2198606573 @default.
• W4205134693 cites W2247766769 @default.
• W4205134693 cites W2333286569 @default.
• W4205134693 cites W2344602241 @default.
• W4205134693 cites W2345512687 @default.
• W4205134693 cites W2395905799 @default.
• W4205134693 cites W2523285811 @default.
• W4205134693 cites W2530292798 @default.
• W4205134693 cites W2567008309 @default.
• W4205134693 cites W2596726365 @default.
• W4205134693 cites W2735099323 @default.
• W4205134693 cites W2752211734 @default.
• W4205134693 cites W2781657900 @default.
• W4205134693 cites W2792734199 @default.
• W4205134693 cites W2795583235 @default.
• W4205134693 cites W2804974840 @default.
• W4205134693 cites W2887454912 @default.
• W4205134693 cites W2901303766 @default.
• W4205134693 cites W2918014537 @default.
• W4205134693 cites W2921983621 @default.
• W4205134693 cites W2927575800 @default.
• W4205134693 cites W2928665623 @default.
• W4205134693 cites W2949423586 @default.
• W4205134693 cites W2951218167 @default.
• W4205134693 cites W2952935243 @default.
• W4205134693 cites W2952947531 @default.
• W4205134693 cites W2970602317 @default.
• W4205134693 cites W2982376588 @default.
• W4205134693 cites W2993022331 @default.
• W4205134693 cites W3003909932 @default.
• W4205134693 cites W3013411594 @default.
• W4205134693 cites W3019879298 @default.
• W4205134693 cites W3021661024 @default.
• W4205134693 cites W3041895828 @default.
• W4205134693 cites W3046151504 @default.
• W4205134693 cites W3099969680 @default.
• W4205134693 cites W3124680305 @default.
• W4205134693 cites W3147833596 @default.
• W4205134693 cites W3186634360 @default.
• W4205134693 cites W3205525370 @default.
• W4205134693 doi "https://doi.org/10.1093/bib/bbab602" @default.
• W4205134693 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/35077535" @default.
• W4205134693 hasPublicationYear "2022" @default.
• W4205134693 type Work @default.
• W4205134693 citedByCount "1" @default.
• W4205134693 countsByYear W42051346932023 @default.
• W4205134693 crossrefType "journal-article" @default.
• W4205134693 hasAuthorship W4205134693A5000444357 @default.
• W4205134693 hasAuthorship W4205134693A5024537538 @default.
• W4205134693 hasAuthorship W4205134693A5075372002 @default.
• W4205134693 hasAuthorship W4205134693A5081156337 @default.
• W4205134693 hasAuthorship W4205134693A5085706122 @default.
• W4205134693 hasAuthorship W4205134693A5088654871 @default.
• W4205134693 hasConcept C104317684 @default.
• W4205134693 hasConcept C111936080 @default.
• W4205134693 hasConcept C119857082 @default.
• W4205134693 hasConcept C154945302 @default.
• W4205134693 hasConcept C2775905019 @default.
• W4205134693 hasConcept C41008148 @default.
• W4205134693 hasConcept C54355233 @default.
• W4205134693 hasConcept C70721500 @default.
• W4205134693 hasConcept C83640560 @default.
• W4205134693 hasConcept C84525736 @default.
• W4205134693 hasConcept C86339819 @default.
• W4205134693 hasConcept C86803240 @default.
• W4205134693 hasConcept C93946551 @default.
• W4205134693 hasConceptScore W4205134693C104317684 @default.
• W4205134693 hasConceptScore W4205134693C111936080 @default.
• W4205134693 hasConceptScore W4205134693C119857082 @default.

• next