FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W3164793609> ?p ?o ?g. }

• W3164793609 abstract "Understanding the functional effects of non-coding variants is important as they are often associated with gene-expression alteration and disease development. Over the past few years, many computational tools have been developed to predict their functional impact. However, the intrinsic difficulty in dealing with the scarcity of data leads to the necessity to further improve the algorithms. In this work, we propose a novel method, employing a semi-supervised deep-learning model with pseudo labels, which takes advantage of learning from both experimentally annotated and unannotated data.We prepared known functional non-coding variants with histone marks, DNA accessibility, and sequence context in GM12878, HepG2, and K562 cell lines. Applying our method to the dataset demonstrated its outstanding performance, compared with that of existing tools. Our results also indicated that the semi-supervised model with pseudo labels achieves higher predictive performance than the supervised model without pseudo labels. Interestingly, a model trained with the data in a certain cell line is unlikely to succeed in other cell lines, which implies the cell-type-specific nature of the non-coding variants. Remarkably, we found that DNA accessibility significantly contributes to the functional consequence of variants, which suggests the importance of open chromatin conformation prior to establishing the interaction of non-coding variants with gene regulation.The semi-supervised deep learning model coupled with pseudo labeling has advantages in studying with limited datasets, which is not unusual in biology. Our study provides an effective approach in finding non-coding mutations potentially associated with various biological phenomena, including human diseases." @default.
• W3164793609 created "2021-06-07" @default.
• W3164793609 creator A5044110621 @default.
• W3164793609 creator A5054681585 @default.
• W3164793609 creator A5059530002 @default.
• W3164793609 date "2021-06-02" @default.
• W3164793609 modified "2023-10-14" @default.
• W3164793609 title "A semi-supervised deep learning approach for predicting the functional effects of genomic non-coding variations" @default.
• W3164793609 cites W2011582941 @default.
• W3164793609 cites W2084160423 @default.
• W3164793609 cites W2092390808 @default.
• W3164793609 cites W2117446594 @default.
• W3164793609 cites W2160995259 @default.
• W3164793609 cites W2198606573 @default.
• W3164793609 cites W2212528563 @default.
• W3164793609 cites W2225726427 @default.
• W3164793609 cites W2256981962 @default.
• W3164793609 cites W2259938310 @default.
• W3164793609 cites W2270152626 @default.
• W3164793609 cites W2547988844 @default.
• W3164793609 cites W2799622612 @default.
• W3164793609 cites W2903347564 @default.
• W3164793609 cites W2903864929 @default.
• W3164793609 cites W2905035870 @default.
• W3164793609 cites W2951962793 @default.
• W3164793609 cites W2979805229 @default.
• W3164793609 cites W2981537718 @default.
• W3164793609 cites W2998404125 @default.
• W3164793609 doi "https://doi.org/10.1186/s12859-021-03999-8" @default.
• W3164793609 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/8171027" @default.
• W3164793609 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/34078253" @default.
• W3164793609 hasPublicationYear "2021" @default.
• W3164793609 type Work @default.
• W3164793609 sameAs 3164793609 @default.
• W3164793609 citedByCount "4" @default.
• W3164793609 countsByYear W31647936092022 @default.
• W3164793609 countsByYear W31647936092023 @default.
• W3164793609 crossrefType "journal-article" @default.
• W3164793609 hasAuthorship W3164793609A5044110621 @default.
• W3164793609 hasAuthorship W3164793609A5054681585 @default.
• W3164793609 hasAuthorship W3164793609A5059530002 @default.
• W3164793609 hasBestOaLocation W31647936091 @default.
• W3164793609 hasConcept C104317684 @default.
• W3164793609 hasConcept C105795698 @default.
• W3164793609 hasConcept C108583219 @default.
• W3164793609 hasConcept C119857082 @default.
• W3164793609 hasConcept C136389625 @default.
• W3164793609 hasConcept C150194340 @default.
• W3164793609 hasConcept C151730666 @default.
• W3164793609 hasConcept C154945302 @default.
• W3164793609 hasConcept C179518139 @default.
• W3164793609 hasConcept C2779343474 @default.
• W3164793609 hasConcept C33923547 @default.
• W3164793609 hasConcept C41008148 @default.
• W3164793609 hasConcept C50644808 @default.
• W3164793609 hasConcept C54355233 @default.
• W3164793609 hasConcept C70721500 @default.
• W3164793609 hasConcept C86803240 @default.
• W3164793609 hasConcept C95371953 @default.
• W3164793609 hasConceptScore W3164793609C104317684 @default.
• W3164793609 hasConceptScore W3164793609C105795698 @default.
• W3164793609 hasConceptScore W3164793609C108583219 @default.
• W3164793609 hasConceptScore W3164793609C119857082 @default.
• W3164793609 hasConceptScore W3164793609C136389625 @default.
• W3164793609 hasConceptScore W3164793609C150194340 @default.
• W3164793609 hasConceptScore W3164793609C151730666 @default.
• W3164793609 hasConceptScore W3164793609C154945302 @default.
• W3164793609 hasConceptScore W3164793609C179518139 @default.
• W3164793609 hasConceptScore W3164793609C2779343474 @default.
• W3164793609 hasConceptScore W3164793609C33923547 @default.
• W3164793609 hasConceptScore W3164793609C41008148 @default.
• W3164793609 hasConceptScore W3164793609C50644808 @default.
• W3164793609 hasConceptScore W3164793609C54355233 @default.
• W3164793609 hasConceptScore W3164793609C70721500 @default.
• W3164793609 hasConceptScore W3164793609C86803240 @default.
• W3164793609 hasConceptScore W3164793609C95371953 @default.
• W3164793609 hasFunder F4320334764 @default.
• W3164793609 hasIssue "S6" @default.
• W3164793609 hasLocation W31647936091 @default.
• W3164793609 hasLocation W31647936092 @default.
• W3164793609 hasLocation W31647936093 @default.
• W3164793609 hasOpenAccess W3164793609 @default.
• W3164793609 hasPrimaryLocation W31647936091 @default.
• W3164793609 hasRelatedWork W3192794374 @default.
• W3164793609 hasRelatedWork W4220686584 @default.
• W3164793609 hasRelatedWork W4223943233 @default.
• W3164793609 hasRelatedWork W4225161397 @default.
• W3164793609 hasRelatedWork W4246751904 @default.
• W3164793609 hasRelatedWork W4312200629 @default.
• W3164793609 hasRelatedWork W4360585206 @default.
• W3164793609 hasRelatedWork W4364306694 @default.
• W3164793609 hasRelatedWork W4380075502 @default.
• W3164793609 hasRelatedWork W4380086463 @default.
• W3164793609 hasVolume "22" @default.
• W3164793609 isParatext "false" @default.
• W3164793609 isRetracted "false" @default.
• W3164793609 magId "3164793609" @default.
• W3164793609 workType "article" @default.