Τίτλος:
DIANA-miRGen v4: Indexing promoters and regulators for more than 1500 microRNAs
Γλώσσες Τεκμηρίου:
Αγγλικά
Περίληψη:
Deregulation of microRNA (miRNA) expression plays a critical role in the transition from a physiological to a pathological state. The accurate miRNA promoter identification in multiple cell types is a fundamental endeavor towards understanding and characterizing the underlying mechanisms of both physiological as well as pathological conditions. DIANA-miRGen v4 (www.microrna.gr/mirgenv4) provides cell type specific miRNA transcription start sites (TSSs) for over 1500 miRNAs retrieved from the analysis of >1000 cap analysis of gene expression (CAGE) samples corresponding to 133 tissues, cell lines and primary cells available in FANTOM repository. MiRNA TSS locations were associated with transcription factor binding site (TFBSs) annotation, for >280 TFs, derived from analyzing the majority of ENCODE ChIP-Seq datasets. For the first time, clusters of cell types having common miRNA TSSs are characterized and provided through a user friendly interface with multiple layers of customization. DIANA-miRGen v4 significantly improves our understanding of miRNA biogenesis regulation at the transcriptional level by providing a unique integration of high-quality annotations for hundreds of cell specific miRNA promoters with experimentally derived TFBSs. © 2021 The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
Συγγραφείς:
Perdikopanis, N.
Georgakilas, G.K.
Grigoriadis, D.
Pierros, V.
Kavakiotis, I.
Alexiou, P.
Hatzigeorgiou, A.
Περιοδικό:
Nucleic Acids Research
Εκδότης:
Oxford University Press
Λέξεις-κλειδιά:
microRNA; microRNA; protein binding; transcription factor, Article; binding site; gene expression regulation; gene regulatory network; learning algorithm; molecular interaction; nucleic acid database; primary cell; RNA analysis; transcription initiation site; transcription regulation; cell line; genetic transcription; genetics; genome; human; Internet; metabolism; molecular genetics; nucleotide sequence; primary cell culture; promoter region; software, Base Sequence; Cell Line; Databases, Nucleic Acid; Genome; Humans; Internet; MicroRNAs; Molecular Sequence Annotation; Primary Cell Culture; Promoter Regions, Genetic; Protein Binding; Software; Transcription Factors; Transcription Initiation Site; Transcription, Genetic
DOI:
10.1093/nar/gkaa1060
