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Table 2 Database of ncRNAs

From: Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application

Cancer or basis Database Species Website Short description Ref
Cancer Lnc2Cancer v2.0 lncRNA An updated database that provides comprehensive experimentally supported associations between lncRNAs and human cancers. [180]
  TANRIC lncRNA This database characterizes the expression profiles of lncRNAs in large patient cohorts of 20 cancer types, including TCGA and independent datasets (> 8000 samples overall). [179]
  lnCaNet lncRNA This database provides a comprehensive co-expression data resource which reveals the interactions between lncRNA and non-neighbouring cancer genes. [181]
  LncRNADisease 2.0 lncRNA A database integrating comprehensive experimentally supported and predicted lncRNA-disease associations. [182]
  The Cancer LncRNome Atlas lncRNA An academic research database to explore the lncRNA alternations across multiple human cancer types. [194]
  SELER lncRNA A database of super-enhancer-associated lncRNA-directed transcriptional regulation in human cancers. [195]
  CSCD circRNA A database that focuses on distinguishing cancer-specific circRNAs from noncancerous circRNAs, and reports predicted cellular location, RBP sites, and ORFs. [183]
  Circ2Traits circRNA Provide cirRNA-disease association based on the interaction of circRNAs with disease-related miRNAs and SNP mapped on circRNA loci. [184]
  CircR2Disease circRNA Provide a comprehensive resource for circRNA deregulation in various diseases, containing 725 associations between 661 circRNAs and 100 diseases. [185]
  CircRNA disease circRNA A manually curated database of experimentally supported circRNA-disease associations. [196]
  MiOncoCirc circRNA circRNA detection in 2093 clinical human cancer samples using exome capture sequencing. [119]
  CircRiC circRNA A database focusing on lineage-specific circRNAs in 935 cancer cell lines including drug response. [197]
  miRCancer miRNA A database currently documents more than 9000 relationships between 57,984 miRNAs and 196 human cancers. [186]
  SomamiR 2.0 miRNA A database of cancer somatic mutations in microRNAs (miRNA) and their target sites that potentially alter the interactions between miRNAs and competing endogenous RNAs (ceRNA). [187]
  OncomiR miRNA An online resource for exploring miRNA dysregulation in cancer. [188]
  miRCancerdb miRNA An easy-to-use database to investigate the microRNAs-dependent regulation of target genes involved in development of cancer. [189]
  miR2Disease miRNA A database aiming at providing a comprehensive resource of microRNA deregulation in various human diseases. [198]
  YM500v3 small ncRNA A database which contains more than 8000 small RNA-seq dataseta and focuses on piRNAs, tRFs, snRNAs, snoRNAs, and miRNAs. [191]
  tRF2Cancer small ncRNA A web server to detect tRFs and their expression in multiple cancers. [192]
  MINTbase v2.0 Small ncRNA A framework for the interactive exploration of mitochondrial and nuclear tRNA fragments. [193]
Basis LNCipedia lncRNA A public database for lncRNA sequence and annotation. [199]
  LNCediting lncRNA This database provides a comprehensive resource for the functional prediction of RNA editing in lncRNAs. [200]
  lncRNAdb v2.0 lncRNA This database provides comprehensive annotations of eukaryotic lncRNAs. [201]
  LncRNAWiki lncRNA This database is a publicly editable and open-content platform for community curation of human lncRNAs. [202]
  LncBook lncRNA This database is a curated knowledgebase of human lncRNAs. [203]
  MONOCLdb lncRNA 20,728 mouse lncRNA genes. [204]
  NONCODE lncRNA An interactive database that aims to present the most complete collection and annotation of ncRNAs especially lncRNAs from 17 species. [205]
  CircAtlas circRNA An integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes. [206]
  circBase circRNA A database containing thousands of recently identified circRNAs in eukaryotic cells. [207]
  CIRCpedia v2 circRNA A database for comprehensive circRNA annotation from over 180 RNA-seq datasets across six different species. [208]
  TSCD circRNA A tissue-specific circRNA database from RNA-seq datasets and characterized the features of circRNAs in human and mouse. [209]
  starBase v2.0 miRNA A database decoding miRNA-ceRNA, miRNA-ncRNA, and protein–RNA interaction networks from large-scale CLIP-Seq data. [210]
  miRTarBase miRNA A resource for experimentally validated microRNA-target interactions. [211]
  miRmine miRNA A database of human miRNA expression profiles. [212]
  EVmiRNA miRNA!/ A database focusing on miRNA expression profiles in extracellular vesicles. [213]
  miRGate miRNA A curated database of human, mouse, and rat miRNA–mRNA targets. [214]
  miRBase miRNA A database containing microRNA sequences from 271 organisms: 38,589 hairpin precursors and 48,860 mature microRNAs. [215]
  DIANA-TarBase v8 miRNA A reference database devoted to the indexing of experimentally supported miRNA targets. [216]
  DASHR 2.0 small ncRNA A database that integrates human small ncRNA gene and mature products derived from all major RNA classes. [217]