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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 http://www.bio-bigdata.net/lnc2cancer An updated database that provides comprehensive experimentally supported associations between lncRNAs and human cancers. [180]
  TANRIC lncRNA http://bioinformatics.mdanderson.org/main/TANRIC:Overview 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 http://lncanet.bioinfo-minzhao.org/ 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 http://www.rnanut.net/lncrnadisease/ A database integrating comprehensive experimentally supported and predicted lncRNA-disease associations. [182]
  The Cancer LncRNome Atlas lncRNA http://tcla.fcgportal.org/ An academic research database to explore the lncRNA alternations across multiple human cancer types. [194]
  SELER lncRNA http://www.seler.cn/download.php A database of super-enhancer-associated lncRNA-directed transcriptional regulation in human cancers. [195]
  CSCD circRNA http://gb.whu.edu.cn/CSCD A database that focuses on distinguishing cancer-specific circRNAs from noncancerous circRNAs, and reports predicted cellular location, RBP sites, and ORFs. [183]
  Circ2Traits circRNA http://gyanxet-beta.com/circdb/ Provide cirRNA-disease association based on the interaction of circRNAs with disease-related miRNAs and SNP mapped on circRNA loci. [184]
  CircR2Disease circRNA http://bioinfo.snnu.edu.cn/CircR2Disease/ Provide a comprehensive resource for circRNA deregulation in various diseases, containing 725 associations between 661 circRNAs and 100 diseases. [185]
  CircRNA disease circRNA http://cgga.org.cn:9091/circRNADisease/ A manually curated database of experimentally supported circRNA-disease associations. [196]
  MiOncoCirc circRNA https://nguyenjoshvo.github.io/ circRNA detection in 2093 clinical human cancer samples using exome capture sequencing. [119]
  CircRiC circRNA https://hanlab.uth.edu/cRic A database focusing on lineage-specific circRNAs in 935 cancer cell lines including drug response. [197]
  miRCancer miRNA http://mircancer.ecu.edu/ A database currently documents more than 9000 relationships between 57,984 miRNAs and 196 human cancers. [186]
  SomamiR 2.0 miRNA http://compbio.uthsc.edu/SomamiR/ 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 http://www.oncomir.org/ An online resource for exploring miRNA dysregulation in cancer. [188]
  miRCancerdb miRNA https://mahshaaban.shinyapps.io/miRCancerdb/ An easy-to-use database to investigate the microRNAs-dependent regulation of target genes involved in development of cancer. [189]
  miR2Disease miRNA http://www.miR2Disease.org A database aiming at providing a comprehensive resource of microRNA deregulation in various human diseases. [198]
  YM500v3 small ncRNA http://ngs.ym.edu.tw/ym500/ A database which contains more than 8000 small RNA-seq dataseta and focuses on piRNAs, tRFs, snRNAs, snoRNAs, and miRNAs. [191]
  tRF2Cancer small ncRNA http://rna.sysu.edu.cn/tRFfinder/ A web server to detect tRFs and their expression in multiple cancers. [192]
  MINTbase v2.0 Small ncRNA https://cm.jefferson.edu/MINTbase/ A framework for the interactive exploration of mitochondrial and nuclear tRNA fragments. [193]
Basis LNCipedia lncRNA https://lncipedia.org A public database for lncRNA sequence and annotation. [199]
  LNCediting lncRNA http://bioinfo.life.hust.edu.cn/LNCediting/ This database provides a comprehensive resource for the functional prediction of RNA editing in lncRNAs. [200]
  lncRNAdb v2.0 lncRNA http://lncrnadb.com/ This database provides comprehensive annotations of eukaryotic lncRNAs. [201]
  LncRNAWiki lncRNA http://lncrna.big.ac.cn This database is a publicly editable and open-content platform for community curation of human lncRNAs. [202]
  LncBook lncRNA http://bigd.big.ac.cn/lncbook This database is a curated knowledgebase of human lncRNAs. [203]
  MONOCLdb lncRNA https://www.monocldb.org/ 20,728 mouse lncRNA genes. [204]
  NONCODE lncRNA http://www.bioinfo.org/noncode/ An interactive database that aims to present the most complete collection and annotation of ncRNAs especially lncRNAs from 17 species. [205]
  CircAtlas circRNA http://circatlas.biols.ac.cn/ An integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes. [206]
  circBase circRNA http://www.circbase.org/ A database containing thousands of recently identified circRNAs in eukaryotic cells. [207]
  CIRCpedia v2 circRNA http://www.picb.ac.cn/rnomics/circpedia A database for comprehensive circRNA annotation from over 180 RNA-seq datasets across six different species. [208]
  TSCD circRNA http://gb.whu.edu.cn/TSCD A tissue-specific circRNA database from RNA-seq datasets and characterized the features of circRNAs in human and mouse. [209]
  starBase v2.0 miRNA http://starbase.sysu.edu.cn/ A database decoding miRNA-ceRNA, miRNA-ncRNA, and protein–RNA interaction networks from large-scale CLIP-Seq data. [210]
  miRTarBase miRNA http://mirtarbase.cuhk.edu.cn/php/index.php A resource for experimentally validated microRNA-target interactions. [211]
  miRmine miRNA http://guanlab.ccmb.med.umich.edu/mirmine A database of human miRNA expression profiles. [212]
  EVmiRNA miRNA http://bioinfo.life.hust.edu.cn/EVmiRNA#!/ A database focusing on miRNA expression profiles in extracellular vesicles. [213]
  miRGate miRNA http://mirgate.bioinfo.cnio.es/miRGate/ A curated database of human, mouse, and rat miRNA–mRNA targets. [214]
  miRBase miRNA http://www.mirbase.org/ A database containing microRNA sequences from 271 organisms: 38,589 hairpin precursors and 48,860 mature microRNAs. [215]
  DIANA-TarBase v8 miRNA http://www.microrna.gr/tarbase A reference database devoted to the indexing of experimentally supported miRNA targets. [216]
  DASHR 2.0 small ncRNA http://lisanwanglab.org/DASHR A database that integrates human small ncRNA gene and mature products derived from all major RNA classes. [217]