Table 2 Database of ncRNAs
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] | |
| Â | 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] | |
| Â | lnCaNet | lncRNA | This database provides a comprehensive co-expression data resource which reveals the interactions between lncRNA and non-neighbouring cancer genes. | [181] | |
| Â | LncRNADisease 2.0 | lncRNA | A database integrating comprehensive experimentally supported and predicted lncRNA-disease associations. | [182] | |
| Â | The Cancer LncRNome Atlas | lncRNA | An academic research database to explore the lncRNA alternations across multiple human cancer types. | [194] | |
| Â | SELER | lncRNA | A database of super-enhancer-associated lncRNA-directed transcriptional regulation in human cancers. | [195] | |
| Â | CSCD | circRNA | A database that focuses on distinguishing cancer-specific circRNAs from noncancerous circRNAs, and reports predicted cellular location, RBP sites, and ORFs. | [183] | |
| Â | Circ2Traits | circRNA | Provide cirRNA-disease association based on the interaction of circRNAs with disease-related miRNAs and SNP mapped on circRNA loci. | [184] | |
| Â | CircR2Disease | circRNA | Provide a comprehensive resource for circRNA deregulation in various diseases, containing 725 associations between 661 circRNAs and 100 diseases. | [185] | |
| Â | CircRNA disease | circRNA | A manually curated database of experimentally supported circRNA-disease associations. | [196] | |
| Â | MiOncoCirc | circRNA | circRNA detection in 2093 clinical human cancer samples using exome capture sequencing. | [119] | |
| Â | CircRiC | circRNA | A database focusing on lineage-specific circRNAs in 935 cancer cell lines including drug response. | [197] | |
| Â | miRCancer | miRNA | A database currently documents more than 9000 relationships between 57,984 miRNAs and 196 human cancers. | [186] | |
| Â | 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] | |
| Â | OncomiR | miRNA | An online resource for exploring miRNA dysregulation in cancer. | [188] | |
| Â | miRCancerdb | miRNA | An easy-to-use database to investigate the microRNAs-dependent regulation of target genes involved in development of cancer. | [189] | |
| Â | miR2Disease | miRNA | A database aiming at providing a comprehensive resource of microRNA deregulation in various human diseases. | [198] | |
| Â | YM500v3 | small ncRNA | A database which contains more than 8000 small RNA-seq dataseta and focuses on piRNAs, tRFs, snRNAs, snoRNAs, and miRNAs. | [191] | |
| Â | tRF2Cancer | small ncRNA | A web server to detect tRFs and their expression in multiple cancers. | [192] | |
| Â | 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] | |
| Â | LNCediting | lncRNA | This database provides a comprehensive resource for the functional prediction of RNA editing in lncRNAs. | [200] | |
| Â | lncRNAdb v2.0 | lncRNA | This database provides comprehensive annotations of eukaryotic lncRNAs. | [201] | |
| Â | LncRNAWiki | lncRNA | This database is a publicly editable and open-content platform for community curation of human lncRNAs. | [202] | |
| Â | LncBook | lncRNA | This database is a curated knowledgebase of human lncRNAs. | [203] | |
| Â | MONOCLdb | lncRNA | 20,728 mouse lncRNA genes. | [204] | |
| Â | NONCODE | lncRNA | An interactive database that aims to present the most complete collection and annotation of ncRNAs especially lncRNAs from 17 species. | [205] | |
| Â | CircAtlas | circRNA | An integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes. | [206] | |
| Â | circBase | circRNA | A database containing thousands of recently identified circRNAs in eukaryotic cells. | [207] | |
| Â | CIRCpedia v2 | circRNA | A database for comprehensive circRNA annotation from over 180 RNA-seq datasets across six different species. | [208] | |
| Â | 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] | |
| Â | miRTarBase | miRNA | A resource for experimentally validated microRNA-target interactions. | [211] | |
| Â | miRmine | miRNA | A database of human miRNA expression profiles. | [212] | |
| Â | 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] | |
| Â | miRBase | miRNA | A database containing microRNA sequences from 271 organisms: 38,589 hairpin precursors and 48,860 mature microRNAs. | [215] | |
| Â | DIANA-TarBase v8 | miRNA | A reference database devoted to the indexing of experimentally supported miRNA targets. | [216] | |
| Â | DASHR 2.0 | small ncRNA | A database that integrates human small ncRNA gene and mature products derived from all major RNA classes. | [217] |