Table 2.
List of the database resources with related information extracted and used in Arena-Idb platform. Legend: BI= Basic Information; S=Sequences; CR=Cross references;); ncRNAs (non-coding RNA); pcRNAs (protein coding RNA); G=Gene; Ps=Pseudogene; D=Disease; P=Protein, GO=Ontology, I=Interactions (NN:ncRNA-ncRNA, NM:ncRNA-pcRNA, NG:ncRNA-Gene, NS:ncRNA-Pseudogene, ND:ncRNA-Disease, NO:ncRNA-Others)
| Database | Biological Entities extracted | Annotated Information | Description |
|---|---|---|---|
| HGNC [1] | ncRNA, pcRNA, G, D | BI, CR | A curated collection of approved Human Gene Nomenclature |
| Genecode [39] | ncRNA, pcRNA, G, PS | BI, S | Reference gene annotation and experimental validation for human and mouse. |
| VEGA/Havana [40] | ncRNA | BI, S | A repository for gene model produced by the manual annotation. |
| Ensembl [41] | ncRNA | BI, S, CR | Genome browser database for vertebrate with annotate gene. |
| miRBase[42] | ncRNA | BI, S | Database of of published miRNA sequences and annotation. |
| RefSeq [43] | ncRNA | BI, S | Collection of integrated, non-redundant and well annotated set of transcript and genomic data. |
| GtRNAdb [44] | ncRNA | BI, S | Genomic tRNA database. |
| piRNAbank [45] | ncRNA | BI, S | Resource on classified and clustered piRNAs. |
| Disease Ontology [46] | D, GO | CR | Database of standardized ontology of human disease. |
| Circ2Traits [47] | ncRNA, pcRNA, G, D | NN, NM, NG, ND | A comprehensive database of human circRNAs associated with diseases and traits. |
| HMDD [48] | ncRNA, G, D | NG, ND | A collection of experimentally supported human miRNAs and disease associations. |
| Lnc2Cancer [49] | ncRNA, D | CR, ND | A manually curated database of experimentally lncRNAs associated with cancer. |
| LncActDB [50] | ncRNA, D | NN, NG, ND | Database containing a list of lncRNA and mRNA with regulatory roles. |
| LncRNAdb [51] | ncRNA, G, P | NN, NG, NP | A database of functional lncRNAs. |
| LncRNADisease [52] | ncRNA, D | NP, ND | A curated DB of lncRNA with diseases. |
| Mir2diseases [53] | ncRNA, G, D | NG, ND | A manually curated database for miRNA deregulation in human diseases. |
| MiRandola [6] | ncRNA, D | ND | Collection of extracellular circulating miRNAs and their deregulation in human disease. |
| miRecords [54] | ncRNA, G | NG | A collection of validate miRNA target interaction with the exclusion of predicted interactions. |
| miRTarBase [55] | ncRNA, G | NG | A database of experimentally validate miRNA target interactions. |
| mirSponge [56] | ncRNA, pcRNA, G, Ps, D | NN, NM, NG, NP, ND | Manually curated database of miRNA spanges and ceRNAs. |
| NONCODE [57] | ncRNA | CR | A database of ncRNA with integrated only the Cross-References. |
| NPInter [18] | ncRNA, P | NN, NP | Database of experimentally verified interaction between ncRNA and other biomolecules. |
| PSMIR [58] | ncRNA | NO | A database of potential associations between small molecules and miRNAs. |
| StarBase [59] | ncRNA, G, P, Ps | NN, NG, NS, NP | A database of miRNA-mRNA interactions. |
| TarBase [60] | ncRNA, Gene | NG | A database of curated experimentally validate miRNA targets. |