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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)

From: Arena-Idb: a platform to build human non-coding RNA interaction networks

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.