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Table 1 Summary table of the most popular databases and tools storing information about micro and long ncRNAs

From: Non-coding RNAs in cancer: platforms and strategies for investigating the genomic “dark matter”

DATABASE and TOOLS BRIEF DESCRIPTION LINK AVAILABILITY PROS (+)/CONS (−)
NONCODE Contains a total of 487.164 lncRNA transcripts and 324.646 lncRNAs genes for 16 different species and allows searching sequences, expression, orthologs, functions and diseases related, to a given input gene or transcript. http://www.noncode.org/ PA (+) High Number of sequences
(+) 17 different species
(+) Disease Association
(+) Simple Analysis
(+) High level of manual
curation
LncRNAMap Is a web resource for studying lncRNAs in the human genome and currently contains 23.355 lncRNAs with sequences retrieved from Ensembl 65 (GRCH37) http://lncrnamap.mbc.nctu.edu.tw/php/ PA (−) No Analytic potential
(−) No recent updates
LNCipedia Includes 127.802 human lncRNAs transcripts, provides sequence, annotations and manually curated lncRNA articles https://lncipedia.org/ PA (+) Recent Web Interface
(+) API Interface for data integration
(+) Submission of novel sequences
LncRNADisease Integrates approximately 1000 lncRNAs-to-disease associations, including cancer, obtained using lncRNA -disease prediction tools that compare lncRNA genomic location with the closer gene http://www.cuilab.cn/lncrnadisease PA (+) Prediction of associations on the basis of user-provided sequences
(+) High level of manual curation
(+) Submission of novel sequences
(−) Web Interface Obsolete
lncRNAdb Is a database of long-noncoding RNAs in eukaryotes storing both raw data about sequence as well as other referenced information such as structural information, genomic context, levels of expression, and functional information https://rnacentral.org/expert-database/lncrnadb PA (−) Limited number of sequences
(+) Extensive annotation and biological knowledge is provided
(+) High level of manual curation
LncRNA2Target Expression profiling analysis following lncRNA Knockdown or Overexpression http://123.59.132.21/lncrna2target/ PA (−) Limited Scope
(−) Obsolete web interface
NRED Provides comprehensive information on lncRNAs and lncRNA expression data from microarray and In situ Hybridization data https://www.hsls.pitt.edu/obrc/index.php?page=URL1237993821 PA (−) Limited Scope
(−) Obsolete web interface
GENCODE Contains ncRNA gene annotations in .gtf format and ncRNA transcript sequences in .fasta format. Its goal is the investigation of gene features based on biological evidence https://www.gencodegenes.org/ PA (−) Limited access (only by FTP)
(−) Limited Query Capabilities
ENCORI Is focused on miRNA-target interaction, including miRNA-lncRNA and protein-lncRNA interaction data http://starbase.sysu.edu.cn/ Upon Request (−) No Simple Access
NPInter Stores functional interactions between ncRNAs and other molecules (DNAs, RNAs and proteins) and is regularly updated with novel interactions coming from manual curation of literature, high throughput screening and in silico predictions. https://omictools.com/npinter-tool PA (+) Regular Updating
(+) High level of manual curation
DIANA TOOLS Is a tool for determining miRNA and lncRNA interaction based on experimental studies and computational prediction http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=lncbasev2%2Findex PA (+) Prediction of Interactions
(−) Limited number of stored information on interactions
GeneCards Provides comprehensive information about coding and non coding genes https://www.genecards.org/ PA (−) No Analytic Capabilities
SomamiR Includes information about somatic mutations in miRNA or miRNA-target site sequences and on biological pathways affected by these alterations http://compbio.uthsc.edu/SomamiR/ PA (+) Somatic Information
PROGmiR Give information about the potential role of miRNAs as cancer biomarker https://omictools.com/progmir-tool PA (+) Highly Tailored for cancer
(−) No information for other diseases
miRCancer Contain data about miRNA-cancer association obtained through data mining http://mircancer.ecu.edu PA (+) Highly Tailored for cancer
(−) No information for other diseases
miRBase Includes published miRNA sequence and annotation, available for download http://www.mirbase.org/index.shtml PA (+) Highly Tailored for cancer
(−) No information for other diseases
miRwalk Provides information about miRNA-target interaction http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2/ PA (+) High potential for custom analysis
miRDB microRNA target prediction tools http://mirdb.org/ PA (−) Limited Analysis
TargetScan http://www.targetscan.org/vert_72/ PA (+) High potential for custom analysis
miRTar.human http://mirtar.mbc.nctu.edu.tw/human/ PA (+) Possibility of downloading and use in local for batch analysis
miRmap https://mirmap.ezlab.org/ PA (+) High potential for custom analysis
miRDeep2 microRNA deep sequencing tools http://ibis.tau.ac.il/miRNAkey/ PA (−) Not user friendy
(−) Requires programming skills
(−) No recent updates
miRNAkey https://bio.tools/mirnakey PA (−) Not user friendy
(−) Requires programming skills
- No recent updates
  1. PA Public Available