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Table 1 Summary of computational approaches for identifying the ceRNA networks

From: The emerging roles of non-coding competing endogenous RNA in hepatocellular carcinoma

Databases

Brief description

Link

Ref

starBase v2.0

Database supplies comprehensive interaction network of ncRNAs (lncRNAs, miRNAs, and ceRNAs), mRNA, and proteins in cancer cells and normal tissues based on 108 CLIP-Seq

http://starbase.sysu.edu.cn/

[31]

NPInter v3.0

Database supplies comprehensive interaction among ncRNAs (except tRNAs and rRNAs), lncRNAs and others. It provides different types of basic information about the interaction

http://www.bioinfo.org/NPInter/

[32]

DIANA-LncBase v2

Database supplies two different miRNA–lncRNA interaction modules. One module is experimentally supported, and the other is in silico predicted interactions

http://www.microrna.gr/LncBase/

[33, 34]

circBase

Database provides scripts to identify known and novel circRNAs in sequencing data.

http://www.circbase.org/

[35]

LNCediting

Database supplies information about RNA editing in lncRNAs and miRNA–lncRNA interactions

http://bioinfo.life.hust.edu.cn/LNCediting/

[36]

CircInteractome

Database supplies information about circRNAs and their interaction with proteins or miRNAs

http://circinteractome.nia.nih.gov/

[37]

Cancer-Specific-CirRNA-Database (CSCD)

Database for cancer-specific circRNAs

http://gb.whu.edu.cn/CSCD/

[38]

spongeScan

Database supplies information about microRNA binding elements in lncRNA sequences

http://spongescan.rc.ufl.edu

[39]

SomamiR 2.0

Database provides information and functional analysis of expected miRNA–ceRNA interaction

http://compbio.uthsc.edu/SomamiR

[40]

lnCeDB

Database provides information of human lncRNA that acts as ceRNAs

http://gyanxet-beta.com/lncedb/

[41]

miRBase

Database provides miRNA gene hunters with unique names for novel miRNA genes prior to publication of results

http://www.mirbase.org/

[42]

Targetscan

Database provides information of predicted microRNA targets

http://www.targetscan.org/vert_72/

[43]

miRcode

Database provides “whole transcriptome” human microRNA target predictions based on the comprehensive GENCODE gene annotation.

http://www.mircode.org/

[44]

  1. ncRNA: noncoding RNA; ceRNA: competing endogenous RNA; lncRNA: long noncoding RNA; mRNAs: messenger RNAs; miRNA: microRNA; circRNA: circularRNA; Ref: reference