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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