Novel RNA Markers in Prostate Cancer: Functional Considerations and Clinical Translation

Table 1

Databases and tools for functional annotation of miRNAs and lncRNAs.

Database name	Description	URL
miRNA
TargetScan	miRNA target prediction based on sequence complementarity	http://www.targetscan.org/
PITA	miRNA target prediction based on target site accessibility	http://genie.weizmann.ac.il/pubs/mir07/mir07_data.html
MiRecords	Collection of miRNA target prediction programs	http://mirecords.biolead.org/
MicroPIR	Prediction of miRNA-promoter interactions	http://www4a.biotec.or.th/micropir/
miRvestigator	Identification of miRNAs responsible for coregulated gene expression patterns discovered through transcriptome profiling	http://baliga.systemsbiology.net/drupal/content/mirvestigator-web-application-identify-mirnas-responsible-co-regulated-gene-expression
DIANA miRPath v.2.0	Combinatorial effect of microRNAs in pathways	http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=mirpath/index
miRGator v2.0	Integrated system for functional investigation of microRNAs	http://mirgator.kobic.re.kr/
mirConnX	Condition-specific mRNA-microRNA network integrator	http://mirconnx.csb.pitt.edu/job_config
MAGIA	Tool for miRNA and genes integrated analysis	http://gencomp.bio.unipd.it/magia/start/
lncRNA
ChIPBase	Platform decoding transcription factor binding maps, expression profiles, and transcriptional regulation of ncRNAs from ChIP-Seq data	http://deepbase.sysu.edu.cn/chipbase/
DIANA-LncBase	Database for experimentally verified and computationally predicted miRNA targets on lncRNAs	http://www.microrna.gr/LncBase
lncRNome	Biologically oriented knowledge base for lncRNAs in humans	http://genome.igib.res.in/lncRNome
starBase v2.0	RNA interaction networks based on CLIP-Seq data	http://starbase.sysu.edu.cn/
NONCODE v3.0	Expression and functional lncRNA data obtained from reannotated microarray studies	http://www.noncode.org
lncRNAdb	Database of annotated eukaryotic lncRNAs	http://www.lncrnadb.org
LncRNADisease database	lncRNAs associated with a number of diseases	http://www.cuilab.cn/lncrnadisease
Functional lncRNA Database	Mammalian long non-protein-coding transcripts that have been experimentally shown to be both noncoding and functional	http://www.valadkhanlab.org/database
LNCipedia 2.0	Database for annotated human lncRNA transcript sequences and structures	http://www.lncipedia.org
ncRNA Expression Database (NRED)	Integration tool for annotated expression data of ncRNAs from mouse and human	http://jsm-research.imb.uq.edu.au/nred/cgi-bin/ncrnadb.pl
circBase	Database of circular RNAs	http://www.circbase.org
Linc2GO	Functional annotation of human lincRNA based on the ceRNA hypothesis	http://www.bioinfo.tsinghua.edu.cn/~liuke/Linc2GO/index.html
ceRDB-Competing Endogenous; mRNA DataBase/CEFINDER	Web-server for identification of ceRNA for a given mRNA target based on the homology of miRNA binding sites present in the 3′UTR sequence	http://www.oncomir.umn.edu/cefinder/