miRCancerdb: a database for correlation analysis between microRNA and gene expression in cancer

BMC Research Notes
Mahmoud AhmedDeok Ryong Kim

Abstract

microRNAs regulate expression of target genes by specifically binding to their transcripts, subsequently leading to translational inhibition or mRNA degradation. Gene regulation by microRNAs has been implicated in a wide range of physiological and pathological conditions. Here, we leverage the use of public-access data and the available genomic annotations to pre-calculate the correlation of the expression of a large number of microRNAs with gene at the mRNA and protein level in the context of cancers. Expression data of miRNAs, mRNAs and proteins in cancer patients from The Cancer Genome Atlas along with TargetScan miRNAs-target annotations were used to calculate the expression correlations between miRNAs and features (mRNAs/proteins) in a number of cancer studies. We then packed the output of this analysis into a database and made it available through an interactive web application. The miRCancerdb is an easy-to-use database to investigate the microRNAs-dependent regulation of target genes involved in development of cancer.

References

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Citations

Mar 1, 2019·Molecular Medicine Reports·Luca FalzoneSaverio Candido
Dec 14, 2018·BMC Cancer·Aaron L SarverSubbaya Subramanian
Mar 21, 2019·Animal Models and Experimental Medicine·Kewei WangMang Li
Jun 4, 2021·BMC Bioinformatics·Gulden OlgunOznur Tastan
Jun 3, 2021·Purinergic Signalling·Rafael Paschoal de CamposGuido Lenz

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Methods Mentioned

BETA
Protein Arrays
RNAseq
Protein Array
ChIP-seq

Software Mentioned

SQLite
R
Hs
db
RTCGA
R package targetscan
Rstudio
TargetScan
eg
miRCancerdb

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