A database for microRNA-gene/protein correlation in cancer.
A web interactive interface for this database is available here
A compressed built database file is available here here
miRCancerdb is database of expression correlation of expression of microRNAs and genes/proteins. The web interface provides an easy access to the database without having to write any code. Among other features, users can search, choose, visualize and downlaod the particular subsets of the data.
The expression data was obtained from The Cancer Genome Atlas (TCGA) using RTCGA R package. And the targets data were obtained form TargetScan using targetscan.Hs.eg.db Bioconductor package.
(TCGA) expression data for microRNAs, mRNA and proteins were obtained using RTCGA R package. The expression correlation were calculated for each microRNA to each feature; gene/protein in each (TCGA) study. An SQLite database were build using these corelations. In addition, expression profiles of each miroRNA and microRNA targets data were obtained from targetscan.Hs.eg.db Bioconductor package and added to the database.
A collection of funtions needed to build the database is provided as an R package called sqlome. The package is available on github and can be installed using:
devtools::install_github('MahShaaban/sqlome')Clone or download this repository, navigate to the miRCancerdb directory and run make to build the database from scratch and launch a shiny browser application.
git clone https://github.com/MahShaaban/miRCancerdb
cd miRCancerdb
make
Indeed, the same can be achieved through Rstudio and the sqlite db file can be accessed using DBI library in R.
Citation:
Usign cRegulome: https://github.com/MahShaaban/cRegulome