https://github.com/mahshaaban/mircancerdb

A database for microRNA-gene/protein expression correlation in cancer.
https://github.com/mahshaaban/mircancerdb

cancer-genomics database microrna r sqlite tcga-data

Last synced: about 2 months ago
JSON representation

A database for microRNA-gene/protein expression correlation in cancer.

• Host: GitHub
• URL: https://github.com/mahshaaban/mircancerdb
• Owner: MahShaaban
• Created: 2017-09-01T05:50:47.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2017-11-07T02:27:40.000Z (about 7 years ago)
• Last Synced: 2023-10-26T05:15:54.938Z (about 1 year ago)
• Topics: cancer-genomics, database, microrna, r, sqlite, tcga-data
• Language: R
• Homepage: https://mahshaaban.shinyapps.io/miRCancerdb/
• Size: 1.37 MB
• Stars: 9
• Watchers: 2
• Forks: 5
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
![version](https://img.shields.io/badge/version-v1.0-blue.svg)

[![status](https://img.shields.io/badge/shinyapps.io-running-green.svg)](https://mahshaaban.shinyapps.io/miRCancerdb/)  

# miRCancerdb  

A database for microRNA-gene/protein correlation in cancer.  

A web interactive interface for this database is available [here](https://mahshaaban.shinyapps.io/miRCancerdb/)  

A compressed built database file is available here [here](https://figshare.com/articles/miRCancer_db_gz/5576329)

# Overview  

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.  

# Datasets  

The expression data was obtained from The Cancer Genome Atlas [(TCGA)](https://tcga-data.nci.nih.gov) using [RTCGA](http://bioconductor.org/packages/release/bioc/html/RTCGA.html) R package.

And the targets data were obtained form [TargetScan](http://www.targetscan.org) using [targetscan.Hs.eg.db](http://www.bioconductor.org/packages/devel/data/annotation/html/targetscan.Hs.eg.db.html) [Bioconductor](http://bioconductor.org) package.  

# Workflow

[(TCGA)](https://tcga-data.nci.nih.gov) expression data for microRNAs, mRNA and proteins were obtained using [RTCGA](http://bioconductor.org/packages/release/bioc/html/RTCGA.html) R package. 

The expression correlation were calculated for each microRNA to each feature; gene/protein in each [(TCGA)](https://tcga-data.nci.nih.gov) 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](http://www.bioconductor.org/packages/devel/data/annotation/html/targetscan.Hs.eg.db.html) [Bioconductor](http://bioconductor.org) package and added to the database.

# Installation  

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:

```r

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.

## More  

Citation:   

Usign cRegulome: https://github.com/MahShaaban/cRegulome