IMMP Integration of MicroRNA, mRNA, and Protein Expression Data for the Identification of Cancer-Related MicroRNA

 

 
News
2016/09/27: Source codes and data sets are updated.
Introduction
This study explores two approaches for the investigation of gene-miRNA relationships by integrating mRNA expression and protein expression data. This study presents ranked miRNAs lists according to their effects on cancer development and constructed modules containing mRNAs, proteins, and miRNAs, in which these three molecular types are highly correlated.
Paper Seo, Y., Jin, D., Choi, C., and Lee, H. (2016) Integration of MicroRNA, mRNA, and Protein Expression Data for the Identification of Cancer-Related MicroRNA.
Source codes
Source codes were implemented in r and are available here. Instructions for running source codes are here. Example input files can be downloaded from here. Note that the attached input and output example files are not real data but have the same format with them. Required input files for each step are described in instructions.
Data sets

The glioblastoma (GBM) data sets including the expression data of mRNA, protein, miRNA used in this paper were collected from TCGA. The information about GBM-related miRNAs was collected from Human miRNA & Disease Database v2.0 (HMDD v2.0). Protein-protein interaction data sets were collected from the Human Protein Reference Database (HPRD) (Prasad et al.,2009).

Contacts
sjyjoy at gist.ac.kr, hyunjulee at gist.ac.kr