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.<br>Paper: Jiyoun Seo, Daeyong Jin, Chan-Hun Choi and Hyunju Lee* (2016) Integration of MicroRNA, mRNA, and Protein Expression Data for the Identification of Cancer-Related MicroRNAs. PLoS One, In Press.<br>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.<br><br><br>Description: Source codes were implemented in r and are available here. Instructions and example input files for running source codes 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.<br>Data sets: <b>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 &amp; 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).</b>