mRExp: mRNA expression data

In miRSM: Inferring miRNA sponge modules in heterogeneous data

Description

mRNA expression data

Format

mRExp: A SummarizedExperiment object with 72 BRCA and 72 normal samples (rows) and 226 miRNAs (columns).

Details

The matched breast invasive carcinoma (BRCA) miRNA, lncRNA and mRNA expression data is obtained from TCGA (http://cancergenome.nih.gov/). The data focuses on 72 individuals for which the complete sets of tumor and matched normal (i.e., normal tissue taken from the same patient) profiles are available. A mRNA which has missing values in more than 10 are imputed using the k-nearest neighbours (KNN) algorithm from the impute R package. We use the limma R package to infer differentially expressed mRNAs between tumour and normal samples. After the analysis, we select top 500 mRNAs which are differentially expressed at a significant level (adjusted p-value < 1E-02, adjusted by Benjamini & Hochberg method).

miRSM documentation built on April 16, 2021, 6 p.m.