ceRExp: ceRNA expression data

In miRSM: Inferring miRNA sponge modules in heterogeneous data

Description

ceRNA expression data

Format

ceRExp: A SummarizedExperiment object with 72 BRCA and 72 normal samples (rows) and 305 lncRNAs (columns).

Details

The matched breast invasive carcinoma (BRCA) miRNA, lncRNA and mRNA expression data is obtained from TCGA (http://cancergenome.nih.gov/). lncRNA expression data is regarded as ceRNA expression data. 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 lncRNA 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 lncRNAs between tumour and normal samples. After the analysis, we select top 305 lncRNAs 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.