ceRNAAnslysis: Competing endogenous RNAs (ceRNAs) analysis

In zexllin/lncRNAtools: Do lncRNA bioinformatics Advanced analysis,includes routine analysis of mRNA/miRNA

Description

Identify ceRNAs by (1) number of shared miRNAs between lncRNA and mRNA; (2) expression correlation of lncRNA and mRNA; (3) regulation similarity of shared miRNAs on lncRNA and mRNA; (4) sensitivity correlation

Usage

ceRNAAnslysis(
  lnc,
  pc,
  deMIR = NULL,
  lnc.targets = "starBase",
  pc.targets = "starBase",
  rna.expr,
  mir.expr
)

Arguments

lnc	a vector of Ensembl long non-coding gene ids
pc	a vector of Ensembl protein coding gene ids
deMIR	a vector of differentially expressed miRNAs. Default is NULL
lnc.targets	a character string specifying the database of miRNA-lncRNA interactions. Should be one of 'spongeScan', 'starBase', and 'miRcode'. Default is 'starBase'. Or a list of miRNA-lncRNA interactions generated by users
pc.targets	a character string specifying the database of miRNA-lncRNA interactions. Should be one of 'spongeScan', 'starBase', and 'miRcode'. Default is 'starBase'. Or a list of miRNA-lncRNA interactions generated by users
rna.expr	normalization mRNAs counts datafram,contain lnc and pc transformed gene expression data
mir.expr	normalization miRNAs counts datafram transformed mature miRNA expression data

Value

A dataframe containing ceRNA pairs, expression correlation between lncRNA and mRNA, the number and hypergeometric significance of shared miRNAs, regulation similarity score, and the mean sensitity correlation (the difference between Pearson correlation and partial correlation) of multiple lncRNA-miRNA-mRNA triplets, etc.

References

Paci P, Colombo T, Farina L. Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer. BMC systems biology. 2014 Jul 17;8(1):83.

zexllin/lncRNAtools documentation built on Jan. 1, 2021, 1:52 p.m.