Getting_started

Getting Started with the MoonFinder package

Lixin Cheng

2019-10-01

Overview:

MoonFinder is developed for the identification of moonlighting RNAs at the genome level based on the functional annotation and interactome data of ncRNAs and proteins. MoonFinder provides an extensive framework for the detection of protein modules and establishment of RNA-module associations.

Citation:

Identification and characterization of moonlighting long non-coding RNAs based on RNA and protein interactome. Bioinformatics, 2018.
A network-based algorithm for the identification of moonlighting non-coding RNAs and its application in sepsis. Briefings in Bioinformatics, 2019

Getting started:

Identify the moonlight lncRNAs

library(MoonFinder)
#> 
#> 
data("ppi","simMatBP.Resnik","moduleList","rna2module")
rnaStatMat = moonlightingCoefficient(rna2module,simMatBP.Resnik)
head(rnaStatMat)
#>      ncRNA   Module Number SDI     
#> [1,] "CRNDE" "5"           "0.4044"
#> [2,] "NEAT1" "5"           "0.4606"
#> [3,] "ZFAS1" "6"           "0.3003"
#> [4,] "GAS5"  "5"           "0.3271"
#> [5,] "JPX"   "7"           "0.3058"
#> [6,] "SNHG1" "3"           "0.6424"

Set up the SDI threshold according to SDI distributions

sdi = as.numeric(rnaStatMat[,3])
dev.new(width=4, height=4)
hist(sdi,border=FALSE,xlab="MC",xlim=c(0,1),ylim=c(0,4),
    breaks=seq(0,1,0.02),prob=TRUE,main="Resnik")
lines(density(sdi),lwd=2,col="orange")
mlncRNA = rnaStatMat[sdi>0.4,1]

Illustration of the mediated modules for a given moonlighting ncRNA.

library(igraph)
#> Warning: package 'igraph' was built under R version 3.5.3
#> 
#> Attaching package: 'igraph'
#> The following objects are masked from 'package:stats':
#> 
#>     decompose, spectrum
#> The following object is masked from 'package:base':
#> 
#>     union
g <- graph.edgelist(ppi,directed=FALSE)
moduleHeatmap("CRNDE",rna2module,moduleList,g)

Comparison of the functions enriched by different modules:

library(clusterProfiler)
#> clusterProfiler v3.10.1  For help: https://guangchuangyu.github.io/software/clusterProfiler
#> 
#> If you use clusterProfiler in published research, please cite:
#> Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
#> 
#> Attaching package: 'clusterProfiler'
#> The following object is masked from 'package:igraph':
#> 
#>     simplify
dev.new(width=14, height=7)
moduleFunctionComparing("CRNDE",rna2module,moduleList)