Introduction

CORALIS is an R package for analyzing interactions between non-coding RNA (ncRNA) and their target genes (mRNA). To this end CORALIS gathers experimentally validated records (ncRNA - mRNA interactions) from miRTarbase and RNAInter v4 database that will be used as as background during the analysis. CORALIS employs a hypergeometric distribution test to determine enriched target genes given a list of non-coding RNAs in miRBase format for microRNA-target enrichment analysis (ie: ‘hsa-miR-3196’) or Official Gene Symbol format for the rest of ncRNAs (i.e: ‘RUNX2’). So far, CORALIS supports miRNA, lncRNA, snRNA and snoRNA target enrichment analysis for several species such as Homo sapiens, Rattus norvegicus, Caenorhabditis elegans and Drosophila melanogaster, among others.

Installation

You can install both the release and the development version of CORALIS from GitHub with:

# install.packages("devtools")
devtools::install_github(repo = "Daniel-VM/CORALIS",
                         ref = "dev",
                         dependencies = T, 
                         build_vignettes = T
                         )

Make sure you have installed R (>= 4.2) and the R package devtools (>= 2.4.4) before installing CORALIS.

USAGE

Target Enrichment Analysis

The CORALIS's tienrich() function performs enrichment analysis for ncRNA-target interactions. A basic usage example for human microRNA target analysis is shown below:

# LOAD PACKAGES
library(CORALIS)

# LOAD TEST DATASET
data(rnasID)

# SET OF HUMAN microRNA IDs
head(ids[["miRNAs"]])
#> [1] "hsa-miR-1291"     "hsa-miR-642a-3p"  "hsa-miR-485-5p"   "hsa-miR-98-5p"   
#> [5] "hsa-miR-4433b-3p" "hsa-miR-3605-3p"

# RUN microRNA TARGET ENRICHMENT ANALYSIS WITH tienrich()
# ?tienrich() # Access to help page
tar_mir <- tienrich(input_list=ids[['miRNAs']], min = 2, fdr = 1, organism='Homo sapiens', type = 'miRNA_mRNA')
#> No targets found for:
#> hsa-miR-10399-3p
#> hsa-miR-11400
#> 
#> Analyzing  target genes with >=2 hits for'miRNA'in the input.
#> 
#> Analysis complete

# OUTPUT 1 (microRNA-target analysis output)
head(tar_mir@results)
#>   Gene_symbol num_interactions
#> 1       CASC4                3
#> 2        OLR1                8
#> 3       USP36                5
#> 4     RHOBTB3                7
#> 5     MAGEA2B                2
#> 6      ZNF350                4
#>                                                                                                                                  ncRNAs
#> 1                                                                                     hsa-miR-151a-3p / hsa-miR-381-3p / hsa-miR-485-5p
#> 2 hsa-miR-98-5p / hsa-miR-122-5p / hsa-miR-4433b-3p / hsa-miR-590-3p / hsa-miR-7977 / hsa-miR-493-5p / hsa-miR-889-3p / hsa-miR-642a-5p
#> 3                                                      hsa-miR-98-5p / hsa-miR-342-5p / hsa-miR-151a-3p / hsa-miR-4531 / hsa-miR-101-5p
#> 4               hsa-miR-98-5p / hsa-miR-432-5p / hsa-miR-664b-5p / hsa-miR-381-3p / hsa-miR-181b-2-3p / hsa-miR-590-3p / hsa-miR-342-5p
#> 5                                                                                                          hsa-miR-9-5p / hsa-miR-98-5p
#> 6                                                                   hsa-miR-642a-3p / hsa-miR-4433b-5p / hsa-miR-21-3p / hsa-miR-150-5p
#>         pvalue        FDR        OR     OR.SE OR.IC.lower OR.IC.upper
#> 1 5.765227e-05 0.05697310 84.966667 0.9251745   13.859214   520.90503
#> 2 8.614884e-05 0.05697310  6.789041 0.4050953    3.068956    15.01849
#> 3 5.677196e-05 0.05697310 15.495716 0.5256257    5.530931    43.41352
#> 4 1.181216e-04 0.05858829  7.606707 0.4307033    3.270253    17.69343
#> 5 3.341132e-04 0.11048011       Inf       Inf         NaN         Inf
#> 6 3.240906e-04 0.11048011 15.369697 0.5829136    4.903299    48.17728

# OUTPUT 2 (microRNA in the input with no target records found)
head(tar_mir@not_found)
#> [1] "hsa-miR-10399-3p" "hsa-miR-11400"

Visualization

The function nodevisu() display a series of graphs to visualize the target interaction analysis results. Two formats are supported:

Barplot:

nodeVisu(obj = tar_mir,
         top=25,
         type = "barplot")

Chord plot:

nodeVisu(obj = tar_mir, 
         top = 25, 
         type = "chord")

Interactive network plot:

nodeVisu(obj = tar_mir, 
         top = 25, 
         fixedsize = FALSE, # if true, default node size is fixed
         type = "network")

Case-stude example

Case-study example and further information about CORALIS is available in CORAILS vignettes (preferred web browsers: Google Chrome and Mozilla Firefox).

browseVignettes("CORALIS")