mirTarBase: MicroRNA-target interactions in human.

In mirIntegrator: Integrating microRNA expression into signaling pathways for pathway analysis

Description

Dataset of miRNA-target interactions in human obtained from mirTarBase release 4.5: Nov. 1, 2013.

Usage

data(mirTarBase)

Format

A data.frame with 39083 interactions and 9 variables. The columns needed for this package are:

• miRNA: which contains the miRNA ID,

• Target.ID: contains the entrez ID of the gene targeted by the miRNA

Details

This dataset is licensed by its authors (Hsu et al.), see http://mirtarbase.mbc.nctu.edu.tw/cache/download/LICENSE.

Value

A data.frame with human miRNA-targets interactions

Source

Downloaded from http://mirtarbase.mbc.nctu.edu.tw/ on 4/1/2015. A script which downloads the file and constructs the mirTarBase object may be found in 'inst/scripts/get_mirTarBase.R', see the example.

References

S.-D. Hsu, Y.-T. Tseng, S. Shrestha, Y.-L. Lin, A. Khaleel, C.-H. Chou, C.-F. Chu, H.-Y. Huang, C.-M. Lin, S.-Y. Ho, T.-Y. Jian, F.-M. Lin, T.-H. Chang, S.-L. Weng, K.-W. Liao, I.-E. Liao, C.-C. Liu, and H.-D. Huang, miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions, Nucleic Acids Research, vol. 42, pp. D78 - D85, Jan. 2014.

Examples

data(mirTarBase)
head(mirTarBase)

script <- system.file("scripts", "get_mirTarBase.R", 
                      package = "mirIntegrator")
script
readLines(script)

Example output

  miRTarBase.ID           miRNA Species..miRNA. Target.Gene Target.ID
1    MIRT006481 hsa-miR-181a-5p    Homo sapiens       DUSP6      1848
2    MIRT000002  hsa-miR-20a-5p    Homo sapiens       HIF1A      3091
3    MIRT000006 hsa-miR-146a-5p    Homo sapiens       CXCR4      7852
4    MIRT000006 hsa-miR-146a-5p    Homo sapiens       CXCR4      7852
5    MIRT006511 hsa-miR-200b-3p    Homo sapiens        RND3       390
6    MIRT006477  hsa-miR-328-3p    Homo sapiens       PTPRJ      5795
  Species..Target.Gene.
1          Homo sapiens
2          Homo sapiens
3          Homo sapiens
4          Homo sapiens
5          Homo sapiens
6          Homo sapiens
                                                      Experiments
1                         Luciferase reporter assay//Western blot
2 Luciferase reporter assay//Western blot//Northern blot//qRT-PCR
3                qRT-PCR//Luciferase reporter assay//Western blot
4                                                      Microarray
5                                       Luciferase reporter assay
6                                           qRT-PCR//Western blot
           Support.Type References..PMID.
1        Functional MTI          17382377
2        Functional MTI          18632605
3        Functional MTI          18568019
4 Functional MTI (Weak)          20375304
5        Functional MTI          20683643
6        Functional MTI          22564856
[1] "/usr/local/lib/R/site-library/mirIntegrator/scripts/get_mirTarBase.R"
 [1] "# The following script downloads and constructs the mirTarBase dataset,"                   
 [2] "# included in the mirIntegrator package. "                                                 
 [3] "# This dataset was published by Hsu SD et al. (2014) Nucleic acids research."              
 [4] "# This dataset is included for demostration purposes and it should be used "               
 [5] "# according to its licensing terms:"                                                       
 [6] "# http://mirtarbase.mbc.nctu.edu.tw/cache/download/LICENSE"                                
 [7] ""                                                                                          
 [8] "# 1. Download the file from mirTarBase website."                                           
 [9] ""                                                                                          
[10] "download.file(url = \"http://mirtarbase.mbc.nctu.edu.tw/cache/download/4.5/hsa_MTI.xls\", "
[11] "              destfile = \"~/hsa_MTI.xls\")"                                               
[12] "# 2. Load the table"                                                                       
[13] "library(\"gdata\")  # gdata needs perl"                                                    
[14] "mirTarBase <- read.xls (\"~/hsa_MTI.xls\", sheet = 1, header = TRUE)"                      
[15] ""                                                                                          
[16] "# 3. Rename columns"                                                                       
[17] "col.nam <- names(mirTarBase) "                                                             
[18] "col.nam[5] <- \"Target.ID\""                                                               
[19] "names(mirTarBase) <- col.nam"                                                              
[20] ""                                                                                          
[21] ""                                                                                          
[22] "# 4. Delete the empty rows"                                                                
[23] "targets_db <- mirTarBase[,c(\"miRNA\",\"Target.ID\")]"                                     
[24] "mirTarBase <- mirTarBase[!(is.na(targets_db[,2])),]"                                       
[25] ""                                                                                          
[26] "# 5. Save files"                                                                           
[27] "save(mirTarBase, file = \"mirTarBase.rda\")"                                               
[28] "library(tools)"                                                                            
[29] "resaveRdaFiles(\"mirTarBase.rda\")"                                                        
[30] ""                                                                                          
[31] "# 6. Now you can delete the downloaded file from your home directory"                      
[32] "if (file.exists(\"~/hsa_MTI.xls\")) file.remove(\"~/hsa_MTI.xls\")"                        

mirIntegrator documentation built on Nov. 8, 2020, 8:28 p.m.