Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
MicroRNA-target interactions in human.DescriptionDataset of miRNA-target interactions in human obtained from mirTarBase release 4.5: Nov. 1, 2013. Usagedata(mirTarBase) FormatA data.frame with 39083 interactions and 9 variables. The columns needed for this package are:
DetailsThis dataset is licensed by its authors (Hsu et al.), see http://mirtarbase.mbc.nctu.edu.tw/cache/download/LICENSE. ValueA data.frame with human miRNA-targets interactions SourceDownloaded 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. ReferencesS.-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)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(mirIntegrator)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mirIntegrator/mirTarBase.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mirTarBase
> ### Title: MicroRNA-target interactions in human.
> ### Aliases: mirTarBase
> ### Keywords: datasets
>
> ### ** Examples
>
> data(mirTarBase)
> head(mirTarBase)
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
>
> script <- system.file("scripts", "get_mirTarBase.R",
+ package = "mirIntegrator")
> script
[1] "/home/ddbj/local/lib64/R/library/mirIntegrator/scripts/get_mirTarBase.R"
> readLines(script)
[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")"
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> dev.off()
null device
1
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