| Title: | TargetScoreData |
|---|---|
| Description: | Precompiled and processed miRNA-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct miRNAs. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each miRNA-mRNA interaction. Thus, the user can use these static sequence-based scores together with user-supplied tissue/cell-specific fold-change due to miRNA overexpression to predict miRNA targets using the package TargetScore (download separately) |
| Authors: | Yue Li |
| Maintainer: | Yue Li <[email protected]> |
| License: | GPL-2 |
| Version: | 1.48.0 |
| Built: | 2026-10-10 11:04:40 UTC |
| Source: | https://github.com/bioc/TargetScoreData |
To automate the pipeline of calculating targetScore using targetScore, we compiled, processed and generated miRNA-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct miRNAs. To our knowledge, this is by far the largest miRNA-pertubation data compendium. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each miRNA-mRNA interaction. Thus, the user can use these static sequence-based scores together with user-supplied tissue/cell-specific fold-change due to miRNA overexpression to predict miRNA targets using targetScore.
| Package: | TargetScoreData |
| Type: | Package |
| Version: | 0.99.4 |
| Date: | 2013-07-13 |
| License: | GPL-2 |
get_TargetScanHuman_contextScore: TargetScan context score for all of the predicted sites (including conserved and nonconserved sites) downloaded from TargetScan 6 website (http://www.targetscan.org/cgi-bin/targetscan/data_download.cgi?db=vert_61)
get_TargetScanHuman_PCT: TargetScan PCT for all of the predicted sites (including conserved and nonconserved sites) downloaded from TargetScan 6 website (http://www.targetscan.org/cgi-bin/targetscan/data_download.cgi?db=vert_61)
get_miRNA_family_info: Get miRNA family information obtained TargetScanHuman 6
get_precomputed_targetScores: Pre-calculated targetScores for 112 miRNAs using logFC and sequence scores from TargetScan context score and PCT from the RData files above.
get_precomputed_logFC: We combined all of the logFC data columns into a single N x M matrix for all of the N = 19177 RefSeq mRNAs (NM_* obtained from UCSC) and M = 286 datasets. Missing data (logFC) for some genes across studies were imputed using impute from impute.knn.
get_miRNA_transfection_data: Get log fold-changes (logFC) from each study organized in a list with each item corresponding to a miRNA. Notably, some miRNAs (e.g., hsa-miR-1) appear more than once in the list corresponding to different studies.
get_validated_targets: Get validated targets of human miRNA obtained from mirTarBase v3.5
Yue Li
Maintainer: Yue Li <[email protected]>
miRTarBase: a database curates experimentally validated microRNA-target interactions. (2011). miRTarBase: a database curates experimentally validated microRNA-target interactions., 39(Database issue), D163-9. doi:10.1093/nar/gkq1107
Friedman, R. C., Farh, K. K.-H., Burge, C. B., & Bartel, D. P. (2009). Most mammalian mRNAs are conserved targets of microRNAs. Genome Research, 19(1), 92-105. doi:10.1101/gr.082701.108
Garcia, D. M., Baek, D., Shin, C., Bell, G. W., Grimson, A., & Bartel, D. P. (2011). Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nature structural & molecular biology, 18(10), 1139-1146. doi:10.1038/nsmb.2115
Please follow the GEO series number to find the references for each microRNA-transfection dataset.
get_TargetScanHuman_contextScore,
get_TargetScanHuman_PCT,
get_validated_targets,
get_miRNA_family_info,
get_precomputed_targetScores,
get_precomputed_logFC,
get_miRNA_transfection_data
ls("package:TargetScoreData")ls("package:TargetScoreData")
Get human miRNA family information obtained frin TargetScanHuman 6 website
get_miRNA_family_info(datapath = system.file("extdata/miR_Family_Info.txt", package = "TargetScoreData"))get_miRNA_family_info(datapath = system.file("extdata/miR_Family_Info.txt", package = "TargetScoreData"))
datapath |
data path |
Get log fold-changes (logFC) from each study organized in a list with each item corresponding to a miRNA. Notably, some miRNAs (e.g., hsa-miR-1) appear more than once in the list corresponding to different studies.
get_miRNA_transfection_data(datapath = system.file("extdata/miRNA_transfection_data.RData", package = "TargetScoreData"))get_miRNA_transfection_data(datapath = system.file("extdata/miRNA_transfection_data.RData", package = "TargetScoreData"))
datapath |
data path |
We combined all of the logFC data columns into a single N x M matrix for all of the N = 19177 RefSeq mRNAs (NM_* obtained from UCSC) and M = 286 datasets. Missing data (logFC) for some genes across studies were imputed using impute from impute.knn.
get_precomputed_logFC(datapath = system.file("extdata/logFC.RData", package = "TargetScoreData"))get_precomputed_logFC(datapath = system.file("extdata/logFC.RData", package = "TargetScoreData"))
datapath |
data path |
Pre-calculated targetScores for 112 miRNAs using logFC and sequence scores from TargetScan context score and PCT from the RData files above.
get_precomputed_targetScores(datapath = system.file("extdata/targetScores.RData", package = "TargetScoreData"))get_precomputed_targetScores(datapath = system.file("extdata/targetScores.RData", package = "TargetScoreData"))
datapath |
data path |
TargetScan context score for all of the predicted sites (including conserved and nonconserved sites) downloaded from TargetScan 6 website (http://www.targetscan.org/cgi-bin/targetscan/data_download.cgi?db=vert_61)
get_TargetScanHuman_contextScore(datapath = system.file("extdata/TargetScanHuman_contextScore.RData", package = "TargetScoreData"))get_TargetScanHuman_contextScore(datapath = system.file("extdata/TargetScanHuman_contextScore.RData", package = "TargetScoreData"))
datapath |
data path |
TargetScan PCT for all of the predicted sites (including conserved and nonconserved sites) downloaded from TargetScan 6 website (http://www.targetscan.org/cgi-bin/targetscan/data_download.cgi?db=vert_61)
get_TargetScanHuman_PCT(datapath = system.file("extdata/TargetScanHuman_PCT.RData", package = "TargetScoreData"))get_TargetScanHuman_PCT(datapath = system.file("extdata/TargetScanHuman_PCT.RData", package = "TargetScoreData"))
datapath |
data path |
Get validated targets of human miRNA obtained from mirTarBase v3.5
get_validated_targets(datapath = system.file("extdata/hsa_MTI.xls", package = "TargetScoreData"))get_validated_targets(datapath = system.file("extdata/hsa_MTI.xls", package = "TargetScoreData"))
datapath |
data path |