muleaData - GMT Datasets for the mulea Package
muleaData is an ExperimentHubData Bioconductor package providing
pre-processed gene set data for use with the
mulea R package, a
comprehensive tool for overrepresentation and functional enrichment
analysis. mulea leverages ontologies (gene and protein sets) stored in
the standardized Gene Matrix Transposed (GMT) format.
We provide these GMT files for 27 different model organisms, ranging
from Escherichia coli to human. These files are compiled from publicly
available sources and include various gene and protein identifiers like
UniProt protein IDs, Entrez, Gene Symbol, and Ensembl gene IDs.
The GMT files and the scripts we applied to create them are available at
the
GMT_files_for_mulea
repository. For the muleaData we read these GMT files with the
mulea::read_gmt() function and saved them to .rds files with the
standard R saveRDS() function.
List of species muleaData covers:
- Arabidopsis thaliana
- Bacillus subtilis
- Bacteroides thetaiotaomicron VPI-5482
- Bifidobacterium longum
- Bos taurus
- Caenorhabditis elegans
- Chlamydomonas reinhardtii
- Danio rerio
- Daphnia pulex
- Dictyostelium discoideum
- Drosophila melanogaster
- Drosophila simulans
- Escherichia coli
- Gallus gallus
- Homo sapiens
- Macaca mulatta
- Mus musculus
- Mycobacterium tuberculosis
- Neurospora crassa
- Pan troglodytes
- Rattus norvegicus
- Saccharomyces cerevisiae
- Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
- Schizosaccharomyces pombe
- Tetrahymena thermophila
- Xenopus tropicalis
- Zea mays
Type, name, link and citation of the databases muleaData covers:
| Ontology category | Ontology name | Short description of content | Reference |
| Gene expression | FlyAtlas | Tissue-specific expression data for Drosophila melanogaster. | Chintapalli,V.R. et al. (2007) Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nat Genet, 39, 715–720. |
| ModEncode | Functional characterization (cell line, temporal expression, tissue expression, treatment) of elements for Caenorhabditis elegans and Drosophila melanogaster. | The Modencode Consortium et al. (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science, 330, 1787–1797. | |
| Genomic location | Chromosomal Bands | Location of genes on the chromosome. | Martin,F.J. et al. (2023) Ensembl 2023. Nucleic Acids Res, 51, D933–D941. |
| Consecutive genes | n consecutive genes on the chromosome. | ||
| miRNA regulation | miRTarBase | Experimentally validated miRNA - target interactions. | Huang,H.-Y. et al. (2022) miRTarBase update 2022: an informative resource for experimentally validated miRNA–target interactions. Nucleic Acids Res, 50, D222–D230. |
| Gene Ontology | GO | Gene Ontology (GO) categorizes genes into unified categories and attributes. | The Gene Ontology Consortium et al. (2023) The Gene Ontology knowledgebase in 2023. Genetics, 224, iyad031. |
| Pathway | Pathway Commons | Collection of biological pathway and interaction data. | Rodchenkov,I. et al. (2020) Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic Acids Res, 48, D489–D497. |
| Reactome | Collection of biological pathway and interaction data. | Jassal,B. et al. (2020) The reactome pathway knowledgebase. Nucleic Acids Res, 48, D498–D503. | |
| Signalink | Interaction database focussing on pathways and interactions of pathways. | Csabai,L. et al. (2022) SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks. Nucleic Acids Res, 50, D701–D709. | |
| Wikipathways | Collection of biological pathway and interaction data. | Martens,M. et al. (2021) WikiPathways: connecting communities. Nucleic Acids Res, 49, D613–D621. | |
| Protein domain | PFAM | Protein domain structure database. | Mistry,J. et al. (2021) Pfam: The protein families database in 2021. Nucleic Acids Res, 49, D412–D419. |
| Transcription factor regulation | ATRM | Transcription factor - target gene interactions for Arabidopsis thaliana. | Jin,J. et al. (2015) An Arabidopsis transcriptional regulatory map reveals distinct functional and evolutionary features of novel transcription factors. Mol Biol Evol, 32, 1767–1773. |
| dorothEA | Transcription factor - target gene interactions for human and mouse. | Garcia-Alonso,L. et al. (2019) Benchmark and integration of resources for the estimation of human transcription factor activities. Genome Res, 29, 1363–1375. | |
| RegulonDB | Transcription factor - target gene interactions for Escherichia coli bacteria. | Tierrafría,V.H. et al. (2022) RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12. Microb Genom, 8, 000833. | |
| TFLink | Small- and large-scale transcription factor - target gene interactions for human and 6 model organisms. | Liska,O. et al. (2022) TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species. Database, 2022, baac083. | |
| TRRUST | Transcription factor - target gene interactions for human. | Han,H. et al. (2018) TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions. Nucleic Acids Res, 46, D380–D386. | |
| Yeastract | Transcription factor - target gene interactions for Saccharomyces cerevisiae. | Teixeira,M.C. et al. (2018) YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae. Nucleic Acids Res, 46, D348–D353. |
Install the developmental version of R from
CRAN. Then install the
developmental version of Bioconductor and
the ExperimentHub library using the following code:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ExperimentHub")
BiocManager::install("muleaData")This is a basic example which shows you how to use the muleaData:
# Calling the ExperimentHub library.
library(ExperimentHub)
#> Loading required package: BiocGenerics
#>
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
#>
#> IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#>
#> anyDuplicated, aperm, append, as.data.frame, basename, cbind,
#> colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
#> get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
#> match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#> Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
#> tapply, union, unique, unsplit, which.max, which.min
#> Loading required package: AnnotationHub
#> Loading required package: BiocFileCache
#> Loading required package: dbplyr
# Downloading the metadata from ExperimentHub.
eh <- ExperimentHub()
# Creating the muleaData variable.
muleaData <- query(eh, "muleaData")
# Checking the muleaData variable.
muleaData
#> ExperimentHub with 879 records
#> # snapshotDate(): 2024-03-06
#> # $dataprovider: muleaData
#> # $species: Drosophila melanogaster, Homo sapiens, Mus musculus, Caenorhabdi...
#> # $rdataclass: data.frame
#> # additional mcols(): taxonomyid, genome, description,
#> # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#> # rdatapath, sourceurl, sourcetype
#> # retrieve records with, e.g., 'object[["EH8571"]]'
#>
#> title
#> EH8571 | Genomic_location_Ensembl_Arabidopsis_thaliana_10genes_EnsemblID.rds
#> EH8572 | Genomic_location_Ensembl_Arabidopsis_thaliana_10genes_EntrezID.rds
#> EH8573 | Genomic_location_Ensembl_Arabidopsis_thaliana_10genes_GeneSymbol...
#> EH8574 | Genomic_location_Ensembl_Arabidopsis_thaliana_10genes_UniprotID.rds
#> EH8575 | Genomic_location_Ensembl_Arabidopsis_thaliana_20genes_EnsemblID.rds
#> ... ...
#> EH9445 | Genomic_location_Ensembl_Zea_mays_5genes_UniprotID.rds
#> EH9446 | Protein_domain_PFAM_Zea_mays_EnsemblID.rds
#> EH9447 | Protein_domain_PFAM_Zea_mays_EntrezID.rds
#> EH9448 | Protein_domain_PFAM_Zea_mays_GeneSymbol.rds
#> EH9449 | Protein_domain_PFAM_Zea_mays_UniprotID.rds
# Looking for the ExperimentalHub ID of i.e. target genes of transcription
# factors from TFLink in Caenorhabditis elegans.
mcols(muleaData) %>%
as.data.frame() %>%
dplyr::filter(species == "Caenorhabditis elegans" &
sourceurl == "https://tflink.net/")
#> title
#> EH8727 Transcription_factor_TFLink_Caenorhabditis_elegans_All_EnsemblID.rds
#> EH8728 Transcription_factor_TFLink_Caenorhabditis_elegans_All_EntrezID.rds
#> EH8729 Transcription_factor_TFLink_Caenorhabditis_elegans_All_GeneSymbol.rds
#> EH8730 Transcription_factor_TFLink_Caenorhabditis_elegans_All_UniprotID.rds
#> EH8731 Transcription_factor_TFLink_Caenorhabditis_elegans_LS_EnsemblID.rds
#> EH8732 Transcription_factor_TFLink_Caenorhabditis_elegans_LS_EntrezID.rds
#> EH8733 Transcription_factor_TFLink_Caenorhabditis_elegans_LS_GeneSymbol.rds
#> EH8734 Transcription_factor_TFLink_Caenorhabditis_elegans_LS_UniprotID.rds
#> EH8735 Transcription_factor_TFLink_Caenorhabditis_elegans_SS_EnsemblID.rds
#> EH8736 Transcription_factor_TFLink_Caenorhabditis_elegans_SS_EntrezID.rds
#> EH8737 Transcription_factor_TFLink_Caenorhabditis_elegans_SS_GeneSymbol.rds
#> EH8738 Transcription_factor_TFLink_Caenorhabditis_elegans_SS_UniprotID.rds
#> dataprovider species taxonomyid genome
#> EH8727 muleaData Caenorhabditis elegans 6239 <NA>
#> EH8728 muleaData Caenorhabditis elegans 6239 <NA>
#> EH8729 muleaData Caenorhabditis elegans 6239 <NA>
#> EH8730 muleaData Caenorhabditis elegans 6239 <NA>
#> EH8731 muleaData Caenorhabditis elegans 6239 <NA>
#> EH8732 muleaData Caenorhabditis elegans 6239 <NA>
#> EH8733 muleaData Caenorhabditis elegans 6239 <NA>
#> EH8734 muleaData Caenorhabditis elegans 6239 <NA>
#> EH8735 muleaData Caenorhabditis elegans 6239 <NA>
#> EH8736 muleaData Caenorhabditis elegans 6239 <NA>
#> EH8737 muleaData Caenorhabditis elegans 6239 <NA>
#> EH8738 muleaData Caenorhabditis elegans 6239 <NA>
#> description
#> EH8727 ExperimentHubData package for the 'mulea' comprehensive overrepresentation and functional enrichment analyser R package. Here we provide ontologies (gene sets) in a data.frame for 27 different organisms, ranging from Escherichia coli to human, all acquired from publicly available data sources. Each ontology is provided with multiple gene and protein identifiers.
#> EH8728 ExperimentHubData package for the 'mulea' comprehensive overrepresentation and functional enrichment analyser R package. Here we provide ontologies (gene sets) in a data.frame for 27 different organisms, ranging from Escherichia coli to human, all acquired from publicly available data sources. Each ontology is provided with multiple gene and protein identifiers.
#> EH8729 ExperimentHubData package for the 'mulea' comprehensive overrepresentation and functional enrichment analyser R package. Here we provide ontologies (gene sets) in a data.frame for 27 different organisms, ranging from Escherichia coli to human, all acquired from publicly available data sources. Each ontology is provided with multiple gene and protein identifiers.
#> EH8730 ExperimentHubData package for the 'mulea' comprehensive overrepresentation and functional enrichment analyser R package. Here we provide ontologies (gene sets) in a data.frame for 27 different organisms, ranging from Escherichia coli to human, all acquired from publicly available data sources. Each ontology is provided with multiple gene and protein identifiers.
#> EH8731 ExperimentHubData package for the 'mulea' comprehensive overrepresentation and functional enrichment analyser R package. Here we provide ontologies (gene sets) in a data.frame for 27 different organisms, ranging from Escherichia coli to human, all acquired from publicly available data sources. Each ontology is provided with multiple gene and protein identifiers.
#> EH8732 ExperimentHubData package for the 'mulea' comprehensive overrepresentation and functional enrichment analyser R package. Here we provide ontologies (gene sets) in a data.frame for 27 different organisms, ranging from Escherichia coli to human, all acquired from publicly available data sources. Each ontology is provided with multiple gene and protein identifiers.
#> EH8733 ExperimentHubData package for the 'mulea' comprehensive overrepresentation and functional enrichment analyser R package. Here we provide ontologies (gene sets) in a data.frame for 27 different organisms, ranging from Escherichia coli to human, all acquired from publicly available data sources. Each ontology is provided with multiple gene and protein identifiers.
#> EH8734 ExperimentHubData package for the 'mulea' comprehensive overrepresentation and functional enrichment analyser R package. Here we provide ontologies (gene sets) in a data.frame for 27 different organisms, ranging from Escherichia coli to human, all acquired from publicly available data sources. Each ontology is provided with multiple gene and protein identifiers.
#> EH8735 ExperimentHubData package for the 'mulea' comprehensive overrepresentation and functional enrichment analyser R package. Here we provide ontologies (gene sets) in a data.frame for 27 different organisms, ranging from Escherichia coli to human, all acquired from publicly available data sources. Each ontology is provided with multiple gene and protein identifiers.
#> EH8736 ExperimentHubData package for the 'mulea' comprehensive overrepresentation and functional enrichment analyser R package. Here we provide ontologies (gene sets) in a data.frame for 27 different organisms, ranging from Escherichia coli to human, all acquired from publicly available data sources. Each ontology is provided with multiple gene and protein identifiers.
#> EH8737 ExperimentHubData package for the 'mulea' comprehensive overrepresentation and functional enrichment analyser R package. Here we provide ontologies (gene sets) in a data.frame for 27 different organisms, ranging from Escherichia coli to human, all acquired from publicly available data sources. Each ontology is provided with multiple gene and protein identifiers.
#> EH8738 ExperimentHubData package for the 'mulea' comprehensive overrepresentation and functional enrichment analyser R package. Here we provide ontologies (gene sets) in a data.frame for 27 different organisms, ranging from Escherichia coli to human, all acquired from publicly available data sources. Each ontology is provided with multiple gene and protein identifiers.
#> coordinate_1_based maintainer rdatadateadded
#> EH8727 1 Eszter Ari arieszter@gmail.com 2024-02-07
#> EH8728 1 Eszter Ari arieszter@gmail.com 2024-02-07
#> EH8729 1 Eszter Ari arieszter@gmail.com 2024-02-07
#> EH8730 1 Eszter Ari arieszter@gmail.com 2024-02-07
#> EH8731 1 Eszter Ari arieszter@gmail.com 2024-02-07
#> EH8732 1 Eszter Ari arieszter@gmail.com 2024-02-07
#> EH8733 1 Eszter Ari arieszter@gmail.com 2024-02-07
#> EH8734 1 Eszter Ari arieszter@gmail.com 2024-02-07
#> EH8735 1 Eszter Ari arieszter@gmail.com 2024-02-07
#> EH8736 1 Eszter Ari arieszter@gmail.com 2024-02-07
#> EH8737 1 Eszter Ari arieszter@gmail.com 2024-02-07
#> EH8738 1 Eszter Ari arieszter@gmail.com 2024-02-07
#> preparerclass tags rdataclass
#> EH8727 muleaData Arabidop.... data.frame
#> EH8728 muleaData Arabidop.... data.frame
#> EH8729 muleaData Arabidop.... data.frame
#> EH8730 muleaData Arabidop.... data.frame
#> EH8731 muleaData Arabidop.... data.frame
#> EH8732 muleaData Arabidop.... data.frame
#> EH8733 muleaData Arabidop.... data.frame
#> EH8734 muleaData Arabidop.... data.frame
#> EH8735 muleaData Arabidop.... data.frame
#> EH8736 muleaData Arabidop.... data.frame
#> EH8737 muleaData Arabidop.... data.frame
#> EH8738 muleaData Arabidop.... data.frame
#> rdatapath
#> EH8727 muleaData/Transcription_factor_TFLink_Caenorhabditis_elegans_All_EnsemblID.rds
#> EH8728 muleaData/Transcription_factor_TFLink_Caenorhabditis_elegans_All_EntrezID.rds
#> EH8729 muleaData/Transcription_factor_TFLink_Caenorhabditis_elegans_All_GeneSymbol.rds
#> EH8730 muleaData/Transcription_factor_TFLink_Caenorhabditis_elegans_All_UniprotID.rds
#> EH8731 muleaData/Transcription_factor_TFLink_Caenorhabditis_elegans_LS_EnsemblID.rds
#> EH8732 muleaData/Transcription_factor_TFLink_Caenorhabditis_elegans_LS_EntrezID.rds
#> EH8733 muleaData/Transcription_factor_TFLink_Caenorhabditis_elegans_LS_GeneSymbol.rds
#> EH8734 muleaData/Transcription_factor_TFLink_Caenorhabditis_elegans_LS_UniprotID.rds
#> EH8735 muleaData/Transcription_factor_TFLink_Caenorhabditis_elegans_SS_EnsemblID.rds
#> EH8736 muleaData/Transcription_factor_TFLink_Caenorhabditis_elegans_SS_EntrezID.rds
#> EH8737 muleaData/Transcription_factor_TFLink_Caenorhabditis_elegans_SS_GeneSymbol.rds
#> EH8738 muleaData/Transcription_factor_TFLink_Caenorhabditis_elegans_SS_UniprotID.rds
#> sourceurl sourcetype
#> EH8727 https://tflink.net/ Multiple
#> EH8728 https://tflink.net/ Multiple
#> EH8729 https://tflink.net/ Multiple
#> EH8730 https://tflink.net/ Multiple
#> EH8731 https://tflink.net/ Multiple
#> EH8732 https://tflink.net/ Multiple
#> EH8733 https://tflink.net/ Multiple
#> EH8734 https://tflink.net/ Multiple
#> EH8735 https://tflink.net/ Multiple
#> EH8736 https://tflink.net/ Multiple
#> EH8737 https://tflink.net/ Multiple
#> EH8738 https://tflink.net/ Multiple
# Creating a variable for the GMT data.frame of EH8735.
# EH8735 contains small-scale measurement results, where the target genes are
# coded with Ensembl ID-s
Transcription_factor_TFLink_Caenorhabditis_elegans_SS_EnsemblID <- muleaData[["EH8735"]]
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#> CRAN: https://cloud.r-project.org
#> Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable)
#> (2024-02-21 r85967)
#> Installing package(s) 'muleaData'
#> Warning: package 'muleaData' is not available for Bioconductor version '3.19'
#>
#> A version of this package for your version of R might be available elsewhere,
#> see the ideas at
#> https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages
#> Installation paths not writeable, unable to update packages
#> path: /usr/local/lib/R/library
#> packages:
#> boot
#> loading from cachesessionInfo()
#> R Under development (unstable) (2024-02-21 r85967)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 22.04.3 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
#>
#> locale:
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#> time zone: Etc/UTC
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#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] ExperimentHub_2.11.1 AnnotationHub_3.11.1 BiocFileCache_2.11.1
#> [4] dbplyr_2.4.0 BiocGenerics_0.49.1
#>
#> loaded via a namespace (and not attached):
#> [1] rappdirs_0.3.3 utf8_1.2.4 generics_0.1.3
#> [4] BiocVersion_3.19.1 RSQLite_2.3.5 digest_0.6.34
#> [7] magrittr_2.0.3 evaluate_0.23 fastmap_1.1.1
#> [10] blob_1.2.4 AnnotationDbi_1.65.2 GenomeInfoDb_1.39.7
#> [13] DBI_1.2.2 BiocManager_1.30.22 httr_1.4.7
#> [16] purrr_1.0.2 fansi_1.0.6 Biostrings_2.71.2
#> [19] cli_3.6.2 rlang_1.1.3 crayon_1.5.2
#> [22] XVector_0.43.1 Biobase_2.63.0 bit64_4.0.5
#> [25] withr_3.0.0 cachem_1.0.8 yaml_2.3.8
#> [28] tools_4.4.0 memoise_2.0.1 dplyr_1.1.4
#> [31] GenomeInfoDbData_1.2.11 filelock_1.0.3 curl_5.2.1
#> [34] mime_0.12 vctrs_0.6.5 R6_2.5.1
#> [37] png_0.1-8 stats4_4.4.0 lifecycle_1.0.4
#> [40] zlibbioc_1.49.0 KEGGREST_1.43.0 S4Vectors_0.41.4
#> [43] IRanges_2.37.1 bit_4.0.5 pkgconfig_2.0.3
#> [46] pillar_1.9.0 glue_1.7.0 xfun_0.42
#> [49] tibble_3.2.1 tidyselect_1.2.0 rstudioapi_0.15.0
#> [52] knitr_1.45 htmltools_0.5.7 rmarkdown_2.26
#> [55] compiler_4.4.0To cite package muleaData in publications use:
C. Turek, M. Olbei, T. Stirling, G. Fekete, E. Tasnadi, L. Gul, B. Bohar, B. Papp, W. Jurkowski, E. Ari: mulea - an R package for enrichment analysis using multiple ontologies and empirical FDR correction. bioRxiv (2024), doi:10.1101/2024.02.28.582444.