{ "_id": "6a1b07a91d7bb097a0a04ab4", "Package": "TENET", "Title": "R package for TENET (Tracing regulatory Element Networks using\nEpigenetic Traits) to identify key transcription factors", "Description": "TENET identifies key transcription factors (TFs) and\nregulatory elements (REs) linked to a specific cell type by\nfinding significantly correlated differences in gene expression\nand RE DNA methylation between case and control input datasets,\nand identifying the top genes by number of significant RE DNA\nmethylation site links. It also includes many tools for\nvisualization and analysis of the results, including plots\ndisplaying and comparing methylation and expression data and\nmethylation site link counts, survival analysis, TF motif\nsearching in the vicinity of linked RE DNA methylation sites,\ncustom TAD and peak overlap analysis, and UCSC Genome Browser\ntrack file generation. A utility function is also provided to\ndownload methylation, expression, and patient survival data\nfrom The Cancer Genome Atlas (TCGA) for use in TENET or other\nanalyses.", "Version": "1.5.0", "Authors@R": "c(person(\"Rhie Lab at the University of Southern California\", email = \"rhielab@gmail.com\", role = \"cre\"), person(\"Daniel\", \"Mullen\", role = \"aut\", comment = c(ORCID = \"0000-0002-7639-0549\")), person(\"Zexun\", \"Wu\", role = \"aut\", comment = c(ORCID = \"0000-0003-2566-1326\")), person(\"Ethan\", \"Nelson-Moore\", role = \"aut\", comment = c(ORCID = \"0009-0001-6903-9232\")), person(\"Suhn\", \"Rhie\", role = \"aut\", comment = c(ORCID = \"0000-0002-5522-5296\")))", "URL": "https://github.com/rhielab/TENET", "BugReports": "https://github.com/rhielab/TENET/issues", "License": "GPL-2", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "BiocType": "Software", "biocViews": "Software, BiomedicalInformatics, CellBiology, Genetics,\nEpigenetics, MultipleComparison, GeneExpression,\nDifferentialExpression, DNAMethylation,\nDifferentialMethylation, MethylationArray, Sequencing,\nMethylSeq, RNASeq, FunctionalGenomics, GeneRegulation,\nGeneTarget, HistoneModification, Transcription,\nTranscriptomics, Survival, Visualization", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev libjpeg-dev\nliblzma-dev libpng-dev libxml2-dev libssl-dev libx11-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:04:36 UTC", "RemoteUrl": "https://github.com/bioc/TENET", "RemoteRef": "HEAD", "RemoteSha": "a1cd8ef1918b8a9cb0cff3fbbe4b850fdda54473", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 10:05:38 UTC", "User": "root" }, "Author": "Rhie Lab at the University of Southern California [cre],\nDaniel Mullen [aut] (ORCID: ),\nZexun Wu [aut] (ORCID: ),\nEthan Nelson-Moore [aut] (ORCID:\n),\nSuhn Rhie [aut] (ORCID: )", "Maintainer": "Rhie Lab at the University of Southern California ", "MD5sum": "35cac90122b76463811b17a31705e4a8", "_user": "bioc", "_type": "src", "_file": "TENET_1.5.0.tar.gz", "_fileid": "e85ec82f929c4b065e2fa8fcc8975249d6656ca84bf1d35e75c78f8b02bbdce7", "_filesize": 1941790, "_sha256": "e85ec82f929c4b065e2fa8fcc8975249d6656ca84bf1d35e75c78f8b02bbdce7", "_created": "2026-05-30T10:05:38.000Z", "_published": "2026-05-30T15:52:09.514Z", "_jobs": [ { "job": 78641576983, "time": 318, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307644131" }, { "job": 78641577000, "time": 528, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307665670" }, { "job": 78641577023, "time": 912, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307702650" }, { "job": 78641577018, "time": 279, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7309287281" }, { "job": 78641577004, "time": 1380, "config": "macos-release-arm64", 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"TF.tested.by.PBM.", "Conditional.Binding.Requirements", "Original.Comments", "Vaquerizas.2009.classification", "CisBP.considers.it.a.TF.", "TFCat.classification", "Is.a.GO.TF.", "Initial.assessment", "Curator.1", "Curator.2", "TFclass.considers.it.a.TF.", "Go.Evidence", "Pfam.Domains..By.ENSP.ID.", "Is.C2H2.ZF.KRAB.." ], "rows": 2765, "table": true, "tojson": true }, { "name": "humanTranscriptionFactorList", "title": "Human transcription factor list", "object": "humanTranscriptionFactorList", "file": "humanTranscriptionFactorList.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "easyTENET", "title": "Run the step 1 through step 6 functions with default arguments", "topics": [ "easyTENET" ] }, { "page": "humanTranscriptionFactorDb", "title": "Human transcription factor database", "topics": [ "humanTranscriptionFactorDb" ] }, { "page": "humanTranscriptionFactorList", "title": "Human transcription factor list", "topics": [ "humanTranscriptionFactorList" ] }, { "page": "step1MakeExternalDatasets", "title": "Create a GRanges object representing putative regulatory element regions, based on the data sources selected for inclusion, to be used in later TENET steps", "topics": [ "step1MakeExternalDatasets" ] }, { "page": "step2GetDifferentiallyMethylatedSites", "title": "Identify differentially methylated RE DNA methylation sites", "topics": [ "step2GetDifferentiallyMethylatedSites" ] }, { "page": "step3GetAnalysisZScores", "title": "Calculate Z-scores comparing the mean expression of each gene in the case samples that are hyper- and/or hypomethylated for each RE DNA methylation site identified in step 2", "topics": [ "step3GetAnalysisZScores" ] }, { "page": "step4SelectMostSignificantLinksPerDNAMethylationSite", "title": "Select the most significant RE DNA methylation site-gene links to each RE DNA methylation site", "topics": [ "step4SelectMostSignificantLinksPerDNAMethylationSite" ] }, { "page": "step5OptimizeLinks", "title": "Find final RE DNA methylation site-gene links using various optimization metrics", "topics": [ "step5OptimizeLinks" ] }, { "page": "step6DNAMethylationSitesPerGeneTabulation", "title": "Tabulate the total number of RE DNA methylation sites linked to each gene", "topics": [ "step6DNAMethylationSitesPerGeneTabulation" ] }, { "page": "step7ExpressionVsDNAMethylationScatterplots", "title": "Create scatterplots displaying the expression of the top genes and the methylation levels of each of their linked RE DNA methylation sites, optionally incorporating copy number variation, somatic mutation, and purity data", "topics": [ "step7ExpressionVsDNAMethylationScatterplots" ] }, { "page": "step7LinkedDNAMethylationSiteCountHistograms", "title": "Create histograms displaying the number of total genes and transcription factor genes linked to a given number of RE DNA methylation sites", "topics": [ "step7LinkedDNAMethylationSiteCountHistograms" ] }, { "page": "step7LinkedDNAMethylationSitesMotifSearching", "title": "Search for transcription factor motifs in the vicinity of DNA methylation sites and/or within custom regions defined by the user", "topics": [ "step7LinkedDNAMethylationSitesMotifSearching" ] }, { "page": "step7SelectedDNAMethylationSitesCaseVsControlBoxplots", "title": "Generate boxplots or violin plots comparing the methylation level of the specified RE DNA methylation sites in case and control samples", "topics": [ "step7SelectedDNAMethylationSitesCaseVsControlBoxplots" ] }, { "page": "step7StatesForLinks", "title": "Identify which of the case samples harbor each of the identified regulatory element DNA methylation site-gene links", "topics": [ "step7StatesForLinks" ] }, { "page": "step7TopGenesCaseVsControlExpressionBoxplots", "title": "Generate boxplots or violin plots comparing the expression level of the top genes and transcription factors in case and control samples", "topics": [ "step7TopGenesCaseVsControlExpressionBoxplots" ] }, { "page": "step7TopGenesCircosPlots", "title": "Generate Circos plots displaying the links between the top identified genes and each of the RE DNA methylation sites linked to them", "topics": [ "step7TopGenesCircosPlots" ] }, { "page": "step7TopGenesDNAMethylationHeatmaps", "title": "Generate heatmaps displaying the methylation level of all RE DNA methylation sites linked to the top genes and transcription factors, along with the expression of those genes in the column headers, in the case samples within the supplied MultiAssayExperiment object", "topics": [ "step7TopGenesDNAMethylationHeatmaps" ] }, { "page": "step7TopGenesExpressionCorrelationHeatmaps", "title": "Generate mirrored heatmaps displaying the correlation of the expression values of the top genes and TFs", "topics": [ "step7TopGenesExpressionCorrelationHeatmaps" ] }, { "page": "step7TopGenesOverlappingLinkedDNAMethylationSitesHeatmaps", "title": "Generate binary heatmaps displaying which of the top genes and transcription factors share links with each of the unique regulatory element DNA methylation sites linked to at least one top gene/TF", "topics": [ "step7TopGenesOverlappingLinkedDNAMethylationSitesHeatmaps" ] }, { "page": "step7TopGenesSurvival", "title": "Perform Kaplan-Meier and Cox regression analyses to assess the association of patient survival with the expression of top genes and transcription factors and methylation of their linked RE DNA methylation sites", "topics": [ "step7TopGenesSurvival" ] }, { "page": "step7TopGenesTADTables", "title": "Create tables using user-supplied topologically associating domain (TAD) information which identify the TADs containing each RE DNA methylation site linked to the top genes and transcription factors, as well as other genes in the same TAD as potential downstream targets", "topics": [ "step7TopGenesTADTables" ] }, { "page": "step7TopGenesUCSCBedFiles", "title": "Create BED-formatted interact files 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to be used in later TENET steps", "step2GetDifferentiallyMethylatedSites: Identify differentially methylated RE DNA methylation sites", "step3GetAnalysisZScores: Calculate Z-scores comparing the mean expression of each gene in the case samples that are hyper- and/or hypomethylated for each RE DNA methylation site identified in step 2", "step4SelectMostSignificantLinksPerDNAMethylationSite: Select the most significant RE DNA methylation site-gene links to each RE DNA methylation site", "step5OptimizeLinks: Find final RE DNA methylation site-gene links using various optimization metrics", "step6DNAMethylationSitesPerGeneTabulation: Tabulate the total number of RE DNA methylation sites linked to each gene", "TCGADownloader: Download TCGA gene expression, DNA methylation, and clinical datasets and compile them into a MultiAssayExperiment object", "TENETCacheAllData: Cache all online datasets required by TENET examples and optional features", "Overview of downstream step 7 functions", "step7ExpressionVsDNAMethylationScatterplots: Create scatterplots displaying the expression of the top genes and the methylation levels of each of their linked RE DNA methylation sites, optionally incorporating copy number variation, somatic mutation, and purity data", "step7LinkedDNAMethylationSiteCountHistograms: Create histograms displaying the number of total genes and transcription factor genes linked to a given number of RE DNA methylation sites", "step7LinkedDNAMethylationSitesMotifSearching: Search for transcription factor motifs in the vicinity of DNA methylation sites and/or within custom regions defined by the user", "step7SelectedDNAMethylationSitesCaseVsControlBoxplots: Generate boxplots or violin plots comparing the methylation level of the specified RE DNA methylation sites in case and control samples", "step7StatesForLinks: Identify which of the case samples harbor each of the identified regulatory element DNA methylation site-gene links", "step7TopGenesCaseVsControlExpressionBoxplots: Generate boxplots or violin plots comparing the expression level of the top genes and transcription factors in case and control samples", "step7TopGenesCircosPlots: Generate Circos plots displaying the links between the top identified genes and each of the RE DNA methylation sites linked to them", "step7TopGenesExpressionCorrelationHeatmaps: Generate mirrored heatmaps displaying the correlation of the expression values of the top genes and TFs", "step7TopGenesDNAMethylationHeatmaps: Generate heatmaps displaying the methylation level of all RE DNA methylation sites linked to the top genes and transcription factors, along with the expression of those genes in the column headers, in the case samples within the supplied MultiAssayExperiment object", "step7TopGenesOverlappingLinkedDNAMethylationSitesHeatmaps: Generate binary heatmaps displaying which of the top genes and transcription factors share links with each of the unique regulatory element DNA methylation sites linked to at least one top gene/TF", "step7TopGenesSurvival: Perform Kaplan-Meier and Cox regression analyses to assess the association of patient survival with the expression of top genes and transcription factors and methylation of their linked RE DNA methylation sites", "step7TopGenesTADTables: Create tables using user-supplied topologically associating domain (TAD) information which identify the TADs containing each RE DNA methylation site linked to the top genes and transcription factors, as well as other genes in the same TAD as potential downstream targets", "step7TopGenesUCSCBedFiles: Create BED-formatted interact files which can be loaded on the UCSC Genome Browser to display links between top genes and transcription factors and their linked RE DNA methylation sites", "step7TopGenesUserPeakOverlap: Identify if RE DNA methylation sites linked to top genes and transcription factors are located within a specific distance of specified genomic regions", "Datasets included in the TENET package", "humanTranscriptionFactorList: Human transcription factor list", "humanTranscriptionFactorDb: Human transcription factor database", "Acknowledgements", "Session info" ], "created": "2024-10-15 22:54:53", "modified": "2025-10-28 11:21:23", "commits": 11 } ], "_score": 4.778151250383644, "_indexed": true, "_nocasepkg": "tenet", "_universes": [ "bioc", "rhielab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.5.0", "date": "2026-05-30T10:50:37.000Z", "distro": "noble", "commit": "a1cd8ef1918b8a9cb0cff3fbbe4b850fdda54473", "fileid": "26ae4a669116b277cc5ac4845d35975c2a99bda60c5e03f67e11e3141a3f772c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676272546" }, { "r": "4.6.0", "os": "linux", "version": "1.5.0", "date": "2026-05-30T10:50:45.000Z", "distro": "noble", "commit": "a1cd8ef1918b8a9cb0cff3fbbe4b850fdda54473", "fileid": 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