Package: TENET 1.5.0

Rhie Lab at the University of Southern California

TENET: R package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key transcription factors

TENET identifies key transcription factors (TFs) and regulatory elements (REs) linked to a specific cell type by finding significantly correlated differences in gene expression and RE DNA methylation between case and control input datasets, and identifying the top genes by number of significant RE DNA methylation site links. It also includes many tools for visualization and analysis of the results, including plots displaying and comparing methylation and expression data and methylation site link counts, survival analysis, TF motif searching in the vicinity of linked RE DNA methylation sites, custom TAD and peak overlap analysis, and UCSC Genome Browser track file generation. A utility function is also provided to download methylation, expression, and patient survival data from The Cancer Genome Atlas (TCGA) for use in TENET or other analyses.

Authors:Rhie Lab at the University of Southern California [cre], Daniel Mullen [aut], Zexun Wu [aut], Ethan Nelson-Moore [aut], Suhn Rhie [aut]

TENET_1.5.0.tar.gz
TENET_1.5.0.zip(r-4.7)TENET_1.5.0.zip(r-4.6)TENET_1.5.0.zip(r-4.5)
TENET_1.5.0.tgz(r-4.6-any)TENET_1.5.0.tgz(r-4.5-any)
TENET_1.5.0.tar.gz(r-4.7-any)TENET_1.5.0.tar.gz(r-4.6-any)
TENET_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
TENET/json (API)
NEWS

# Install 'TENET' in R:
install.packages('TENET', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rhielab/tenet/issues

Datasets:

On BioConductor:TENET-1.5.0(bioc 3.24)TENET-1.4.0(bioc 3.23)

softwarebiomedicalinformaticscellbiologygeneticsepigeneticsmultiplecomparisongeneexpressiondifferentialexpressiondnamethylationdifferentialmethylationmethylationarraysequencingmethylseqrnaseqfunctionalgenomicsgeneregulationgenetargethistonemodificationtranscriptiontranscriptomicssurvivalvisualization

4.78 score 1 stars 20 scripts 249 downloads 23 exports 197 dependencies

Last updated from:a1cd8ef191. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE318
linux-devel-x86_64OK528
source / vignettesOK1401
linux-release-x86_64OK912
macos-release-arm64OK1380
macos-oldrel-arm64OK279
windows-develOK1294
windows-releaseOK526
windows-oldrelOK513
wasm-releaseOK257

Exports:easyTENETstep1MakeExternalDatasetsstep2GetDifferentiallyMethylatedSitesstep3GetAnalysisZScoresstep4SelectMostSignificantLinksPerDNAMethylationSitestep5OptimizeLinksstep6DNAMethylationSitesPerGeneTabulationstep7ExpressionVsDNAMethylationScatterplotsstep7LinkedDNAMethylationSiteCountHistogramsstep7LinkedDNAMethylationSitesMotifSearchingstep7SelectedDNAMethylationSitesCaseVsControlBoxplotsstep7StatesForLinksstep7TopGenesCaseVsControlExpressionBoxplotsstep7TopGenesCircosPlotsstep7TopGenesDNAMethylationHeatmapsstep7TopGenesExpressionCorrelationHeatmapsstep7TopGenesOverlappingLinkedDNAMethylationSitesHeatmapsstep7TopGenesSurvivalstep7TopGenesTADTablesstep7TopGenesUCSCBedFilesstep7TopGenesUserPeakOverlapTCGADownloaderTENETCacheAllData

Dependencies:abindAnnotationDbiAnnotationHubapeaskpassbackportsBAMMtoolsBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbitbit64bitopsblobbootbroomBSgenomeBSgenome.Hsapiens.UCSC.hg38cachemcarcarDatacaToolscigarilloclicliprcodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDerivdigestdoBydownloaderdplyrevaluateexactRankTestsExperimentHubfarverfastmapfilelockforecastformatRFormulafracdifffutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggplot2ggpubrggrepelggsciggsignifggtextgluegplotsgridExtragridtextgtablegtoolshighrhmshttrhttr2IRangesisobandjpegjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelifecyclelitedownlme4lmtestmagrittrmarkdownMASSmatlabMatrixMatrixGenericsMatrixModelsmatrixStatsmaxstatmemoisemgcvmicrobenchmarkmimeminqamodelrMotifDbMultiAssayExperimentmvtnormnlmenloptrnnetnumDerivopensslpastecspbkrtestpillarpkgconfigplyrpngpolynompreprocessCoreprettyunitsprogresspurrrquantregR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRCircosRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreadrreformulasreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLiterstatixrtracklayerrvestS4ArraysS4VectorsS7scalesselectrSeqinfoseqLogosesamesesameDatasnowSparseArraySparseMsplitstackshapestringistringrSummarizedExperimentsurvivalsurvminersysTCGAbiolinksTCGAbiolinksGUI.dataTENET.ExperimentHubtibbletidyrtidyselecttimeDatetzdbUCSC.utilsurcautf8vctrsviridisLitevroomwheatmapwithrxfunXMLxml2XVectoryamlzoo

Using TENET

Rhie Lab at the University of Southern California

Rendered fromTENET_vignette.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-10-28
Started: 2024-10-15

Readme and manuals

Help Manual

Help pageTopics
Run the step 1 through step 6 functions with default argumentseasyTENET
Human transcription factor databasehumanTranscriptionFactorDb
Human transcription factor listhumanTranscriptionFactorList
Create a GRanges object representing putative regulatory element regions, based on the data sources selected for inclusion, to be used in later TENET stepsstep1MakeExternalDatasets
Identify differentially methylated RE DNA methylation sitesstep2GetDifferentiallyMethylatedSites
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 2step3GetAnalysisZScores
Select the most significant RE DNA methylation site-gene links to each RE DNA methylation sitestep4SelectMostSignificantLinksPerDNAMethylationSite
Find final RE DNA methylation site-gene links using various optimization metricsstep5OptimizeLinks
Tabulate the total number of RE DNA methylation sites linked to each genestep6DNAMethylationSitesPerGeneTabulation
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 datastep7ExpressionVsDNAMethylationScatterplots
Create histograms displaying the number of total genes and transcription factor genes linked to a given number of RE DNA methylation sitesstep7LinkedDNAMethylationSiteCountHistograms
Search for transcription factor motifs in the vicinity of DNA methylation sites and/or within custom regions defined by the userstep7LinkedDNAMethylationSitesMotifSearching
Generate boxplots or violin plots comparing the methylation level of the specified RE DNA methylation sites in case and control samplesstep7SelectedDNAMethylationSitesCaseVsControlBoxplots
Identify which of the case samples harbor each of the identified regulatory element DNA methylation site-gene linksstep7StatesForLinks
Generate boxplots or violin plots comparing the expression level of the top genes and transcription factors in case and control samplesstep7TopGenesCaseVsControlExpressionBoxplots
Generate Circos plots displaying the links between the top identified genes and each of the RE DNA methylation sites linked to themstep7TopGenesCircosPlots
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 objectstep7TopGenesDNAMethylationHeatmaps
Generate mirrored heatmaps displaying the correlation of the expression values of the top genes and TFsstep7TopGenesExpressionCorrelationHeatmaps
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/TFstep7TopGenesOverlappingLinkedDNAMethylationSitesHeatmaps
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 sitesstep7TopGenesSurvival
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 targetsstep7TopGenesTADTables
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 sitesstep7TopGenesUCSCBedFiles
Identify if RE DNA methylation sites linked to top genes and transcription factors are located within a specific distance of specified genomic regionsstep7TopGenesUserPeakOverlap
Download TCGA gene expression, DNA methylation, and clinical datasets and compile them into a MultiAssayExperiment objectTCGADownloader
Cache all online datasets required by TENET examples and optional featuresTENETCacheAllData