Author: Christophe Tav

# rChEA3: An R client for ChEA3 transcription factor enrichment API

#### Christophe Tav

#### October 2025

# Introduction

rChEA3 is an R client for the ChEA3 transcription factor enrichment API.

While ChEA3 is only available online as a web server, rChEA3 provides access to this tool directly in R, streamlining transcription factor enrichment into your workflow. Submit gene lists, retrieve TF rankings from multiple evidence sources (ChIP-seq, co-expression, literature), and integrate results into your R/Bioconductor analysis pipeline.

The package includes convenient functions to query the API, retrieve results across collections, prepare outputs for downstream analysis, and generate publication-ready figures.

# Example workflow

This section demonstrates a typical workflow with rChEA3, from submitting a gene list to retrieving transcription factor enrichment results. The examples illustrate how to interact with the ChEA3 API, explore the different collections, and visualize results in a clear, publication-ready format.

We start by loading the package:

    library(rChEA3)

## 1. Submit a gene list

Provide a vector of gene symbols as input. The gene list should consist of HGNC-approved gene symbols, as ChEA3 only accepts these standardized gene identifiers.

    genes <- c("TP53", "ESR1", "MYC", "NIPBL", "BRCA1")
    results <- queryChEA3(genes)
    #> Available results
    #> ──────────────────────────────
    #>   ► Integrated Results
    #>     ✔ Mean Rank — Average integrated ranks across libraries
    #>         Use <your_result>[["Integrated--meanRank"]]
    #>     ✔ Top Rank — Top integrated rank across libraries
    #>         Use <your_result>[["Integrated--topRank"]]
    #>   ────────────────────
    #>   ► ChIP-Seq
    #>     ✔ ENCODE — Interactions mined from the ENCODE project
    #>         Use <your_result>[["ENCODE--ChIP-seq"]]
    #>     ✔ ReMap — Interactions mined from the ReMap project
    #>         Use <your_result>[["ReMap--ChIP-seq"]]
    #>     ✔ Literature — Interactions mined from the literature
    #>         Use <your_result>[["Literature--ChIP-seq"]]
    #>   ────────────────────
    #>   ► Coexpression
    #>     ✔ ARCHS4 — TF-target coexpression in the ARCHS4 dataset
    #>         Use <your_result>[["ARCHS4--Coexpression"]]
    #>     ✔ GTEx — TF-target coexpression in the GTEx dataset
    #>         Use <your_result>[["GTEx--Coexpression"]]
    #>   ────────────────────
    #>   ► Co-occurrence
    #>     ✔ Enrichr — TF-target co-occurrence in Enrichr queries
    #>         Use <your_result>[["Enrichr--Queries"]]
    #>   ────────────────────

> Note: For detailed information about the different ChEA3 collections and their underlying methodology, see Keenan et al., 2019.

## 2. Inspect top results

The function displayTopN() allows a quick inspection of the results by showing the top transcription factors from each collection. By default, the top 10 transcription factors are displayed without applying thresholds.

    displayTopN(results)
    #> Top 10 per collection
    #> ──────────────────────────────
    #>   ► Integrated Results
    #>     ✔ Mean Rank - Average integrated ranks across libraries
    #>          Rank     TF Score
    #>             1  ZBED6 15.00
    #>             2    PGR 41.25
    #>             3    SON 45.50
    #>             4 ZBTB21 46.50
    #>             5   BPTF 58.50
    #>             6   SPEN 58.50
    #>             7  SMAD4 69.20
    #>             8  ZNF12 78.33
    #>             9   ARNT 87.00
    #>            10   SAFB 93.00
    #>
    #>     ✔ Top Rank - Top integrated rank across libraries
    #>          Rank      TF     Score
    #>             1 TGIF2LY 0.0006143
    #>             2  ZNF800 0.0006223
    #>             3   CREB1 0.0007123
    #>             4  RHOXF1 0.0012290
    #>             5  HIVEP1 0.0012450
    #>             6    NFYA 0.0014250
    #>             7  ZNF654 0.0018430
    #>             8    OSR2 0.0018670
    #>             9     SP1 0.0021370
    #>            10     BBX 0.0024570
    #>
    #>   ────────────────────
    #>   ► ChIP-Seq
    #>     ✔ ENCODE - Interactions mined from the ENCODE project
    #>          Rank     TF Scaled Rank               Set_name Intersect FET p-value   FDR
    #>             1  CEBPB    0.008475        CEBPB_C2C12_MM9         3    0.009772 0.717
    #>             2 ZNF217    0.016950       ZNF217_MCF7_HG19         3    0.012720 0.717
    #>             3   CTCF    0.025420        CTCF_HEPG2_HG19         4    0.017380 0.717
    #>             4  CEBPD    0.033900        CEBPD_K562_HG19         2    0.018070 0.717
    #>             5 ZNF384    0.042370      ZNF384_CH12LX_MM9         3    0.019260 0.717
    #>             6   ATF2    0.050850       ATF2_H1HESC_HG19         3    0.021370 0.717
    #>             7   RELA    0.059320      RELA_GM12878_HG19         2    0.022770 0.717
    #>             8   FLI1    0.067800 FLI1_MEGAKARYOCYTE_MM9         3    0.024120 0.717
    #>             9    YY1    0.076270       YY1_GM12892_HG19         2    0.031250 0.717
    #>            10   JUND    0.084750       JUND_H1HESC_HG19         3    0.037140 0.717
    #>          Odds Ratio
    #>               9.358
    #>               8.449
    #>               5.697
    #>              12.580
    #>               7.167
    #>               6.871
    #>              11.080
    #>               6.541
    #>               9.289
    #>               5.463
    #>
    #>     ✔ ReMap - Interactions mined from the ReMap project
    #>          Rank     TF Scaled Rank Set_name Intersect FET p-value   FDR Odds Ratio
    #>             1  CXXC4    0.003367    CXXC4         3     0.01325 0.911      8.314
    #>             2   MBD3    0.006734     MBD3         2     0.07561 0.911      5.558
    #>             3  KMT2B    0.010100    KMT2B         2     0.07561 0.911      5.558
    #>             4   RFX2    0.013470     RFX2         2     0.07569 0.911      5.554
    #>             5   MBD4    0.016840     MBD4         2     0.07578 0.911      5.550
    #>             6  EOMES    0.020200    EOMES         2     0.07578 0.911      5.550
    #>             7   TBXT    0.023570     TBXT         2     0.07604 0.911      5.539
    #>             8   XBP1    0.026940     XBP1         2     0.07613 0.911      5.535
    #>             9 ZBTB33    0.030300   ZBTB33         2     0.07621 0.911      5.531
    #>            10  FOXA1    0.033670    FOXA1         2     0.07621 0.911      5.531
    #>
    #>     ✔ Literature - Interactions mined from the literature
    #>          Rank     TF Scaled Rank                                              Set_name
    #>             1   ESR1    0.006098                     ESR1_15608294_CHIPCHIP_MCF7_HUMAN
    #>             2   E2F4    0.012200                   E2F4_17652178_CHIPCHIP_JURKAT_HUMAN
    #>             3  BACH1    0.018290              BACH1_22875853_CHIPPCR_HELAANDSCP4_HUMAN
    #>             4  PPARD    0.024390                 PPARD_23208498_CHIPSEQ_MDAMB231_HUMAN
    #>             5    JUN    0.030490                       JUN_21703547_CHIPSEQ_K562_HUMAN
    #>             6   E2F7    0.036590                      E2F7_22180533_CHIPSEQ_HELA_HUMAN
    #>             7   CUX1    0.042680 CUX1_19635798_CHIPCHIP_MULTIPLEHUMANCANCERTYPES_HUMAN
    #>             8  NANOG    0.048780                    NANOG_18347094_CHIPCHIP_MESC_MOUSE
    #>             9 POU3F1    0.054880                     POU3F1_26484290_CHIPSEQ_ESC_MOUSE
    #>            10   EGR1    0.060980                     EGR1_19374776_CHIPCHIP_THP1_HUMAN
    #>          Intersect FET p-value   FDR Odds Ratio
    #>                  2    0.000384 0.118     94.090
    #>                  3    0.003138 0.482     14.330
    #>                  3    0.010030 0.494      9.264
    #>                  2    0.010610 0.494     16.770
    #>                  3    0.013300 0.494      8.302
    #>                  1    0.013400 0.494     90.890
    #>                  4    0.016600 0.494      5.783
    #>                  3    0.016690 0.494      7.588
    #>                  3    0.019720 0.494      7.099
    #>                  1    0.019870 0.494     60.590
    #>
    #>   ────────────────────
    #>   ► Coexpression
    #>     ✔ ARCHS4 - TF-target coexpression in the ARCHS4 dataset
    #>          Rank      TF Scaled Rank               Set_name Intersect FET p-value FDR
    #>             1 TGIF2LY   0.0006143 TGIF2LY_ARCHS4_PEARSON         2    0.004325   1
    #>             2  RHOXF1   0.0012290  RHOXF1_ARCHS4_PEARSON         2    0.004352   1
    #>             3  ZNF654   0.0018430  ZNF654_ARCHS4_PEARSON         1    0.084660   1
    #>             4     BBX   0.0024570     BBX_ARCHS4_PEARSON         1    0.084660   1
    #>             5  ZNF407   0.0030710  ZNF407_ARCHS4_PEARSON         1    0.084660   1
    #>             6     RLF   0.0036860     RLF_ARCHS4_PEARSON         1    0.084660   1
    #>             7  ZNF552   0.0043000  ZNF552_ARCHS4_PEARSON         1    0.084660   1
    #>             8     YY2   0.0049140     YY2_ARCHS4_PEARSON         1    0.084660   1
    #>             9    REST   0.0055280    REST_ARCHS4_PEARSON         1    0.084660   1
    #>            10  ZBTB24   0.0061430  ZBTB24_ARCHS4_PEARSON         1    0.084930   1
    #>          Odds Ratio
    #>               26.93
    #>               26.84
    #>               13.51
    #>               13.51
    #>               13.51
    #>               13.51
    #>               13.51
    #>               13.51
    #>               13.51
    #>               13.46
    #>
    #>     ✔ GTEx - TF-target coexpression in the GTEx dataset
    #>          Rank      TF Scaled Rank Set_name Intersect FET p-value   FDR Odds Ratio
    #>             1  ZNF800   0.0006223   ZNF800         3   0.0001677 0.136      40.53
    #>             2  HIVEP1   0.0012450   HIVEP1         3   0.0001694 0.136      40.39
    #>             3    OSR2   0.0018670     OSR2         2   0.0042690 0.538      27.11
    #>             4   ADNP2   0.0024890    ADNP2         2   0.0043250 0.538      26.93
    #>             5   NCOA3   0.0031110    NCOA3         2   0.0043520 0.538      26.84
    #>             6 ZSCAN25   0.0037340  ZSCAN25         2   0.0043520 0.538      26.84
    #>             7  ZNF317   0.0043560   ZNF317         2   0.0043520 0.538      26.84
    #>             8   KLF11   0.0049780    KLF11         2   0.0043520 0.538      26.84
    #>             9 ZNF705E   0.0056000  ZNF705E         2   0.0043520 0.538      26.84
    #>            10     SP1   0.0062230      SP1         2   0.0043520 0.538      26.84
    #>
    #>   ────────────────────
    #>   ► Co-occurrence
    #>     ✔ Enrichr - TF-target co-occurrence in Enrichr queries
    #>          Rank    TF Scaled Rank Set_name Intersect FET p-value      FDR Odds Ratio
    #>             1 CREB1   0.0007123    CREB1         5   1.539e-07 4.39e-05      68.48
    #>             2  NFYA   0.0014250     NFYA         5   1.539e-07 4.39e-05      68.48
    #>             3   SP1   0.0021370      SP1         5   1.565e-07 4.39e-05      68.24
    #>             4 SMAD4   0.0028490    SMAD4         5   1.565e-07 4.39e-05      68.24
    #>             5  ATF2   0.0035610     ATF2         5   1.565e-07 4.39e-05      68.24
    #>             6   SRY   0.0042740      SRY         4   5.135e-06 2.57e-04      55.16
    #>             7 MYOD1   0.0049860    MYOD1         4   5.204e-06 2.57e-04      54.97
    #>             8    AR   0.0056980       AR         4   5.204e-06 2.57e-04      54.97
    #>             9   CRX   0.0064100      CRX         4   5.204e-06 2.57e-04      54.97
    #>            10 NR5A1   0.0071230    NR5A1         4   5.204e-06 2.57e-04      54.97
    #>
    #>   ────────────────────

## 3. Extract the result for one particular collection

Each ChEA3 collection can be accessed by name. For example, to retrieve the integrated ranking:

    meanRank_results <- results[["Integrated--meanRank"]]
    head(meanRank_results)
    #>     Query Name Rank     TF Score
    #> 1 rChEA3_query    1  ZBED6 15.00
    #> 2 rChEA3_query    2    PGR 41.25
    #> 3 rChEA3_query    3    SON 45.50
    #> 4 rChEA3_query    4 ZBTB21 46.50
    #> 5 rChEA3_query    5   BPTF 58.50
    #> 6 rChEA3_query    6   SPEN 58.50
    #>                                                                            Library
    #> 1                                                           ARCHS4 Coexpression,15
    #> 2 ARCHS4 Coexpression,24;Enrichr Queries,11;ReMap ChIP-seq,84;GTEx Coexpression,46
    #> 3                                      ARCHS4 Coexpression,60;GTEx Coexpression,31
    #> 4                                      ARCHS4 Coexpression,26;GTEx Coexpression,67
    #> 5                                      ARCHS4 Coexpression,68;GTEx Coexpression,49
    #> 6                                      ARCHS4 Coexpression,22;GTEx Coexpression,95
    #>     Overlapping_Genes
    #> 1               NIPBL
    #> 2 MYC,BRCA1,ESR1,TP53
    #> 3               NIPBL
    #> 4           NIPBL,MYC
    #> 5               NIPBL
    #> 6               NIPBL

## 4. Generate the visualization

    visualizeRank(meanRank_results)

# Session info

    sessionInfo()
    #> R version 4.5.0 (2025-04-11)
    #> Platform: aarch64-apple-darwin20
    #> Running under: macOS Sequoia 15.6.1
    #>
    #> Matrix products: default
    #> BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib
    #> LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
    #>
    #> locale:
    #> [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
    #>
    #> time zone: America/Toronto
    #> tzcode source: internal
    #>
    #> attached base packages:
    #> [1] stats     graphics  grDevices utils     datasets  methods   base
    #>
    #> other attached packages:
    #> [1] rChEA3_0.2.0
    #>
    #> loaded via a namespace (and not attached):
    #>  [1] gtable_0.3.6       jsonlite_2.0.0     dplyr_1.1.4        compiler_4.5.0
    #>  [5] crayon_1.5.3       tidyselect_1.2.1   dichromat_2.0-0.1  jquerylib_0.1.4
    #>  [9] scales_1.4.0       yaml_2.3.10        fastmap_1.2.0      ggplot2_4.0.0
    #> [13] R6_2.6.1           labeling_0.4.3     generics_0.1.4     curl_7.0.0
    #> [17] knitr_1.50         tibble_3.3.0       lubridate_1.9.4    bslib_0.9.0
    #> [21] pillar_1.11.1      RColorBrewer_1.1-3 rlang_1.1.6        cachem_1.1.0
    #> [25] xfun_0.53          S7_0.2.0           sass_0.4.10        timechange_0.3.0
    #> [29] cli_3.6.5          withr_3.0.2        magrittr_2.0.4     digest_0.6.37
    #> [33] grid_4.5.0         rstudioapi_0.17.1  lifecycle_1.0.4    vctrs_0.6.5
    #> [37] evaluate_1.0.5     glue_1.8.0         farver_2.1.2       rmarkdown_2.30
    #> [41] httr_1.4.7         tools_4.5.0        pkgconfig_2.0.3    htmltools_0.5.8.1

# Citation

If you use this package, please cite:

Keenan, A.B., Torre, D., Lachmann, A., Leong, A.K., Wojciechowicz, M.L., Utti, V., Jagodnik, K.M., Kropiwnicki, E., Wang, Z., & Ma’ayan, A. (2019). ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Research, 47(W1), W212–W224. doi:10.1093/nar/gkz446

# Resources

- ChEA3 Web Server - Interactive tool and detailed documentation
- ChEA3 Publication - Original research article
- rChEA3 GitHub - Package source code and issues