5 - Integrative analysis workshop with TCGAbiolinks and ELMER - Analysis GUI
Introduction
In this section, we will perform the same analysis performed using ELMER, but instead of doing it programmatically we will use TCGAbiolinksGUI (Silva et al. 2017).
First we will launch the TCGAbiolinksGUI.
Downloading data
Please download this two objects:
Analysis
Create MultiAssayExperiment object
To create the MultiAssayExperiment object go to
Integrative analysis/ELMER/Create input data.
Select the DNA methylation object previously downloaded.
Select the gene expression object previously downloaded.
Fill the field Save as: and click on Create MAE
object.
The object will be created.
Perform analysis
To perform ELMER analysis go to
Integrative analysis/ELMER/Analysis.
Select the MAE data created in the previous section.
Select the groups that will be analysed: Primary solid Tumor and Solid Tissue Normal.
We will identify probes that are hypomethylated in Primary solid Tumor compared to Solid Tissue Normal.
For the significant differently methylated probes identified before
we will correlated with the 20 nearest genes. Change the value of the
field Number of permutations to 100,
Raw P-value cut-off to 0.05 and
Empirical P value cut-off to 0.01.
There will be no changes in the step 3.
There will be no changes in the step 4.
Click on Run the analysis.
If the analysis identified significant regulatory TF the results will be saved into an R object.
Visualize results
To visualize the results go to
Integrative analysis/ELMER/Visualize results.
Click on Select results and select the object created on
the previous section.
Or the avarage DNA methylation levels of probes of a Motif vs the expression of a TF.
For each enriched motif you can verify the ranking of sigificances between the correlation of DNA methylation level on the significant paired probes with that motif vs the TF expression (for all human TF).
The enrichement of each motif can be visualized.
You can take a look for a gene which was the probe linked.
You can see the plot and its neraby genes.
It is possible to visualize the table with the significant differently methylated probes.
It is possible to visualize the table with the enriched motifs.
It is possible to visualize the table with the candidates regulatory TF.
Session Info
## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 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-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] MultiAssayExperiment_1.33.1 SummarizedExperiment_1.37.0
## [3] Biobase_2.67.0 MatrixGenerics_1.19.0
## [5] matrixStats_1.4.1 GenomicRanges_1.59.1
## [7] GenomeInfoDb_1.43.2 IRanges_2.41.1
## [9] S4Vectors_0.45.2 sesameData_1.24.0
## [11] ExperimentHub_2.15.0 AnnotationHub_3.15.0
## [13] BiocFileCache_2.15.0 dbplyr_2.5.0
## [15] BiocGenerics_0.53.3 generics_0.1.3
## [17] BiocStyle_2.35.0 dplyr_1.1.4
## [19] DT_0.33 ELMER_2.31.0
## [21] ELMER.data_2.30.0
##
## loaded via a namespace (and not attached):
## [1] BiocIO_1.17.1 bitops_1.0-9
## [3] filelock_1.0.3 tibble_3.2.1
## [5] XML_3.99-0.17 rpart_4.1.23
## [7] lifecycle_1.0.4 httr2_1.0.7
## [9] rstatix_0.7.2 doParallel_1.0.17
## [11] vroom_1.6.5 lattice_0.22-6
## [13] ensembldb_2.31.0 crosstalk_1.2.1
## [15] backports_1.5.0 magrittr_2.0.3
## [17] Hmisc_5.2-0 plotly_4.10.4
## [19] sass_0.4.9 rmarkdown_2.29
## [21] jquerylib_0.1.4 yaml_2.3.10
## [23] Gviz_1.51.0 DBI_1.2.3
## [25] buildtools_1.0.0 RColorBrewer_1.1-3
## [27] abind_1.4-8 zlibbioc_1.52.0
## [29] rvest_1.0.4 purrr_1.0.2
## [31] AnnotationFilter_1.31.0 biovizBase_1.55.0
## [33] RCurl_1.98-1.16 nnet_7.3-19
## [35] VariantAnnotation_1.53.0 rappdirs_0.3.3
## [37] circlize_0.4.16 GenomeInfoDbData_1.2.13
## [39] ggrepel_0.9.6 maketools_1.3.1
## [41] codetools_0.2-20 DelayedArray_0.33.2
## [43] xml2_1.3.6 tidyselect_1.2.1
## [45] shape_1.4.6.1 farver_2.1.2
## [47] UCSC.utils_1.3.0 TCGAbiolinksGUI.data_1.26.0
## [49] base64enc_0.1-3 GenomicAlignments_1.43.0
## [51] jsonlite_1.8.9 GetoptLong_1.0.5
## [53] Formula_1.2-5 iterators_1.0.14
## [55] foreach_1.5.2 tools_4.4.2
## [57] progress_1.2.3 Rcpp_1.0.13-1
## [59] glue_1.8.0 BiocBaseUtils_1.9.0
## [61] gridExtra_2.3 SparseArray_1.7.2
## [63] xfun_0.49 withr_3.0.2
## [65] BiocManager_1.30.25 fastmap_1.2.0
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## [81] prettyunits_1.2.0 httr_1.4.7
## [83] htmlwidgets_1.6.4 S4Arrays_1.7.1
## [85] pkgconfig_2.0.3 gtable_0.3.6
## [87] blob_1.2.4 ComplexHeatmap_2.23.0
## [89] XVector_0.47.0 sys_3.4.3
## [91] htmltools_0.5.8.1 carData_3.0-5
## [93] ProtGenerics_1.39.0 clue_0.3-66
## [95] scales_1.3.0 png_0.1-8
## [97] knitr_1.49 rstudioapi_0.17.1
## [99] tzdb_0.4.0 reshape2_1.4.4
## [101] rjson_0.2.23 checkmate_2.3.2
## [103] curl_6.0.1 cachem_1.1.0
## [105] GlobalOptions_0.1.2 stringr_1.5.1
## [107] BiocVersion_3.21.1 parallel_4.4.2
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## [111] restfulr_0.0.15 pillar_1.9.0
## [113] grid_4.4.2 reshape_0.8.9
## [115] vctrs_0.6.5 ggpubr_0.6.0
## [117] car_3.1-3 cluster_2.1.6
## [119] htmlTable_2.4.3 evaluate_1.0.1
## [121] TCGAbiolinks_2.35.0 readr_2.1.5
## [123] GenomicFeatures_1.59.1 cli_3.6.3
## [125] compiler_4.4.2 Rsamtools_2.23.1
## [127] rlang_1.1.4 crayon_1.5.3
## [129] ggsignif_0.6.4 labeling_0.4.3
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## [145] KEGGREST_1.47.0 broom_1.0.7
## [147] memoise_2.0.1 bslib_0.8.0
## [149] bit_4.5.0 downloader_0.4