Question

GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets

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owen.whitley ▴ 10

@owenwhitley-15693

Last seen 5.8 years ago

Hi,

I noticed that the brainTxDb dataset used with the GSVA tutorial has oligodendrocytic_dn and neuronal_dn with the exact same genesets. Was this intended? Here's a demonstration below:

data("brainTxDbSets")

> brainTxDbSets$neuronal_dn
[1] "DKK3"     "LPHN2"    "AHR"      "NRP1"     "MAP3K15" "GALNTL4" "CNTNAP2" "LHFP"     "CRIP2"    "ABHD8"
[11] "ODZ3"     "DOCK7"    "KCTD1"    "FSTL1"    "BCR"      "EFHD2"    "TUBA4A"   "CCRN4L"   "CRYM"     "FEZF2"
[21] "C17orf76" "PKIG"     "CSDC2"    "SPEG"     "PRKAG2"   "P4HA2"    "NGRN"     "CTGF"     "LRRC48"   "CLYBL"
> brainTxDbSets$oligodendrocytic_dn
[1] "DKK3"     "LPHN2"    "AHR"      "NRP1"     "MAP3K15" "GALNTL4" "CNTNAP2" "LHFP"     "CRIP2"    "ABHD8"
[11] "ODZ3"     "DOCK7"    "KCTD1"    "FSTL1"    "BCR"      "EFHD2"    "TUBA4A"   "CCRN4L"   "CRYM"     "FEZF2"
[21] "C17orf76" "PKIG"     "CSDC2"    "SPEG"     "PRKAG2"   "P4HA2"    "NGRN"     "CTGF"     "LRRC48"   "CLYBL"

> all(brainTxDbSets$neuronal_dn == brainTxDbSets$oligodendrocytic_dn)
[1] TRUE

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C               LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8    
 [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8    LC_PAPER=en_CA.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ComplexHeatmap_1.17.1      GSVAdata_1.14.0            hgu95a.db_3.2.3            org.Hs.eg.db_3.5.0        
 [5] GSEABase_1.40.1            graph_1.56.0               annotate_1.56.2            XML_3.98-1.11             
 [9] AnnotationDbi_1.40.0       reshape2_1.4.3             readxl_1.1.0               mclust_5.4.1              
[13] clusteval_0.1              scales_1.0.0               doParallel_1.0.11          iterators_1.0.10          
[17] foreach_1.4.4              gtools_3.8.1               MOFAtools_0.1              sva_3.26.0                
[21] BiocParallel_1.12.0        genefilter_1.60.0          mgcv_1.8-24                nlme_3.1-137              
[25] gProfileR_0.6.6            ggplot2_3.0.0              kernlab_0.9-27             edgeR_3.20.9              
[29] limma_3.34.9               SummarizedExperiment_1.8.1 DelayedArray_0.4.1         matrixStats_0.54.0        
[33] Biobase_2.38.0             GenomicRanges_1.30.3       GenomeInfoDb_1.14.0        IRanges_2.12.0            
[37] S4Vectors_0.16.0           BiocGenerics_0.24.0        rrcovHD_0.2-5              rrcov_1.4-4               
[41] robustbase_0.93-2         

loaded via a namespace (and not attached):
  [1] shinydashboard_0.7.0                                tidyselect_0.2.4                                   
  [3] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0 RSQLite_2.1.1                                      
  [5] htmlwidgets_1.2                                     munsell_0.5.0                                      
  [7] codetools_0.2-15                                    preprocessCore_1.40.0                              
  [9] statmod_1.4.30                                      withr_2.1.2                                        
 [11] colorspace_1.3-2                                    knitr_1.20                                         
 [13] rstudioapi_0.7                                      GenomeInfoDbData_1.0.0                             
 [15] bit64_0.9-7                                         pheatmap_1.0.10                                    
 [17] rhdf5_2.22.0                                        R6_2.2.2                                           
 [19] ggbeeswarm_0.6.0                                    illuminaio_0.20.0                                  
 [21] locfit_1.5-9.1                                      robustHD_0.5.1                                     
 [23] bitops_1.0-6                                        reshape_0.8.7                                      
 [25] assertthat_0.2.0                                    promises_1.0.1                                     
 [27] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0  nnet_7.3-12                                        
 [29] beeswarm_0.2.3                                      gtable_0.2.0                                       
 [31] methylumi_2.24.1                                    rlang_0.2.2                                        
 [33] GlobalOptions_0.1.0                                 splines_3.4.3                                      
 [35] rtracklayer_1.38.3                                  lazyeval_0.2.1                                     
 [37] acepack_1.4.1                                       GEOquery_2.46.15                                   
 [39] checkmate_1.8.5                                     heatmap.plus_1.3                                   
 [41] yaml_2.2.0                                          GenomicFeatures_1.30.3                             
 [43] backports_1.1.2                                     httpuv_1.4.5                                       
 [45] Hmisc_4.1-1                                         RMySQL_0.10.15                                     
 [47] tools_3.4.3                                         spls_2.2-2                                         
 [49] nor1mix_1.2-3                                       RColorBrewer_1.1-2                                 
 [51] siggenes_1.52.0                                     MultiAssayExperiment_1.4.9                         
 [53] Rcpp_0.12.18                                        plyr_1.8.4                                         
 [55] base64enc_0.1-3                                     progress_1.2.0                                     
 [57] zlibbioc_1.24.0                                     purrr_0.2.5                                        
 [59] RCurl_1.95-4.11                                     BiasedUrn_1.07                                     
 [61] prettyunits_1.0.2                                   rpart_4.1-13                                       
 [63] openssl_1.0.2                                       GetoptLong_0.1.7                                   
 [65] cowplot_0.9.3                                       bumphunter_1.20.0                                  
 [67] ggrepel_0.8.0                                       cluster_2.0.7-1                                    
 [69] magrittr_1.5                                        data.table_1.11.4                                  
 [71] circlize_0.4.4                                      mvtnorm_1.0-8                                      
 [73] hms_0.4.2                                           mime_0.5                                           
 [75] xtable_1.8-2                                        shape_1.4.4                                        
 [77] gridExtra_2.3                                       compiler_3.4.3                                     
 [79] biomaRt_2.34.2                                      minfi_1.24.0                                       
 [81] tibble_1.4.2                                        crayon_1.3.4                                       
 [83] htmltools_0.3.6                                     pcaPP_1.9-73                                       
 [85] later_0.7.3                                         Formula_1.2-3                                      
 [87] tidyr_0.8.1                                         geneplotter_1.56.0                                 
 [89] DBI_1.0.0                                           corrplot_0.84                                      
 [91] MASS_7.3-50                                         Matrix_1.2-14                                      
 [93] readr_1.1.1                                         quadprog_1.5-5                                     
 [95] perry_0.2.0                                         bindr_0.1.1                                        
 [97] pkgconfig_2.0.2                                     GenomicAlignments_1.14.2                           
 [99] registry_0.5                                        IlluminaHumanMethylation450kmanifest_0.4.0         
[101] foreign_0.8-71                                      ExPosition_2.8.19                                  
[103] xml2_1.2.0                                          vipor_0.4.5                                        
[105] rngtools_1.3.1                                      pkgmaker_0.27                                      
[107] multtest_2.34.0                                     beanplot_1.2                                       
[109] XVector_0.18.0                                      ruv_0.9.7                                          
[111] bibtex_0.4.2                                        doRNG_1.7.1                                        
[113] stringr_1.3.1                                       digest_0.6.16                                      
[115] pls_2.7-0                                           Biostrings_2.46.0                                  
[117] cellranger_1.1.0                                    base64_2.0                                         
[119] htmlTable_1.12                                      shiny_1.1.0                                        
[121] Rsamtools_1.30.0                                    rjson_0.2.20                                       
[123] bindrcpp_0.2.2                                      alluvial_0.1-2                                     
[125] pillar_1.3.0                                        lattice_0.20-35                                    
[127] httr_1.3.1                                          DEoptimR_1.0-8                                     
[129] survival_2.42-6                                     GO.db_3.5.0                                        
[131] glue_1.3.0                                          bit_1.1-14                                         
[133] stringi_1.2.4                                       blob_1.1.1                                         
[135] latticeExtra_0.6-28                                 memoise_1.1.0                                      
[137] dplyr_0.7.6

GSVA tutorial • 1.4k views

ADD COMMENT • link updated 6.4 years ago by Robert Castelo ★ 3.4k • written 6.4 years ago by owen.whitley ▴ 10

score 2 · Answer 1 · 2018-09-17

Hi,

thanks for bringing this up. It escaped to our attention since only the *_up signatures (gene sets) are used in the vignette that illustrates their use, and this coincidence is happening with a *_dn gene set. These signatures were derived from the publication by Cahoy et al. (2008) but I cannot recall from where exactly we downloaded them, or whether we derived them ourselves from the transcriptomic data (we did this more than 5 years ago). Luckily, they seem to be well curated in the MSigDb database, at the following URLs:

http://software.broadinstitute.org/gsea/msigdb/cards/CAHOY_NEURONAL.html

http://software.broadinstitute.org/gsea/msigdb/cards/CAHOY_ASTROCYTIC.html

http://software.broadinstitute.org/gsea/msigdb/cards/CAHOY_ASTROGLIAL.html

http://software.broadinstitute.org/gsea/msigdb/cards/CAHOY_OLIGODENDROCUTIC.html

I see that they are only reported to be signatures of up-regulation. So, it may not make sense to look at downregulated signatures of these cells anyway.

I hope this helps,

robert.