GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
1
0
Entering edit mode
@owenwhitley-15693
Last seen 2.4 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 • 498 views
ADD COMMENT
2
Entering edit mode
Robert Castelo ★ 2.7k
@rcastelo
Last seen 11 weeks ago
Barcelona/Universitat Pompeu Fabra

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.

 

 

ADD COMMENT

Login before adding your answer.

Traffic: 166 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6