Introduction.

The goal of goSorensen is to implement the equivalence test introduced in Flores, P., Salicrú, M., Sánchez-Pla, A. and Ocaña, J.(2022) “An equivalence test between features lists, based on the Sorensen - Dice index and the joint frequencies of GO node enrichment”, BMC Bioinformatics, 2022 23:207.

Given two gene lists, L₁ and L₂, (the data) and a given set of n Gene Ontology (GO) terms (the frame of reference for biological significance in these lists), the test is devoted to answer the following question (quite informally stated for the moment): The dissimilarity between the biological information in both lists, is it negligible? To measure the dissimilarity we use the Sorensen-Dice index:

$$ \hat d_S = \hat d(L_1,L_2) = \frac{2n_{11}}{2n_{11} + n_{10} + n_{01}} $$

where n₁₁ corresponds to the number of GO terms (among the n GO terms under consideration) which are enriched in both gene lists, n₁₀ corresponds to the GO terms enriched in L₁ but not in L₂ and n₀₁ the reverse, those enriched in L₂ but not in L₁. For notation completeness, n₀₀ would correspond to those GO terms not enriched in both lists; it is not considered by the Sorensen-Dice index but would be necessary in some computations. Obviously, n = n₁₁ + n₁₀ + n₀₁ + n₀₀.

More precisely, the above problem can be restated as follows: Given a negligibility threshold d₀ for the Sorensen-Dice values, to decide negligibility corresponds to rejecting the null hypothesis H₀ : d_S ≥ d₀ in favour of the alternative H₁ : d_S < d₀, where d_S stands for the “true” value of the Sorensen-Dice dissimilarity (L₁ and L₂ are samples, and the own process of declaring enrichment of a GO term is random, so d̂_S = d̂(L₁, L₂) is an estimate of d_S). Then, a bit more precise statement of the problem is “The dissimilarity between the biological information in two gene lists, is it negligible up to a degree d₀?” Where this information is expressed by means of the Sorensen-Dice dissimilarity measured on the degree of coincidence and non-coincidence in GO terms enrichment among a given set of GO terms.

For the moment, the reference set of GO terms can be only all those GO terms in a given level of one GO ontology, either BP, CC or MF.

if (!requireNamespace("goSorensen", quietly = TRUE)) {
    BiocManager::install("goSorensen")
}
library(goSorensen)

data("allOncoGeneLists")

length(allOncoGeneLists)

## [1] 7

sapply(allOncoGeneLists, length)

##         atlas      cangenes           cis miscellaneous        sanger 
##           991           189           613           187           450 
##    Vogelstein       waldman 
##           419           426

# First 20 gene identifiers of gene lists Vogelstein and sanger:
allOncoGeneLists[["Vogelstein"]][1:20]

##  [1] "10006"  "25"     "27"     "23305"  "91"     "4299"   "3899"   "27125" 
##  [9] "207"    "238"    "139285" "324"    "367"    "23092"  "23365"  "8289"  
## [17] "57492"  "196528" "405"    "79058"

allOncoGeneLists[["sanger"]][1:20]

##  [1] "25"     "27"     "2181"   "57082"  "10962"  "51517"  "27125"  "10142" 
##  [9] "207"    "208"    "217"    "238"    "57714"  "324"    "23365"  "399"   
## [17] "8289"   "405"    "79058"  "171023"

if (!requireNamespace("org.Hs.eg.db", quietly = TRUE)) {
    BiocManager::install("org.Hs.eg.db")
}
library(org.Hs.eg.db)

library(org.Hs.eg.db)

humanEntrezIDs <- keys(org.Hs.eg.db, keytype = "ENTREZID")

Session information.

All software and respective versions used to produce this document are listed below.

sessionInfo()

## 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] org.Hs.eg.db_3.20.0  AnnotationDbi_1.69.0 IRanges_2.41.2      
##  [4] S4Vectors_0.45.2     Biobase_2.67.0       BiocGenerics_0.53.3 
##  [7] generics_0.1.3       goSorensen_1.9.0     BiocStyle_2.35.0    
## [10] rmarkdown_2.29      
## 
## loaded via a namespace (and not attached):
##  [1] DBI_1.2.3               gson_0.1.0              rlang_1.1.4            
##  [4] magrittr_2.0.3          DOSE_4.1.0              compiler_4.4.2         
##  [7] RSQLite_2.3.9           png_0.1-8               vctrs_0.6.5            
## [10] reshape2_1.4.4          stringr_1.5.1           pkgconfig_2.0.3        
## [13] crayon_1.5.3            fastmap_1.2.0           XVector_0.47.0         
## [16] enrichplot_1.27.3       UCSC.utils_1.3.0        purrr_1.0.2            
## [19] bit_4.5.0.1             xfun_0.49               zlibbioc_1.52.0        
## [22] cachem_1.1.0            aplot_0.2.4             GenomeInfoDb_1.43.2    
## [25] jsonlite_1.8.9          blob_1.2.4              BiocParallel_1.41.0    
## [28] parallel_4.4.2          R6_2.5.1                bslib_0.8.0            
## [31] stringi_1.8.4           RColorBrewer_1.1-3      jquerylib_0.1.4        
## [34] GOSemSim_2.33.0         Rcpp_1.0.13-1           knitr_1.49             
## [37] goProfiles_1.69.0       ggtangle_0.0.5          R.utils_2.12.3         
## [40] Matrix_1.7-1            splines_4.4.2           igraph_2.1.2           
## [43] tidyselect_1.2.1        qvalue_2.39.0           yaml_2.3.10            
## [46] codetools_0.2-20        lattice_0.22-6          tibble_3.2.1           
## [49] plyr_1.8.9              treeio_1.31.0           KEGGREST_1.47.0        
## [52] evaluate_1.0.1          gridGraphics_0.5-1      CompQuadForm_1.4.3     
## [55] Biostrings_2.75.3       pillar_1.10.0           BiocManager_1.30.25    
## [58] ggtree_3.15.0           clusterProfiler_4.15.1  ggfun_0.1.8            
## [61] ggplot2_3.5.1           tidytree_0.4.6          munsell_0.5.1          
## [64] scales_1.3.0            glue_1.8.0              lazyeval_0.2.2         
## [67] maketools_1.3.1         tools_4.4.2             sys_3.4.3              
## [70] data.table_1.16.4       fgsea_1.33.0            buildtools_1.0.0       
## [73] fs_1.6.5                fastmatch_1.1-4         cowplot_1.1.3          
## [76] grid_4.4.2              tidyr_1.3.1             ape_5.8-1              
## [79] colorspace_2.1-1        nlme_3.1-166            GenomeInfoDbData_1.2.13
## [82] patchwork_1.3.0         cli_3.6.3               dplyr_1.1.4            
## [85] gtable_0.3.6            R.methodsS3_1.8.2       yulab.utils_0.1.8      
## [88] sass_0.4.9              digest_0.6.37           ggrepel_0.9.6          
## [91] ggplotify_0.1.2         farver_2.1.2            memoise_2.0.1          
## [94] htmltools_0.5.8.1       R.oo_1.27.0             lifecycle_1.0.4        
## [97] httr_1.4.7              GO.db_3.20.0            bit64_4.5.2

Bibliography.

Flores, P., Salicrú, M., Sánchez-Pla, A. et al. An equivalence test between features lists, based on the Sorensen–Dice index and the joint frequencies of GO term enrichment. BMC Bioinformatics 23, 207 (2022). https://doi.org/10.1186/s12859-022-04739-2