Contents

1 Overview

ADAM is a GSEA R package created to group a set of genes from comparative samples (control versus experiment) according to their respective functions (Gene Ontology and KEGG pathways as default) and show their significance by calculating p-values referring to gene diversity and activity (Castro et al. (2009)). Each group of genes is called GFAG (Group of Functionally Associated Genes). The package has support for many species in regards to the genes and their respective functions.

In the package’s analysis, all genes present in the expression data are grouped by their respective functions according to the domains described by AnalysisDomain argument. The relationship between genes and functions are made based on the species annotation package. If there is no annotation package, a three column file (gene, function and function description) must be provided. For each GFAG, gene diversity and activity in each sample are calculated. As the package always compare two samples (control versus experiment), relative gene diversity and activity for each GFAG are calculated. Using bootstrap method, for each GFAG, according to relative gene diversity and activity, two p-values are calculated. The p-values are then corrected, by using the correction method defined by PCorrectionMethod argument, generating a q-value (Molan (2018)). The significative GFAGs will be those whose q-value stay under the cutoff set by PCorrection argument. Optionally, it’s possible to run Wilcoxon ranck sum test and/or Fisher’s exact test (Fontoura and Mombach (2016)). These tests also provide a corrected p-value, and siginificative groups can be seen through them.

2 GFAGAnalysis

GFAGAnalysis function provides a complete analysis, using all available arguments. As an example, lets consider a gene expression set of Aedes aegypti:

suppressMessages(library(ADAM))
data("ExpressionAedes")
head(ExpressionAedes)
##         gene  control1 experiment1  control2 experiment2
## 1 AAEL000372 0.9750520   11.744300 15.432300     0.00000
## 2 AAEL000433 1.5934700   11.876400  0.133743     1.23991
## 3 AAEL000596 0.5680230    3.365710  7.411010    13.06860
## 4 AAEL000599 0.0370953    0.361577  0.154117     0.34019
## 5 AAEL000656 0.0648374    0.278074  1.340890     1.15750
## 6 AAEL000759 2.3512100   48.762500  6.276890    25.02600

The first column refers to the gene names, while the others are the expression obtained by a specific experiment (in this case, RNA-seq). ADAM always need two samples (control versus experiment). This way, we must select two sample columns from the expression data for each comparison:

Comparison <- c("control1,experiment1","control2,experiment2")

Each GFAG has a number of genes associated to it. This way, the analysis can consider all GFAGs or just those with a certain number of genes:

Minimum <- 3
Maximum <- 20

The p-values for each GFAG is calculated through the bootstrap method, which demands a seed for generating random numbers and a number of bootstraps steps (the number of bootstraps should be a value that ensures the p-value precision):

SeedBootstrap <- 1049
StepsBootstrap <- 1000

The p-values will be corrected by a specific method with a certain cutoff value:

CutoffValue <- 0.05
MethodCorrection <- "fdr"

In order to group the genes according to their biological functions, it’s necessary an annotation package or a file relating genes and functions. In this case, Aedes aegypti doesn’t have an annotation package. This way, we build our own file:

data("KeggPathwaysAedes")
head(KeggPathwaysAedes)
##         gene pathwayID                 pathwayDescription
## 1 AAEL012172  aag00270 Cysteine and methionine metabolism
## 2 AAEL026440  aag00270 Cysteine and methionine metabolism
## 3 AAEL026231  aag00270 Cysteine and methionine metabolism
## 4 AAEL001176  aag00270 Cysteine and methionine metabolism
## 5 AAEL002399  aag00270 Cysteine and methionine metabolism
## 6 AAEL026357  aag00270 Cysteine and methionine metabolism

It’s necessary to inform which function domain and gene nomenclature are being used. As Aedes agypti doesn’t have an annotation package, the domain will be “own” and the nomenclature “gene”:

Domain <- "own"
Nomenclature <- "geneStableID"

Wilcoxon rank sum test and Fisher’s exact test will be run:

Wilcoxon <- TRUE
Fisher <- TRUE

As all arguments were defined, then we can run GFAGAnalysis function:

ResultAnalysis <- suppressMessages(GFAGAnalysis(ComparisonID = Comparison, 
                            ExpressionData = ExpressionAedes,
                            MinGene = Minimum,
                            MaxGene = Maximum,
                            SeedNumber = SeedBootstrap, 
                            BootstrapNumber = StepsBootstrap,
                            PCorrection = CutoffValue,
                            DBSpecies = KeggPathwaysAedes, 
                            PCorrectionMethod = MethodCorrection,
                            WilcoxonTest = Wilcoxon,
                            FisherTest = Fisher,
                            AnalysisDomain = Domain, 
                            GeneIdentifier = Nomenclature))

In the example above, we used the function supressMessages just to stop showing messages during the GFAGAnalysis function execution. The output of GFAGAnalysis will be a list with two elements. The first corresponds to a data frame showing genes and their respective functions:

head(ResultAnalysis[[1]])
##         gene  GroupID
## 1 AAEL000759 aag00270
## 2 AAEL001176 aag00270
## 3 AAEL001378 aag00270
## 4 AAEL002399 aag00270
## 5 AAEL004059 aag00270
## 6 AAEL004728 aag00270

The second element of the output list result corresponds to data frames according to the argument ComparisonID:

DT::datatable(as.data.frame(ResultAnalysis[[2]][1]), width = 800,
            options = list(scrollX = TRUE))
DT::datatable(as.data.frame(ResultAnalysis[[2]][2]), width = 800, 
            options = list(scrollX = TRUE))

The data frames corresponding to the second element of the list have the following columns:

3 ADAnalysis

ADAnalysis function provides a partial analysis, where is calculated just gene diversity and activity of each GFAG with no signicance by bootstrap, Wilcoxon or Fisher. As an example, lets consider the same gene expression set of Aedes aegypti previously used in GFAGAnalysis funcion example:

suppressMessages(library(ADAM))
data("ExpressionAedes")
data("KeggPathwaysAedes")

As ADAM always need two samples (control versus experiment), let’s select two sample columns from the expression data and define minimum and maximum number of genes per GFAG:

Comparison <- c("control1,experiment1")
Minimum <- 3
Maximum <- 100

Aedes aegypti doesn’t have an annotation package. This way, we build our own file:

SpeciesID <- "KeggPathwaysAedes"

It’s necessary to inform which function domain and gene nomenclature are being used. Aedes agypti doesn’t have an annotation package. So the domain will be “own” and the nomenclature “geneStableID”:

Domain <- "own"
Nomenclature <- "geneStableID"

As all arguments were defined, then we can run ADAnalysis function:

ResultAnalysis <- suppressMessages(ADAnalysis(ComparisonID = Comparison, 
                            ExpressionData = ExpressionAedes,
                            MinGene = Minimum,
                            MaxGene = Maximum,
                            DBSpecies = KeggPathwaysAedes, 
                            AnalysisDomain = Domain, 
                            GeneIdentifier = Nomenclature))

In the example above, we used the function supressMessages just to stop showing messages during the ADAnalysis function execution. The output of ADAnalysis will be a list with two elements. The first corresponds to a data frame showing genes and their respective functions:

head(ResultAnalysis[[1]])
##         gene  GroupID
## 1 AAEL000759 aag00270
## 2 AAEL001176 aag00270
## 3 AAEL001378 aag00270
## 4 AAEL002399 aag00270
## 5 AAEL004059 aag00270
## 6 AAEL004728 aag00270

The second element of the output list result corresponds to data frames according to the argument ComparisonID:

DT::datatable(as.data.frame(ResultAnalysis[[2]][1]), width = 800, 
            options = list(scrollX = TRUE))

The data frames corresponding to the second element of the list have the following columns:

4 Session information

## R version 4.2.0 RC (2022-04-21 r82226)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              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       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] ADAM_1.13.0      BiocStyle_2.25.0
## 
## loaded via a namespace (and not attached):
##  [1] MatrixGenerics_1.9.0        Biobase_2.57.0             
##  [3] httr_1.4.2                  sass_0.4.1                 
##  [5] bit64_4.0.5                 jsonlite_1.8.0             
##  [7] bslib_0.3.1                 assertthat_0.2.1           
##  [9] BiocManager_1.30.17         stats4_4.2.0               
## [11] blob_1.2.3                  GenomeInfoDbData_1.2.8     
## [13] yaml_2.3.5                  pillar_1.7.0               
## [15] RSQLite_2.2.12              lattice_0.20-45            
## [17] glue_1.6.2                  digest_0.6.29              
## [19] GenomicRanges_1.49.0        XVector_0.37.0             
## [21] htmltools_0.5.2             Matrix_1.4-1               
## [23] pkgconfig_2.0.3             bookdown_0.26              
## [25] zlibbioc_1.43.0             purrr_0.3.4                
## [27] GO.db_3.15.0                tibble_3.1.6               
## [29] KEGGREST_1.37.0             generics_0.1.2             
## [31] IRanges_2.31.0              ellipsis_0.3.2             
## [33] DT_0.22                     cachem_1.0.6               
## [35] SummarizedExperiment_1.27.0 pbapply_1.5-0              
## [37] BiocGenerics_0.43.0         cli_3.3.0                  
## [39] magrittr_2.0.3              crayon_1.5.1               
## [41] memoise_2.0.1               evaluate_0.15              
## [43] fansi_1.0.3                 tools_4.2.0                
## [45] lifecycle_1.0.1             matrixStats_0.62.0         
## [47] stringr_1.4.0               S4Vectors_0.35.0           
## [49] DelayedArray_0.23.0         AnnotationDbi_1.59.0       
## [51] Biostrings_2.65.0           compiler_4.2.0             
## [53] jquerylib_0.1.4             GenomeInfoDb_1.33.0        
## [55] rlang_1.0.2                 grid_4.2.0                 
## [57] RCurl_1.98-1.6              htmlwidgets_1.5.4          
## [59] crosstalk_1.2.0             bitops_1.0-7               
## [61] rmarkdown_2.14              DBI_1.1.2                  
## [63] R6_2.5.1                    knitr_1.38                 
## [65] dplyr_1.0.8                 fastmap_1.1.0              
## [67] bit_4.0.4                   utf8_1.2.2                 
## [69] stringi_1.7.6               parallel_4.2.0             
## [71] Rcpp_1.0.8.3                vctrs_0.4.1                
## [73] png_0.1-7                   tidyselect_1.1.2           
## [75] xfun_0.30

References

Castro, Mauro AA, José L Rybarczyk Filho, Rodrigo JS Dalmolin, Marialva Sinigaglia, José CF Moreira, José CM Mombach, and Rita MC de Almeida. 2009. “ViaComplex: Software for Landscape Analysis of Gene Expression Networks in Genomic Context.” Bioinformatics 25 (11): 1468–9.

Fontoura, C.A.R.S., and J.C.M Mombach. 2016. “PATHChange: A Tool for Identification of Differentially Expressed Pathways Using Multi-Statistic Comparison.” https://cran.r-project.org/web/packages/PATHChange/PATHChange.pdf.

Molan, A. L. 2018. “Construction of a Tool for Multispecies Genic Functional Enrichment Analysis Among Comparative Samples.” Master’s thesis, Institute of Biosciences of Botucatu – Univ. Estadual Paulista. http://hdl.handle.net/11449/157105.