Fisher’s Test for Enrichment and Depletion of User-Defined Pathways
fedup is an R package that tests for enrichment and depletion of user-defined pathways using a Fisher’s exact test. The method is designed for versatile pathway annotation formats (eg. gmt, txt, xlsx) to allow the user to run pathway analysis on custom annotations. This package is also integrated with Cytoscape to provide network-based pathway visualization that enhances the interpretability of the results.
This README will quickly demonstrate how to use fedup when testing two sets of genes. Refer to full vignettes for additional information and implementations (e.g., using single or multiple test sets).
System prerequisites
R version ≥ 4.1
R packages:
-
CRAN: openxlsx, tibble, dplyr, data.table, ggplot2, ggthemes, forcats, RColorBrewer
- Bioconductor: RCy3
Installation
Install fedup from Bioconductor:
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("fedup")Or install the development version from Github:
devtools::install_github("rosscm/fedup", quiet = TRUE)Load necessary packages:
Running the package
Input data
Load test genes (geneDouble) and pathway annotations (pathwaysGMT):
Take a look at the data structure:
str(geneDouble)
#> List of 3
#> $ background : chr [1:17804] "SLCO4A1" "PGRMC2" "LDLR" "RABL3" ...
#> $ FASN_negative: chr [1:379] "SLCO4A1" "PGRMC2" "LDLR" "RABL3" ...
#> $ FASN_positive: chr [1:298] "CDC34" "PRKCE" "SMARCC2" "EIF3A" ...
str(head(pathwaysGMT))
#> List of 6
#> $ REGULATION OF PLK1 ACTIVITY AT G2 M TRANSITION%REACTOME%R-HSA-2565942.1 : chr [1:84] "CSNK1E" "DYNLL1" "TUBG1" "CKAP5" ...
#> $ GLYCEROPHOSPHOLIPID BIOSYNTHESIS%REACTOME%R-HSA-1483206.4 : chr [1:126] "PCYT1B" "PCYT1A" "PLA2G4D" "PLA2G4B" ...
#> $ MITOTIC PROPHASE%REACTOME DATABASE ID RELEASE 74%68875 : chr [1:134] "SETD8" "NUMA1" "NCAPG2" "LMNB1" ...
#> $ ACTIVATION OF NF-KAPPAB IN B CELLS%REACTOME%R-HSA-1169091.1 : chr [1:67] "PSMA6" "PSMA3" "PSMA4" "PSMA1" ...
#> $ CD28 DEPENDENT PI3K AKT SIGNALING%REACTOME DATABASE ID RELEASE 74%389357 : chr [1:22] "CD28" "THEM4" "AKT1" "TRIB3" ...
#> $ UBIQUITIN-DEPENDENT DEGRADATION OF CYCLIN D%REACTOME DATABASE ID RELEASE 74%75815: chr [1:52] "PSMA6" "PSMA3" "PSMA4" "PSMA1" ...To see more info on this data, run ?geneDouble or ?pathwaysGMT. You could also run example("prepInput", package = "fedup") or example("readPathways", package = "fedup") to see exactly how the data was generated using the prepInput() and readPathways() functions. ? and example() can be used on any other functions mentioned here to see their documentation and run examples.
Pathway analysis
Now use runFedup on the sample data:
fedupRes <- runFedup(geneDouble, pathwaysGMT)
#> Running fedup with:
#> => 2 test set(s)
#> + FASN_negative: 379 genes
#> + FASN_positive: 298 genes
#> => 17804 background genes
#> => 1437 pathway annotations
#> All done!The fedupRes output is a list of length length(which(names(geneDouble) != "background")), corresponding to the number of test sets in geneDouble (i.e., 2).
View fedup results for FASN_negative sorted by pvalue:
set <- "FASN_negative"
print(head(fedupRes[[set]][which(fedupRes[[set]]$status == "enriched"),]))
#> pathway
#> 1: ASPARAGINE N-LINKED GLYCOSYLATION%REACTOME DATABASE ID RELEASE 74%446203
#> 2: BIOSYNTHESIS OF THE N-GLYCAN PRECURSOR (DOLICHOL LIPID-LINKED OLIGOSACCHARIDE, LLO) AND TRANSFER TO A NASCENT PROTEIN%REACTOME%R-HSA-446193.1
#> 3: DISEASES ASSOCIATED WITH N-GLYCOSYLATION OF PROTEINS%REACTOME DATABASE ID RELEASE 74%3781860
#> 4: INTRA-GOLGI AND RETROGRADE GOLGI-TO-ER TRAFFIC%REACTOME DATABASE ID RELEASE 74%6811442
#> 5: RAB REGULATION OF TRAFFICKING%REACTOME DATABASE ID RELEASE 74%9007101
#> 6: DISEASES OF GLYCOSYLATION%REACTOME%R-HSA-3781865.1
#> size real_frac expected_frac fold_enrichment status
#> 1: 286 8.179420 1.53336329 5.334300 enriched
#> 2: 78 3.693931 0.42125365 8.768901 enriched
#> 3: 17 2.110818 0.09548416 22.106472 enriched
#> 4: 183 4.749340 0.99415862 4.777246 enriched
#> 5: 120 3.693931 0.62345540 5.924933 enriched
#> 6: 139 3.957784 0.74702314 5.298074 enriched
#> real_gene pvalue qvalue
#> 1: MOGS,DOLPP1,ALG9,ALG12,ALG3,MPDU1,... 1.596605e-12 2.294321e-09
#> 2: DOLPP1,ALG9,ALG12,ALG3,MPDU1,ALG8,... 6.358461e-09 4.568554e-06
#> 3: MOGS,ALG9,ALG12,ALG3,MPDU1,MGAT2,... 3.054616e-08 1.463161e-05
#> 4: ARL1,RAB18,RAB3GAP2,VPS52,NAA35,TMED9,... 2.516179e-07 9.039372e-05
#> 5: RAB18,TSC1,RAB3GAP2,TSC2,TBC1D20,RAB10,... 4.945154e-07 1.421237e-04
#> 6: MOGS,ALG9,ALG12,ALG3,MPDU1,MGAT2,... 7.240716e-07 1.734151e-04
print(head(fedupRes[[set]][which(fedupRes[[set]]$status == "depleted"),]))
#> pathway size
#> 1: GPCR LIGAND BINDING%REACTOME%R-HSA-500792.3 454
#> 2: OLFACTORY SIGNALING PATHWAY%REACTOME DATABASE ID RELEASE 74%381753 396
#> 3: CLASS A 1 (RHODOPSIN-LIKE RECEPTORS)%REACTOME%R-HSA-373076.7 323
#> 4: NEURONAL SYSTEM%REACTOME DATABASE ID RELEASE 74%112316 379
#> 5: PEPTIDE LIGAND-BINDING RECEPTORS%REACTOME%R-HSA-375276.5 195
#> 6: KERATINIZATION%REACTOME DATABASE ID RELEASE 74%6805567 217
#> real_frac expected_frac fold_enrichment status real_gene pvalue
#> 1: 0.0000000 2.3702539 0.0000000 depleted 0.000318537
#> 2: 0.0000000 1.9096832 0.0000000 depleted 0.001508862
#> 3: 0.0000000 1.6906313 0.0000000 depleted 0.003316944
#> 4: 0.5277045 2.0950348 0.2518834 depleted KCNK2,PRKAB1 0.026904721
#> 5: 0.0000000 1.0166255 0.0000000 depleted 0.057057149
#> 6: 0.0000000 0.8425073 0.0000000 depleted 0.079543380
#> qvalue
#> 1: 0.01760530
#> 2: 0.05420587
#> 3: 0.10361845
#> 4: 0.42024004
#> 5: 0.57670567
#> 6: 0.67813171Let’s also view fedup results for FASN_positive, sorted by pvalue:
set <- "FASN_positive"
print(head(fedupRes[[set]][which(fedupRes[[set]]$status == "enriched"),]))
#> pathway
#> 1: L13A-MEDIATED TRANSLATIONAL SILENCING OF CERULOPLASMIN EXPRESSION%REACTOME%R-HSA-156827.3
#> 2: GTP HYDROLYSIS AND JOINING OF THE 60S RIBOSOMAL SUBUNIT%REACTOME DATABASE ID RELEASE 74%72706
#> 3: CAP-DEPENDENT TRANSLATION INITIATION%REACTOME DATABASE ID RELEASE 74%72737
#> 4: EUKARYOTIC TRANSLATION INITIATION%REACTOME%R-HSA-72613.3
#> 5: TRANSLATION INITIATION COMPLEX FORMATION%REACTOME%R-HSA-72649.3
#> 6: RIBOSOMAL SCANNING AND START CODON RECOGNITION%REACTOME DATABASE ID RELEASE 74%72702
#> size real_frac expected_frac fold_enrichment status
#> 1: 112 7.382550 0.4718041 15.64749 enriched
#> 2: 113 7.382550 0.4774208 15.46340 enriched
#> 3: 120 7.382550 0.5167378 14.28684 enriched
#> 4: 120 7.382550 0.5167378 14.28684 enriched
#> 5: 59 5.369128 0.2583689 20.78086 enriched
#> 6: 59 5.369128 0.2583689 20.78086 enriched
#> real_gene pvalue qvalue
#> 1: EIF3A,RPL35,EIF3D,RPS3,EIF3G,EIF4H,... 9.628857e-18 8.562503e-15
#> 2: EIF3A,RPL35,EIF3D,RPS3,EIF3G,EIF4H,... 1.191719e-17 8.562503e-15
#> 3: EIF3A,RPL35,EIF3D,RPS3,EIF3G,EIF4H,... 4.970934e-17 1.785808e-14
#> 4: EIF3A,RPL35,EIF3D,RPS3,EIF3G,EIF4H,... 4.970934e-17 1.785808e-14
#> 5: EIF3A,EIF3D,RPS3,EIF3G,EIF4H,RPS5,... 5.796507e-15 1.388264e-12
#> 6: EIF3A,EIF3D,RPS3,EIF3G,EIF4H,RPS5,... 5.796507e-15 1.388264e-12
print(head(fedupRes[[set]][which(fedupRes[[set]]$status == "depleted"),]))
#> pathway
#> 1: GPCR LIGAND BINDING%REACTOME%R-HSA-500792.3
#> 2: NEURONAL SYSTEM%REACTOME DATABASE ID RELEASE 74%112316
#> 3: OLFACTORY SIGNALING PATHWAY%REACTOME DATABASE ID RELEASE 74%381753
#> 4: CLASS A 1 (RHODOPSIN-LIKE RECEPTORS)%REACTOME%R-HSA-373076.7
#> 5: G ALPHA (I) SIGNALLING EVENTS%REACTOME%R-HSA-418594.6
#> 6: TRANSMISSION ACROSS CHEMICAL SYNAPSES%REACTOME DATABASE ID RELEASE 74%112315
#> size real_frac expected_frac fold_enrichment status real_gene pvalue
#> 1: 454 0.0000000 2.370254 0.0000000 depleted 0.002390509
#> 2: 379 0.0000000 2.095035 0.0000000 depleted 0.005261657
#> 3: 396 0.0000000 1.909683 0.0000000 depleted 0.007449873
#> 4: 323 0.0000000 1.690631 0.0000000 depleted 0.017309826
#> 5: 396 0.3355705 2.106268 0.1593199 depleted AHCYL1 0.034808044
#> 6: 238 0.0000000 1.314311 0.0000000 depleted 0.035700272
#> qvalue
#> 1: 0.03240718
#> 2: 0.05953545
#> 3: 0.07989155
#> 4: 0.13667154
#> 5: 0.21016453
#> 6: 0.21198880Dot plot
Prepare data for plotting via dplyr and tidyr:
fedupPlot <- fedupRes %>%
bind_rows(.id = "set") %>%
separate(col = "set", into = c("set", "sign"), sep = "_") %>%
subset(qvalue < 0.05) %>%
mutate(log10qvalue = -log10(qvalue)) %>%
mutate(pathway = gsub("\\%.*", "", pathway)) %>%
mutate(status = factor(status, levels = c("enriched", "depleted"))) %>%
as.data.frame()Plot significant results (qvalue < 0.05) in the form of a dot plot via plotDotPlot. Colour and facet the points by the sign column:
p <- plotDotPlot(
df = fedupPlot,
xVar = "log10qvalue",
yVar = "pathway",
xLab = "-log10(qvalue)",
fillVar = "sign",
fillLab = "Genetic interaction",
fillCol = c("#6D90CA", "#F6EB13"),
sizeVar = "fold_enrichment",
sizeLab = "Fold enrichment") +
facet_grid("sign", scales = "free", space = "free") +
theme(strip.text.y = element_blank())
print(p)
Look at all those chick… enrichments! This is a bit overwhelming, isn’t it? How do we interpret these 156 fairly redundant pathways in a way that doesn’t hurt our tired brains even more? Oh I know, let’s use an enrichment map!
Enrichment map
First, make sure to have Cytoscape downloaded and and open on your computer. You’ll also need to install the EnrichmentMap (≥ v3.3.0) and AutoAnnotate apps.
Then format results for compatibility with EnrichmentMap using writeFemap:
resultsFolder <- tempdir()
writeFemap(fedupRes, resultsFolder)
#> Wrote out EM-formatted fedup results file to /var/folders/mh/_0z2r5zj3k75yhtgm6l7xy3m0000gn/T//Rtmp2Cxw8t/femap_FASN_negative.txt
#> Wrote out EM-formatted fedup results file to /var/folders/mh/_0z2r5zj3k75yhtgm6l7xy3m0000gn/T//Rtmp2Cxw8t/femap_FASN_positive.txtPrepare a pathway annotation file (gmt format) from the pathway list you passed to runFedup using the writePathways function (you don’t need to run this function if your pathway annotations are already in gmt format, but it doesn’t hurt to make sure):
gmtFile <- tempfile("pathwaysGMT", fileext = ".gmt")
writePathways(pathwaysGMT, gmtFile)
#> Wrote out pathway gmt file to /var/folders/mh/_0z2r5zj3k75yhtgm6l7xy3m0000gn/T//Rtmp2Cxw8t/pathwaysGMTd1a71bfa6116.gmtCytoscape is open right? If so, run these lines and let the plotFemap magic happen:
netFile <- tempfile("fedupEM", fileext = ".png")
plotFemap(
gmtFile = gmtFile,
resultsFolder = resultsFolder,
qvalue = 0.05,
chartData = "DATA_SET",
hideNodeLabels = TRUE,
netName = "fedupEM",
netFile = netFile
)To note here, the EM nodes were coloured manually (by the same colours passed to plotDotPlot) in Cytoscape via the Change Colors option in the EM panel. A feature for automated dataset colouring is set to be released in version 3.3.2 of EnrichmentMap.
This has effectively summarized the 156 pathways from our dot plot into 21 unique biological themes (including 4 unclustered pathways). We can now see clear themes in the data pertaining to negative FASN genetic interactions, such as diseases glycosylation, proteins, golgi transport, and rab regulation trafficking. These can be compared and constrasted with the enrichment seen for FASN positive interactions.
Try this out yourself! Hopefully it’s the only fedup you achieve 😬
Versioning
For the versions available, see the tags on this repo.
Shoutouts
✨2020✨
