Source: https://github.com/markziemann/SurveyEnrichmentMethods
suppressPackageStartupMessages({
library("getDEE2")
library("DESeq2")
library("clusterProfiler")
library("org.Hs.eg.db")
library("mitch")
library("kableExtra")
library("eulerr")
})In this piece, I will use the same list of genes to analyse GO and KEGG enrichment with DAVID and clusterprofiler in order to understand the discrepancies I’m seeing in the results.
These gene lists are from Chai et al, 2019.
The foreground list is composed of the downregulated genes shown in Supplementary Table 2, while the background list was obtained from Supplementary Table 1.
To get this to work, I will convert the gene symbols to Ensembl identifiers. There were only ~8000 expressed genes which is a bit low.
I will look at all gene sets with p<0.05, as that is what the authors of the original study did. I know, I know….
bgg <- readLines("PMC6463127_bgg.txt")
head(bgg)## [1] "UBE2Q2" "ATRX" "TCOF1" "NSRP1" "OPA1" "ITGA8"length(bgg)## [1] 8090geneinfo <- read.table("http://dee2.io/data/hsapiens/hsa_gene_info.tsv",header=TRUE)
bge <- geneinfo[which(geneinfo$GeneSymbol %in% bgg),"GeneID"]
bge <- bge[which(!is.na(bge))]
bge <- unique(bge)
length(bge)## [1] 8261writeLines(bge,"background.txt")Now to do the same for the foreground list.
fgg <- readLines("PMC6463127_dn.txt")
head(fgg)## [1] "DEGS1" "TMBIM6" "SSBP3" "SNORA74A" "DPYD" "ALG5"length(fgg)## [1] 202fge <- geneinfo[which(geneinfo$GeneSymbol %in% fgg),"GeneID"]
fge <- fge[which(!is.na(fge))]
fge <- unique(fge)
length(fge)## [1] 205writeLines(fge,"foreground.txt")I ran DAVID and was able to get similar terms with p<0.05 as compared to the original journal article.
dav <- read.table("david_bp_res.tsv",header=TRUE,sep="\t")
dav %>% kbl(caption="Enriched GO:BP terms obtained using DAVID") %>% kable_paper("hover", full_width = F)| Category | Term | Count | X. | PValue | Genes | List.Total | Pop.Hits | Pop.Total | Fold.Enrichment | Bonferroni | Benjamini | FDR |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GOTERM_BP_DIRECT | GO:0061077~chaperone-mediated protein folding | 5 | 2.475248 | 0.0015479 | ENSG00000127022, ENSG00000166794, ENSG00000162735, ENSG00000179218, ENSG00000122642 | 181 | 19 | 6549 | 9.521663 | 0.8295080 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0006465~signal peptide processing | 4 | 1.980198 | 0.0021250 | ENSG00000166562, ENSG00000140612, ENSG00000118363, ENSG00000138600 | 181 | 10 | 6549 | 14.472928 | 0.9119028 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0002474~antigen processing and presentation of peptide antigen via MHC class I | 5 | 2.475248 | 0.0027392 | ENSG00000127022, ENSG00000185825, ENSG00000167004, ENSG00000157020, ENSG00000179218 | 181 | 22 | 6549 | 8.223255 | 0.9563874 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0006506~GPI anchor biosynthetic process | 4 | 1.980198 | 0.0037409 | ENSG00000120697, ENSG00000185808, ENSG00000101464, ENSG00000174227 | 181 | 12 | 6549 | 12.060773 | 0.9861587 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0002576~platelet degranulation | 6 | 2.970297 | 0.0097636 | ENSG00000108679, ENSG00000135218, ENSG00000196937, ENSG00000084234, ENSG00000005893, ENSG00000197746 | 181 | 48 | 6549 | 4.522790 | 0.9999864 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0018279~protein N-linked glycosylation via asparagine | 4 | 1.980198 | 0.0104523 | ENSG00000120697, ENSG00000134910, ENSG00000163902, ENSG00000102595 | 181 | 17 | 6549 | 8.513487 | 0.9999939 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0044829~positive regulation by host of viral genome replication | 3 | 1.485148 | 0.0104776 | ENSG00000166794, ENSG00000124164, ENSG00000047188 | 181 | 6 | 6549 | 18.091160 | 0.9999940 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0036498~IRE1-mediated unfolded protein response | 5 | 2.475248 | 0.0121196 | ENSG00000100219, ENSG00000143870, ENSG00000149428, ENSG00000025796, ENSG00000132432 | 181 | 33 | 6549 | 5.482170 | 0.9999991 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0034975~protein folding in endoplasmic reticulum | 3 | 1.485148 | 0.0144052 | ENSG00000127022, ENSG00000167004, ENSG00000179218 | 181 | 7 | 6549 | 15.506709 | 0.9999999 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0050900~leukocyte migration | 6 | 2.970297 | 0.0158110 | ENSG00000172270, ENSG00000019582, ENSG00000147065, ENSG00000092068, ENSG00000116815, ENSG00000174059 | 181 | 54 | 6549 | 4.020258 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0006509~membrane protein ectodomain proteolysis | 3 | 1.485148 | 0.0292415 | ENSG00000162736, ENSG00000168615, ENSG00000138600 | 181 | 10 | 6549 | 10.854696 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0008543~fibroblast growth factor receptor signaling pathway | 5 | 2.475248 | 0.0342643 | ENSG00000133116, ENSG00000163882, ENSG00000151923, ENSG00000135486, ENSG00000196159 | 181 | 45 | 6549 | 4.020258 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0006888~ER to Golgi vesicle-mediated transport | 7 | 3.465346 | 0.0441722 | ENSG00000104388, ENSG00000185825, ENSG00000170348, ENSG00000124164, ENSG00000086598, ENSG00000138069, ENSG00000149428 | 181 | 94 | 6549 | 2.694428 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0030148~sphingolipid biosynthetic process | 3 | 1.485148 | 0.0480322 | ENSG00000143753, ENSG00000124164, ENSG00000067113 | 181 | 13 | 6549 | 8.349766 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0006898~receptor-mediated endocytosis | 5 | 2.475248 | 0.0506994 | ENSG00000108679, ENSG00000135218, ENSG00000179218, ENSG00000149428, ENSG00000197081 | 181 | 51 | 6549 | 3.547286 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0006486~protein glycosylation | 4 | 1.980198 | 0.0522752 | ENSG00000120697, ENSG00000134910, ENSG00000163902, ENSG00000102595 | 181 | 31 | 6549 | 4.668686 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0046135~pyrimidine nucleoside catabolic process | 2 | 0.990099 | 0.0542189 | ENSG00000188641, ENSG00000122643 | 181 | 2 | 6549 | 36.182320 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:1903298~negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway | 2 | 0.990099 | 0.0542189 | ENSG00000149428, ENSG00000139644 | 181 | 2 | 6549 | 36.182320 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0006611~protein export from nucleus | 3 | 1.485148 | 0.0623955 | ENSG00000124207, ENSG00000082898, ENSG00000179218 | 181 | 15 | 6549 | 7.236464 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0048208~COPII vesicle coating | 4 | 1.980198 | 0.0656033 | ENSG00000170348, ENSG00000086598, ENSG00000157020, ENSG00000138069 | 181 | 34 | 6549 | 4.256744 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0030433~ER-associated ubiquitin-dependent protein catabolic process | 4 | 1.980198 | 0.0656033 | ENSG00000239305, ENSG00000161057, ENSG00000147475, ENSG00000164953 | 181 | 34 | 6549 | 4.256744 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0006890~retrograde vesicle-mediated transport, Golgi to ER | 5 | 2.475248 | 0.0671666 | ENSG00000175582, ENSG00000170348, ENSG00000086598, ENSG00000087502, ENSG00000138069 | 181 | 56 | 6549 | 3.230564 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0006457~protein folding | 7 | 3.465346 | 0.0736553 | ENSG00000127022, ENSG00000167004, ENSG00000100380, ENSG00000143870, ENSG00000179218, ENSG00000122642, ENSG00000086061 | 181 | 107 | 6549 | 2.367068 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0007283~spermatogenesis | 8 | 3.960396 | 0.0777930 | ENSG00000185825, ENSG00000173698, ENSG00000110367, ENSG00000145375, ENSG00000123131, ENSG00000179218, ENSG00000086061, ENSG00000197081 | 181 | 135 | 6549 | 2.144137 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0042985~negative regulation of amyloid precursor protein biosynthetic process | 2 | 0.990099 | 0.0802217 | ENSG00000078596, ENSG00000136156 | 181 | 3 | 6549 | 24.121547 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:1990000~amyloid fibril formation | 2 | 0.990099 | 0.0802217 | ENSG00000135218, ENSG00000148180 | 181 | 3 | 6549 | 24.121547 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0060907~positive regulation of macrophage cytokine production | 2 | 0.990099 | 0.0802217 | ENSG00000019582, ENSG00000135218 | 181 | 3 | 6549 | 24.121547 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0048205~COPI coating of Golgi vesicle | 2 | 0.990099 | 0.0802217 | ENSG00000170348, ENSG00000086598 | 181 | 3 | 6549 | 24.121547 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0060323~head morphogenesis | 2 | 0.990099 | 0.0802217 | ENSG00000182220, ENSG00000157216 | 181 | 3 | 6549 | 24.121547 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0001843~neural tube closure | 4 | 1.980198 | 0.0855226 | ENSG00000100714, ENSG00000167642, ENSG00000086598, ENSG00000164930 | 181 | 38 | 6549 | 3.808665 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0031647~regulation of protein stability | 4 | 1.980198 | 0.0908613 | ENSG00000100219, ENSG00000116030, ENSG00000100225, ENSG00000005893 | 181 | 39 | 6549 | 3.711007 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0006874~cellular calcium ion homeostasis | 4 | 1.980198 | 0.0908613 | ENSG00000152266, ENSG00000124164, ENSG00000179218, ENSG00000133112 | 181 | 39 | 6549 | 3.711007 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0006810~transport | 7 | 3.465346 | 0.0962883 | ENSG00000170348, ENSG00000003989, ENSG00000152661, ENSG00000086598, ENSG00000092068, ENSG00000088386, ENSG00000125304 | 181 | 115 | 6549 | 2.202402 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0010951~negative regulation of endopeptidase activity | 4 | 1.980198 | 0.0963357 | ENSG00000167642, ENSG00000084234, ENSG00000196104, ENSG00000156535 | 181 | 40 | 6549 | 3.618232 | 1.0000000 | 1 | 1 |
| GOTERM_BP_DIRECT | GO:0055114~oxidation-reduction process | 10 | 4.950495 | 0.0982062 | ENSG00000143753, ENSG00000100714, ENSG00000167004, ENSG00000008311, ENSG00000170271, ENSG00000188641, ENSG00000123131, ENSG00000116005, ENSG00000122884, ENSG00000143653 | 181 | 200 | 6549 | 1.809116 | 1.0000000 | 1 | 1 |
Here I’m using the enrichGO function to analyse the data. The algorithm is slightly different and the gene sets might be a different version. First GO biological processes.
cp <- enrichGO(gene = fge, keyType = "ENSEMBL", universe = bge,
OrgDb = org.Hs.eg.db, ont = "BP", pAdjustMethod = "BH", pvalueCutoff = 0.05,
qvalueCutoff = 1, minGSSize = 2, readable = TRUE)
cp <- data.frame(cp)
nrow(cp)## [1] 7cp %>% kbl(caption="Enriched GO terms obtained using clusterProfiler with the correct background") %>% kable_paper("hover", full_width = F)| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | geneID | Count | |
|---|---|---|---|---|---|---|---|---|---|
| GO:0006643 | GO:0006643 | membrane lipid metabolic process | 12/195 | 72/7108 | 5.00e-07 | 0.0009010 | 0.0008525 | FUCA1/DEGS1/SCCPDH/PIGG/PLPP1/SERINC1/PSAP/ESYT1/PIGU/VAPB/TECR/PIGP | 12 |
| GO:0034976 | GO:0034976 | response to endoplasmic reticulum stress | 17/195 | 151/7108 | 7.00e-07 | 0.0009010 | 0.0008525 | TMCO1/PDIA6/RNF103/MANF/DNAJB14/CANX/BCAP31/ERLIN2/TMEM67/HYOU1/TMBIM6/TMED2/UGGT2/PDIA3/VAPB/CALR/XBP1 | 17 |
| GO:1901135 | GO:1901135 | carbohydrate derivative metabolic process | 31/195 | 437/7108 | 8.00e-07 | 0.0009010 | 0.0008525 | FUCA1/DPYD/NCSTN/NME7/SCCPDH/RAB1A/RNF103/UXS1/SEC13/RPN1/PIGG/NUDT9/SPOCK3/NT5C3A/PDK4/AASS/NUP205/CTPS2/OGT/ITM2A/OGN/PTH/STT3A/PSAP/ESYT1/ALG5/ITM2B/UGGT2/PIGU/TECR/PIGP | 31 |
| GO:0006664 | GO:0006664 | glycolipid metabolic process | 7/195 | 35/7108 | 3.68e-05 | 0.0243273 | 0.0230165 | FUCA1/SCCPDH/PIGG/PSAP/ESYT1/PIGU/PIGP | 7 |
| GO:1903509 | GO:1903509 | liposaccharide metabolic process | 7/195 | 35/7108 | 3.68e-05 | 0.0243273 | 0.0230165 | FUCA1/SCCPDH/PIGG/PSAP/ESYT1/PIGU/PIGP | 7 |
| GO:0002576 | GO:0002576 | platelet degranulation | 9/195 | 62/7108 | 4.22e-05 | 0.0243273 | 0.0230165 | SCCPDH/MANF/CD109/CD36/FAM3C/LAMP2/APLP2/PSAP/LGALS3BP | 9 |
| GO:0035966 | GO:0035966 | response to topologically incorrect protein | 12/195 | 117/7108 | 7.97e-05 | 0.0393657 | 0.0372447 | PDIA6/MANF/DNAJB14/CANX/DNAJA1/HYOU1/TMBIM6/TMED2/UGGT2/VAPB/CALR/XBP1 | 12 |
The gene symbols were obtained from the supplementary files.
Here are the results:
gorilla <- read.table("gorilla_res.tsv",sep="\t",header=TRUE)
gorilla %>% kbl(caption="Enriched GO terms obtained using GOrilla with the correct background") %>% kable_paper("hover", full_width = F)| GO.term | Description | P.value | FDR.q.value | Enrichment..N..B..n..b. | Genes |
|---|---|---|---|---|---|
| GO:0006810 | transport | 0.00e+00 | 3.88e-05 | 1.78 (7396,1786,195,84) | [+] Show genes |
| GO:0051234 | establishment of localization | 0.00e+00 | 4.52e-05 | 1.74 (7396,1848,195,85) | [+] Show genes |
| GO:0051179 | localization | 0.00e+00 | 5.73e-05 | 1.66 (7396,2101,195,92) | [+] Show genes |
| GO:0034976 | response to endoplasmic reticulum stress | 2.00e-07 | 6.45e-04 | 4.74 (7396,128,195,16) | [+] Show genes |
| GO:0006643 | membrane lipid metabolic process | 7.00e-07 | 1.78e-03 | 6.52 (7396,64,195,11) | [+] Show genes |
| GO:0071705 | nitrogen compound transport | 3.70e-06 | 7.68e-03 | 1.98 (7396,860,195,45) | [+] Show genes |
| GO:0008104 | protein localization | 5.00e-06 | 8.88e-03 | 1.89 (7396,984,195,49) | [+] Show genes |
| GO:0042886 | amide transport | 5.30e-06 | 8.35e-03 | 2.10 (7396,706,195,39) | [+] Show genes |
| GO:0033036 | macromolecule localization | 7.60e-06 | 1.06e-02 | 1.86 (7396,999,195,49) | [+] Show genes |
| GO:0015833 | peptide transport | 1.08e-05 | 1.36e-02 | 2.06 (7396,700,195,38) | [+] Show genes |
| GO:0006664 | glycolipid metabolic process | 1.22e-05 | 1.39e-02 | 8.56 (7396,31,195,7) | [+] Show genes |
| GO:1903509 | liposaccharide metabolic process | 1.22e-05 | 1.28e-02 | 8.56 (7396,31,195,7) | [+] Show genes |
| GO:0016192 | vesicle-mediated transport | 1.24e-05 | 1.19e-02 | 1.95 (7396,815,195,42) | [+] Show genes |
| GO:0071702 | organic substance transport | 1.30e-05 | 1.17e-02 | 1.86 (7396,960,195,47) | [+] Show genes |
| GO:0015031 | protein transport | 1.97e-05 | 1.65e-02 | 2.03 (7396,691,195,37) | [+] Show genes |
| GO:0002576 | platelet degranulation | 2.06e-05 | 1.61e-02 | 5.79 (7396,59,195,9) | [+] Show genes |
| GO:0055080 | cation homeostasis | 2.50e-05 | 1.85e-02 | 2.92 (7396,247,195,19) | [+] Show genes |
| GO:0045184 | establishment of protein localization | 2.82e-05 | 1.97e-02 | 1.97 (7396,730,195,38) | [+] Show genes |
| GO:0098771 | inorganic ion homeostasis | 3.13e-05 | 2.07e-02 | 2.87 (7396,251,195,19) | [+] Show genes |
| GO:0032940 | secretion by cell | 3.60e-05 | 2.26e-02 | 2.35 (7396,419,195,26) | [+] Show genes |
| GO:0050801 | ion homeostasis | 3.80e-05 | 2.27e-02 | 2.74 (7396,277,195,20) | [+] Show genes |
| GO:0006213 | pyrimidine nucleoside metabolic process | 5.79e-05 | 3.30e-02 | 11.16 (7396,17,195,5) | [+] Show genes |
| GO:0045055 | regulated exocytosis | 1.02e-04 | 5.56e-02 | 2.48 (7396,321,195,21) | [+] Show genes |
| GO:0046903 | secretion | 1.32e-04 | 6.92e-02 | 2.18 (7396,453,195,26) | [+] Show genes |
| GO:0055065 | metal ion homeostasis | 1.65e-04 | 8.28e-02 | 2.82 (7396,215,195,16) | [+] Show genes |
| GO:0006887 | exocytosis | 1.66e-04 | 8.00e-02 | 2.34 (7396,357,195,22) | [+] Show genes |
| GO:1901564 | organonitrogen compound metabolic process | 2.39e-04 | 1.11e-01 | 1.39 (7396,2231,195,82) | [+] Show genes |
| GO:0006457 | protein folding | 2.50e-04 | 1.12e-01 | 3.32 (7396,137,195,12) | [+] Show genes |
| GO:0051604 | protein maturation | 2.61e-04 | 1.13e-01 | 3.83 (7396,99,195,10) | [+] Show genes |
| GO:0098657 | import into cell | 2.77e-04 | 1.16e-01 | 2.60 (7396,248,195,17) | [+] Show genes |
| GO:0009218 | pyrimidine ribonucleotide metabolic process | 2.78e-04 | 1.12e-01 | 11.67 (7396,13,195,4) | [+] Show genes |
| GO:0019882 | antigen processing and presentation | 3.06e-04 | 1.20e-01 | 3.25 (7396,140,195,12) | [+] Show genes |
| GO:1901135 | carbohydrate derivative metabolic process | 3.13e-04 | 1.19e-01 | 2.29 (7396,348,195,21) | [+] Show genes |
| GO:0046467 | membrane lipid biosynthetic process | 3.13e-04 | 1.16e-01 | 6.32 (7396,36,195,6) | [+] Show genes |
| GO:1900038 | negative regulation of cellular response to hypoxia | 3.40e-04 | 1.22e-01 | 18.96 (7396,6,195,3) | [+] Show genes |
| GO:0006465 | signal peptide processing | 3.40e-04 | 1.19e-01 | 18.96 (7396,6,195,3) | [+] Show genes |
| GO:0048194 | Golgi vesicle budding | 3.40e-04 | 1.15e-01 | 18.96 (7396,6,195,3) | [+] Show genes |
| GO:0016485 | protein processing | 3.85e-04 | 1.27e-01 | 4.46 (7396,68,195,8) | [+] Show genes |
| GO:0046907 | intracellular transport | 4.09e-04 | 1.31e-01 | 1.72 (7396,858,195,39) | [+] Show genes |
| GO:0042592 | homeostatic process | 5.03e-04 | 1.58e-01 | 1.91 (7396,576,195,29) | [+] Show genes |
| GO:0006886 | intracellular protein transport | 5.04e-04 | 1.54e-01 | 2.03 (7396,466,195,25) | [+] Show genes |
| GO:0006984 | ER-nucleus signaling pathway | 5.07e-04 | 1.51e-01 | 7.29 (7396,26,195,5) | [+] Show genes |
| GO:0046131 | pyrimidine ribonucleoside metabolic process | 5.09e-04 | 1.49e-01 | 10.11 (7396,15,195,4) | [+] Show genes |
| GO:0034613 | cellular protein localization | 5.18e-04 | 1.48e-01 | 1.91 (7396,577,195,29) | [+] Show genes |
| GO:0002474 | antigen processing and presentation of peptide antigen via MHC class I | 5.19e-04 | 1.45e-01 | 4.27 (7396,71,195,8) | [+] Show genes |
| GO:0044419 | interspecies interaction between organisms | 5.48e-04 | 1.49e-01 | 1.90 (7396,579,195,29) | [+] Show genes |
| GO:0030968 | endoplasmic reticulum unfolded protein response | 5.52e-04 | 1.47e-01 | 4.83 (7396,55,195,7) | [+] Show genes |
| GO:0031293 | membrane protein intracellular domain proteolysis | 5.84e-04 | 1.53e-01 | 16.25 (7396,7,195,3) | [+] Show genes |
| GO:0042984 | regulation of amyloid precursor protein biosynthetic process | 5.84e-04 | 1.50e-01 | 16.25 (7396,7,195,3) | [+] Show genes |
| GO:0070727 | cellular macromolecule localization | 5.96e-04 | 1.50e-01 | 1.89 (7396,582,195,29) | [+] Show genes |
| GO:0072507 | divalent inorganic cation homeostasis | 6.48e-04 | 1.59e-01 | 2.99 (7396,152,195,12) | [+] Show genes |
| GO:0032469 | endoplasmic reticulum calcium ion homeostasis | 6.65e-04 | 1.60e-01 | 9.48 (7396,16,195,4) | [+] Show genes |
| GO:0009247 | glycolipid biosynthetic process | 6.65e-04 | 1.57e-01 | 9.48 (7396,16,195,4) | [+] Show genes |
| GO:0090114 | COPII-coated vesicle budding | 6.92e-04 | 1.61e-01 | 37.93 (7396,2,195,2) | [+] Show genes |
| GO:0002366 | leukocyte activation involved in immune response | 8.09e-04 | 1.84e-01 | 2.30 (7396,297,195,18) | [+] Show genes |
| GO:0051649 | establishment of localization in cell | 8.24e-04 | 1.84e-01 | 1.64 (7396,950,195,41) | [+] Show genes |
| GO:2000241 | regulation of reproductive process | 8.41e-04 | 1.85e-01 | 5.29 (7396,43,195,6) | [+] Show genes |
| GO:2000242 | negative regulation of reproductive process | 8.52e-04 | 1.84e-01 | 8.92 (7396,17,195,4) | [+] Show genes |
| GO:0051445 | regulation of meiotic cell cycle | 8.52e-04 | 1.81e-01 | 8.92 (7396,17,195,4) | [+] Show genes |
| GO:0055074 | calcium ion homeostasis | 8.88e-04 | 1.86e-01 | 3.07 (7396,136,195,11) | [+] Show genes |
| GO:0051641 | cellular localization | 8.95e-04 | 1.84e-01 | 1.54 (7396,1205,195,49) | [+] Show genes |
| GO:0002263 | cell activation involved in immune response | 9.09e-04 | 1.84e-01 | 2.28 (7396,300,195,18) | [+] Show genes |
| GO:0034975 | protein folding in endoplasmic reticulum | 9.17e-04 | 1.82e-01 | 14.22 (7396,8,195,3) | [+] Show genes |
| GO:1900037 | regulation of cellular response to hypoxia | 9.17e-04 | 1.80e-01 | 14.22 (7396,8,195,3) | [+] Show genes |
| GO:0044794 | positive regulation by host of viral process | 9.17e-04 | 1.77e-01 | 14.22 (7396,8,195,3) | [+] Show genes |
sessionInfo()## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## locale:
## [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
## [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
## [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] eulerr_6.1.1 kableExtra_1.3.4
## [3] mitch_1.4.1 org.Hs.eg.db_3.13.0
## [5] AnnotationDbi_1.54.1 clusterProfiler_4.0.5
## [7] DESeq2_1.32.0 SummarizedExperiment_1.22.0
## [9] Biobase_2.52.0 MatrixGenerics_1.4.3
## [11] matrixStats_0.61.0 GenomicRanges_1.44.0
## [13] GenomeInfoDb_1.28.4 IRanges_2.26.0
## [15] S4Vectors_0.30.2 BiocGenerics_0.38.0
## [17] getDEE2_1.2.0
##
## loaded via a namespace (and not attached):
## [1] shadowtext_0.0.9 fastmatch_1.1-3 systemfonts_1.0.3
## [4] plyr_1.8.6 igraph_1.2.8 lazyeval_0.2.2
## [7] splines_4.1.2 BiocParallel_1.26.2 ggplot2_3.3.5
## [10] digest_0.6.28 yulab.utils_0.0.4 htmltools_0.5.2
## [13] GOSemSim_2.18.1 viridis_0.6.2 GO.db_3.13.0
## [16] fansi_0.5.0 magrittr_2.0.1 memoise_2.0.0
## [19] Biostrings_2.60.2 annotate_1.70.0 graphlayouts_0.7.1
## [22] svglite_2.0.0 enrichplot_1.12.3 colorspace_2.0-2
## [25] rvest_1.0.2 blob_1.2.2 ggrepel_0.9.1
## [28] xfun_0.28 dplyr_1.0.7 crayon_1.4.2
## [31] RCurl_1.98-1.5 jsonlite_1.7.2 scatterpie_0.1.7
## [34] genefilter_1.74.1 survival_3.2-13 ape_5.5
## [37] glue_1.5.0 polyclip_1.10-0 gtable_0.3.0
## [40] zlibbioc_1.38.0 XVector_0.32.0 webshot_0.5.2
## [43] htm2txt_2.1.1 DelayedArray_0.18.0 scales_1.1.1
## [46] DOSE_3.18.3 DBI_1.1.1 GGally_2.1.2
## [49] Rcpp_1.0.7 viridisLite_0.4.0 xtable_1.8-4
## [52] gridGraphics_0.5-1 tidytree_0.3.6 bit_4.0.4
## [55] htmlwidgets_1.5.4 httr_1.4.2 fgsea_1.18.0
## [58] gplots_3.1.1 RColorBrewer_1.1-2 ellipsis_0.3.2
## [61] pkgconfig_2.0.3 reshape_0.8.8 XML_3.99-0.8
## [64] farver_2.1.0 sass_0.4.0 locfit_1.5-9.4
## [67] utf8_1.2.2 ggplotify_0.1.0 tidyselect_1.1.1
## [70] rlang_0.4.12 reshape2_1.4.4 later_1.3.0
## [73] munsell_0.5.0 tools_4.1.2 cachem_1.0.6
## [76] downloader_0.4 generics_0.1.1 RSQLite_2.2.8
## [79] evaluate_0.14 stringr_1.4.0 fastmap_1.1.0
## [82] yaml_2.2.1 ggtree_3.0.4 knitr_1.36
## [85] bit64_4.0.5 tidygraph_1.2.0 caTools_1.18.2
## [88] purrr_0.3.4 KEGGREST_1.32.0 ggraph_2.0.5
## [91] nlme_3.1-153 mime_0.12 aplot_0.1.1
## [94] xml2_1.3.2 DO.db_2.9 rstudioapi_0.13
## [97] compiler_4.1.2 beeswarm_0.4.0 png_0.1-7
## [100] treeio_1.16.2 tibble_3.1.6 tweenr_1.0.2
## [103] geneplotter_1.70.0 bslib_0.3.1 stringi_1.7.5
## [106] highr_0.9 lattice_0.20-45 Matrix_1.3-4
## [109] vctrs_0.3.8 pillar_1.6.4 lifecycle_1.0.1
## [112] jquerylib_0.1.4 data.table_1.14.2 cowplot_1.1.1
## [115] bitops_1.0-7 httpuv_1.6.3 patchwork_1.1.1
## [118] qvalue_2.24.0 R6_2.5.1 promises_1.2.0.1
## [121] KernSmooth_2.23-20 echarts4r_0.4.2 gridExtra_2.3
## [124] gtools_3.9.2 MASS_7.3-54 assertthat_0.2.1
## [127] GenomeInfoDbData_1.2.6 grid_4.1.2 ggfun_0.0.4
## [130] tidyr_1.1.4 rmarkdown_2.11 ggforce_0.3.3
## [133] shiny_1.7.1