Source: https://github.com/markziemann/SurveyEnrichmentMethods

Intro

suppressPackageStartupMessages({
library("getDEE2")
library("DESeq2")
library("clusterProfiler")
library("org.Hs.eg.db")
library("mitch")
library("kableExtra")
library("eulerr")
})

In Kaumadi et al 2021 we showed that major problems plague functional enrichment analysis in many journal articles.

Here I will do my best to reproduce and replicate the findings of some studies. These were selected on the following criteria:

  • Included in the 2019 group that was studies in Kaumadi et al 2021.

  • Human study

  • RNA-seq gene expression

  • Performed DAVID gene set analysis

  • Provided gene list

From this subset, four studies were selected

Study Analytical issues
PMC6349697 Background
PMC6425008 Background, FDR
PMC6463127 Background, FDR
PMC6535219 Background

In this document I will be seeing if I can reproduce the same findings by using the same tool with the gene list provided in the article. Also I will correct the method wherever possible. This means using the correct background gene list, using FDR control and performing separate analysis of up and down-regulated gene lists.

The study examined in this document is PMC6535219: Guo et al, 2019.

The focus of this study is anoikis resistance (AR). They performed RNA-seq of CAL27 control cells and CAL27-AR cells. In File S1, they provide the differentially regulated genes (|Loget| ≥ 1, probability ≥ 0.8) , from those genes, they performed extra filtering (|Loget| ≥ 2, probability ≥ 0.9) and the genes passing those filters were subject to DAVID analysis separately for up and downregulated genes.

I have summarised some of the DAVID findings here, which I will try to repeat and replicate with corrected methods.

GO type Direction GO term p-value
BP UP epidermis development 1.01e-21
BP UP keratinocyte differentiation 1.62e-20
BP UP keratinization 1.65e-14
BP DN cell division 4.49e33
BP DN mitotic nuclear division 6.38e-27
BP DN DNA replication 1.24e-21
MF UP structural molecule activity 2.31e-9
MF UP protein heterodimerization activity 4.62e-6
MF UP calcium ion binding 4.12e-5
MF DN protein binding 2.63e-12
CC UP extracellular exosome 1.02e-20
CC DN nucleoplasm 7.76e-22
CC UP extracellular space 1.21e-10
CC UP extracellular region 9.22e-7
CC DN nucleus 1.10e-10

Try to reproduce

So let’s see if I can reproduce their result using DAVID without a background gene list. The study provided the differentially regulated gene lists in Supplementary File S1. I filtered the list as per the methods and submitted to DAVID

Here are the significant GO terms for the up and down directions, along with the downregulated KEGG pathways.

repl1up <- read.table("PMC6535219_repl1_up.tsv",header=TRUE,sep="\t")

repl1up %>% kbl(caption="Upregulated GO terms obtained using article gene list without background") %>% kable_paper("hover", full_width = F)
Upregulated GO terms obtained using article gene list without background
Category Term Count X. PValue List.Total Pop.Hits Pop.Total Fold.Enrichment FDR
GOTERM_BP_DIRECT GO:0008544~epidermis development 27 5.818966 0.0000000 417 85 16792 12.791198 0.0000000
GOTERM_BP_DIRECT GO:0030216~keratinocyte differentiation 25 5.387931 0.0000000 417 76 16792 13.246245 0.0000000
GOTERM_BP_DIRECT GO:0031424~keratinization 17 3.663793 0.0000000 417 48 16792 14.261791 0.0000000
GOTERM_BP_DIRECT GO:0018149~peptide cross-linking 16 3.448276 0.0000000 417 50 16792 12.885947 0.0000000
GOTERM_BP_DIRECT GO:0060337~type I interferon signaling pathway 16 3.448276 0.0000000 417 64 16792 10.067146 0.0000000
GOTERM_BP_DIRECT GO:0006334~nucleosome assembly 19 4.094828 0.0000000 417 119 16792 6.429438 0.0000002
GOTERM_BP_DIRECT GO:0060333~interferon-gamma-mediated signaling pathway 15 3.232759 0.0000000 417 71 16792 8.507448 0.0000005
GOTERM_BP_DIRECT GO:0051607~defense response to virus 20 4.310345 0.0000000 417 165 16792 4.881041 0.0000063
GOTERM_BP_DIRECT GO:0002504~antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 8 1.724138 0.0000001 417 17 16792 18.949922 0.0000158
GOTERM_BP_DIRECT GO:0009615~response to virus 16 3.448276 0.0000001 417 110 16792 5.857249 0.0000158
GOTERM_BP_DIRECT GO:0000183~chromatin silencing at rDNA 10 2.155172 0.0000002 417 37 16792 10.883401 0.0000358
GOTERM_BP_DIRECT GO:0045071~negative regulation of viral genome replication 10 2.155172 0.0000004 417 40 16792 10.067146 0.0000675
GOTERM_BP_DIRECT GO:0044267~cellular protein metabolic process 15 3.232759 0.0000013 417 118 16792 5.118888 0.0001844
GOTERM_BP_DIRECT GO:0032200~telomere organization 8 1.724138 0.0000031 417 27 16792 11.931433 0.0003971
GOTERM_BP_DIRECT GO:0045814~negative regulation of gene expression, epigenetic 10 2.155172 0.0000033 417 50 16792 8.053717 0.0003971
GOTERM_BP_DIRECT GO:0019882~antigen processing and presentation 10 2.155172 0.0000075 417 55 16792 7.321561 0.0008470
GOTERM_BP_DIRECT GO:0045087~innate immune response 28 6.034483 0.0000099 417 430 16792 2.622140 0.0010612
GOTERM_BP_DIRECT GO:0006335~DNA replication-dependent nucleosome assembly 8 1.724138 0.0000107 417 32 16792 10.067146 0.0010809
GOTERM_BP_DIRECT GO:0045815~positive regulation of gene expression, epigenetic 10 2.155172 0.0000205 417 62 16792 6.494933 0.0019527
GOTERM_BP_DIRECT GO:0044597~daunorubicin metabolic process 5 1.077586 0.0000240 417 8 16792 25.167866 0.0020747
GOTERM_BP_DIRECT GO:0044598~doxorubicin metabolic process 5 1.077586 0.0000240 417 8 16792 25.167866 0.0020747
GOTERM_BP_DIRECT GO:0006955~immune response 26 5.603448 0.0000530 417 421 16792 2.486896 0.0043383
GOTERM_BP_DIRECT GO:0030855~epithelial cell differentiation 10 2.155172 0.0000551 417 70 16792 5.752655 0.0043383
GOTERM_BP_DIRECT GO:0032673~regulation of interleukin-4 production 4 0.862069 0.0000593 417 4 16792 40.268585 0.0043383
GOTERM_BP_DIRECT GO:0061436~establishment of skin barrier 6 1.293103 0.0000598 417 18 16792 13.422862 0.0043383
GOTERM_BP_DIRECT GO:0051290~protein heterotetramerization 8 1.724138 0.0000694 417 42 16792 7.670207 0.0048447
GOTERM_BP_DIRECT GO:0042574~retinal metabolic process 5 1.077586 0.0001569 417 12 16792 16.778577 0.0105443
GOTERM_BP_DIRECT GO:0016045~detection of bacterium 5 1.077586 0.0002223 417 13 16792 15.487917 0.0142724
GOTERM_BP_DIRECT GO:0032496~response to lipopolysaccharide 14 3.017241 0.0002282 417 164 16792 3.437562 0.0142724
GOTERM_BP_DIRECT GO:0019886~antigen processing and presentation of exogenous peptide antigen via MHC class II 10 2.155172 0.0004559 417 92 16792 4.377020 0.0275676
GOTERM_BP_DIRECT GO:0031295~T cell costimulation 9 1.939655 0.0006839 417 78 16792 4.646375 0.0400177
GOTERM_BP_DIRECT GO:0042572~retinol metabolic process 6 1.293103 0.0007786 417 30 16792 8.053717 0.0441345
GOTERM_BP_DIRECT GO:0010951~negative regulation of endopeptidase activity 11 2.370690 0.0008576 417 121 16792 3.660780 0.0460036
GOTERM_BP_DIRECT GO:0045653~negative regulation of megakaryocyte differentiation 5 1.077586 0.0008622 417 18 16792 11.185718 0.0460036
GOTERM_BP_DIRECT GO:0051591~response to cAMP 7 1.508621 0.0009030 417 46 16792 6.127828 0.0467995
GOTERM_CC_DIRECT GO:0070062~extracellular exosome 146 31.465517 0.0000000 441 2811 18224 2.146333 0.0000000
GOTERM_CC_DIRECT GO:0001533~cornified envelope 20 4.310345 0.0000000 441 46 18224 17.967071 0.0000000
GOTERM_CC_DIRECT GO:0000786~nucleosome 22 4.741379 0.0000000 441 94 18224 9.671636 0.0000000
GOTERM_CC_DIRECT GO:0005615~extracellular space 73 15.732759 0.0000000 441 1347 18224 2.239548 0.0000000
GOTERM_CC_DIRECT GO:0042613~MHC class II protein complex 8 1.724138 0.0000006 441 22 18224 15.027005 0.0000260
GOTERM_CC_DIRECT GO:0000788~nuclear nucleosome 10 2.155172 0.0000009 441 44 18224 9.391878 0.0000302
GOTERM_CC_DIRECT GO:0005576~extracellular region 71 15.301724 0.0000009 441 1610 18224 1.822374 0.0000302
GOTERM_CC_DIRECT GO:0030057~desmosome 8 1.724138 0.0000011 441 24 18224 13.774754 0.0000317
GOTERM_CC_DIRECT GO:0030658~transport vesicle membrane 9 1.939655 0.0000028 441 38 18224 9.787325 0.0000714
GOTERM_CC_DIRECT GO:0030666~endocytic vesicle membrane 11 2.370690 0.0000038 441 66 18224 6.887377 0.0000877
GOTERM_CC_DIRECT GO:0071556~integral component of lumenal side of endoplasmic reticulum membrane 8 1.724138 0.0000045 441 29 18224 11.399797 0.0000935
GOTERM_CC_DIRECT GO:0030669~clathrin-coated endocytic vesicle membrane 9 1.939655 0.0000051 441 41 18224 9.071180 0.0000982
GOTERM_CC_DIRECT GO:0005882~intermediate filament 13 2.801724 0.0000185 441 113 18224 4.754119 0.0003250
GOTERM_CC_DIRECT GO:0031012~extracellular matrix 21 4.525862 0.0000363 441 296 18224 2.931789 0.0005939
GOTERM_CC_DIRECT GO:0097209~epidermal lamellar body 4 0.862069 0.0000549 441 4 18224 41.324263 0.0008384
GOTERM_CC_DIRECT GO:0012507~ER to Golgi transport vesicle membrane 8 1.724138 0.0002387 441 52 18224 6.357579 0.0034160
GOTERM_CC_DIRECT GO:0000228~nuclear chromosome 8 1.724138 0.0002694 441 53 18224 6.237625 0.0036284
GOTERM_CC_DIRECT GO:0032588~trans-Golgi network membrane 9 1.939655 0.0008785 441 83 18224 4.480944 0.0111759
GOTERM_CC_DIRECT GO:0005765~lysosomal membrane 17 3.663793 0.0010479 441 274 18224 2.563914 0.0126299
GOTERM_CC_DIRECT GO:0005886~plasma membrane 126 27.155172 0.0024042 441 4121 18224 1.263494 0.0275286
GOTERM_MF_DIRECT GO:0005198~structural molecule activity 26 5.603448 0.0000000 416 247 16881 4.271508 0.0000012
GOTERM_MF_DIRECT GO:0032395~MHC class II receptor activity 8 1.724138 0.0000000 416 15 16881 21.642308 0.0000075
GOTERM_MF_DIRECT GO:0050786~RAGE receptor binding 6 1.293103 0.0000036 416 11 16881 22.134178 0.0004938
GOTERM_MF_DIRECT GO:0042605~peptide antigen binding 8 1.724138 0.0000039 416 28 16881 11.594093 0.0004938
GOTERM_MF_DIRECT GO:0046982~protein heterodimerization activity 30 6.465517 0.0000046 416 465 16881 2.618021 0.0004938
GOTERM_MF_DIRECT GO:0005509~calcium ion binding 37 7.974138 0.0000412 416 717 16881 2.094052 0.0036758
GOTERM_MF_DIRECT GO:0004252~serine-type endopeptidase activity 19 4.094828 0.0000639 416 255 16881 3.023558 0.0048847
GOTERM_MF_DIRECT GO:0004032~alditol:NADP+ 1-oxidoreductase activity 4 0.862069 0.0004796 416 7 16881 23.188187 0.0320754
GOTERM_MF_DIRECT GO:0004867~serine-type endopeptidase inhibitor activity 10 2.155172 0.0006372 416 97 16881 4.183436 0.0378796
GOTERM_MF_DIRECT GO:0004745~retinol dehydrogenase activity 5 1.077586 0.0008379 416 18 16881 11.272035 0.0424038
GOTERM_MF_DIRECT GO:0008236~serine-type peptidase activity 8 1.724138 0.0008719 416 63 16881 5.152930 0.0424038 
repl1dn <- read.table("PMC6535219_repl1_dn.tsv",header=TRUE,sep="\t")

repl1dn %>% kbl(caption="Downregulated GO terms obtained using article gene list without background") %>% kable_paper("hover", full_width = F)
Downregulated GO terms obtained using article gene list without background
Category Term Count X. PValue List.Total Pop.Hits Pop.Total Fold.Enrichment FDR
GOTERM_BP_DIRECT GO:0051301~cell division 53 16.2576687 0.0000000 299 350 16792 8.504310 0.0000000
GOTERM_BP_DIRECT GO:0007067~mitotic nuclear division 41 12.5766871 0.0000000 299 248 16792 9.284605 0.0000000
GOTERM_BP_DIRECT GO:0006260~DNA replication 30 9.2024540 0.0000000 299 155 16792 10.869781 0.0000000
GOTERM_BP_DIRECT GO:0007062~sister chromatid cohesion 24 7.3619632 0.0000000 299 103 16792 13.085950 0.0000000
GOTERM_BP_DIRECT GO:0000082~G1/S transition of mitotic cell cycle 21 6.4417178 0.0000000 299 102 16792 11.562463 0.0000000
GOTERM_BP_DIRECT GO:0000070~mitotic sister chromatid segregation 12 3.6809816 0.0000000 299 25 16792 26.957057 0.0000000
GOTERM_BP_DIRECT GO:0007059~chromosome segregation 16 4.9079755 0.0000000 299 68 16792 13.214244 0.0000000
GOTERM_BP_DIRECT GO:0008283~cell proliferation 29 8.8957055 0.0000000 299 366 16792 4.449878 0.0000000
GOTERM_BP_DIRECT GO:0006270~DNA replication initiation 11 3.3742331 0.0000000 299 32 16792 19.305184 0.0000000
GOTERM_BP_DIRECT GO:0000086~G2/M transition of mitotic cell cycle 17 5.2147239 0.0000000 299 137 16792 6.968826 0.0000005
GOTERM_BP_DIRECT GO:0006281~DNA repair 21 6.4417178 0.0000000 299 235 16792 5.018601 0.0000012
GOTERM_BP_DIRECT GO:0000281~mitotic cytokinesis 9 2.7607362 0.0000000 299 29 16792 17.429132 0.0000039
GOTERM_BP_DIRECT GO:0000083~regulation of transcription involved in G1/S transition of mitotic cell cycle 8 2.4539877 0.0000001 299 23 16792 19.534099 0.0000129
GOTERM_BP_DIRECT GO:0007018~microtubule-based movement 12 3.6809816 0.0000002 299 81 16792 8.320079 0.0000222
GOTERM_BP_DIRECT GO:0007080~mitotic metaphase plate congression 9 2.7607362 0.0000002 299 37 16792 13.660671 0.0000249
GOTERM_BP_DIRECT GO:0007019~microtubule depolymerization 6 1.8404908 0.0000004 299 10 16792 33.696321 0.0000396
GOTERM_BP_DIRECT GO:0006268~DNA unwinding involved in DNA replication 6 1.8404908 0.0000004 299 10 16792 33.696321 0.0000396
GOTERM_BP_DIRECT GO:0051310~metaphase plate congression 6 1.8404908 0.0000012 299 12 16792 28.080268 0.0001142
GOTERM_BP_DIRECT GO:0000910~cytokinesis 9 2.7607362 0.0000018 299 48 16792 10.530100 0.0001621
GOTERM_BP_DIRECT GO:0000731~DNA synthesis involved in DNA repair 8 2.4539877 0.0000023 299 35 16792 12.836694 0.0001915
GOTERM_BP_DIRECT GO:0090307~mitotic spindle assembly 8 2.4539877 0.0000028 299 36 16792 12.480119 0.0002230
GOTERM_BP_DIRECT GO:0006271~DNA strand elongation involved in DNA replication 6 1.8404908 0.0000044 299 15 16792 22.464214 0.0003242
GOTERM_BP_DIRECT GO:0007076~mitotic chromosome condensation 6 1.8404908 0.0000044 299 15 16792 22.464214 0.0003242
GOTERM_BP_DIRECT GO:0000732~strand displacement 7 2.1472393 0.0000051 299 26 16792 15.120144 0.0003567
GOTERM_BP_DIRECT GO:0000724~double-strand break repair via homologous recombination 10 3.0674847 0.0000062 299 74 16792 7.589262 0.0004111
GOTERM_BP_DIRECT GO:0007051~spindle organization 6 1.8404908 0.0000063 299 16 16792 21.060201 0.0004111
GOTERM_BP_DIRECT GO:0007049~cell cycle 16 4.9079755 0.0000080 299 217 16792 4.140869 0.0004985
GOTERM_BP_DIRECT GO:0034080~CENP-A containing nucleosome assembly 8 2.4539877 0.0000096 299 43 16792 10.448472 0.0005804
GOTERM_BP_DIRECT GO:0031145~anaphase-promoting complex-dependent catabolic process 10 3.0674847 0.0000107 299 79 16792 7.108929 0.0006217
GOTERM_BP_DIRECT GO:0032508~DNA duplex unwinding 8 2.4539877 0.0000113 299 44 16792 10.211006 0.0006217
GOTERM_BP_DIRECT GO:0030071~regulation of mitotic metaphase/anaphase transition 5 1.5337423 0.0000114 299 9 16792 31.200297 0.0006217
GOTERM_BP_DIRECT GO:0051726~regulation of cell cycle 12 3.6809816 0.0000131 299 124 16792 5.434890 0.0006893
GOTERM_BP_DIRECT GO:0006302~double-strand break repair 9 2.7607362 0.0000211 299 66 16792 7.658255 0.0010527
GOTERM_BP_DIRECT GO:0007094~mitotic spindle assembly checkpoint 6 1.8404908 0.0000212 299 20 16792 16.848160 0.0010527
GOTERM_BP_DIRECT GO:0051382~kinetochore assembly 5 1.5337423 0.0000430 299 12 16792 23.400223 0.0020740
GOTERM_BP_DIRECT GO:0000079~regulation of cyclin-dependent protein serine/threonine kinase activity 7 2.1472393 0.0000592 299 39 16792 10.080096 0.0027756
GOTERM_BP_DIRECT GO:0042787~protein ubiquitination involved in ubiquitin-dependent protein catabolic process 12 3.6809816 0.0000915 299 153 16792 4.404748 0.0041755
GOTERM_BP_DIRECT GO:0030335~positive regulation of cell migration 13 3.9877301 0.0001126 299 184 16792 3.967864 0.0050007
GOTERM_BP_DIRECT GO:0007052~mitotic spindle organization 6 1.8404908 0.0001685 299 30 16792 11.232107 0.0072941
GOTERM_BP_DIRECT GO:1900264~positive regulation of DNA-directed DNA polymerase activity 4 1.2269939 0.0001837 299 7 16792 32.091734 0.0077517
GOTERM_BP_DIRECT GO:0000722~telomere maintenance via recombination 6 1.8404908 0.0002313 299 32 16792 10.530100 0.0095242
GOTERM_BP_DIRECT GO:0085020~protein K6-linked ubiquitination 4 1.2269939 0.0002900 299 8 16792 28.080268 0.0113860
GOTERM_BP_DIRECT GO:0051983~regulation of chromosome segregation 4 1.2269939 0.0002900 299 8 16792 28.080268 0.0113860
GOTERM_BP_DIRECT GO:0051276~chromosome organization 5 1.5337423 0.0003053 299 19 16792 14.779088 0.0117106
GOTERM_BP_DIRECT GO:0006974~cellular response to DNA damage stimulus 13 3.9877301 0.0003512 299 208 16792 3.510033 0.0131735
GOTERM_BP_DIRECT GO:0031572~G2 DNA damage checkpoint 5 1.5337423 0.0003763 299 20 16792 14.040134 0.0138073
GOTERM_BP_DIRECT GO:1904668~positive regulation of ubiquitin protein ligase activity 4 1.2269939 0.0004294 299 9 16792 24.960238 0.0154204
GOTERM_BP_DIRECT GO:0032467~positive regulation of cytokinesis 6 1.8404908 0.0004658 299 37 16792 9.107114 0.0163793
GOTERM_BP_DIRECT GO:0042060~wound healing 8 2.4539877 0.0005427 299 80 16792 5.616053 0.0186950
GOTERM_BP_DIRECT GO:0034501~protein localization to kinetochore 4 1.2269939 0.0006053 299 10 16792 22.464214 0.0204358
GOTERM_BP_DIRECT GO:0051439~regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle 5 1.5337423 0.0006595 299 23 16792 12.208812 0.0218265
GOTERM_BP_DIRECT GO:0008284~positive regulation of cell proliferation 20 6.1349693 0.0006963 299 466 16792 2.410323 0.0226030
GOTERM_BP_DIRECT GO:0000278~mitotic cell cycle 6 1.8404908 0.0007557 299 41 16792 8.218615 0.0239025
GOTERM_BP_DIRECT GO:0045737~positive regulation of cyclin-dependent protein serine/threonine kinase activity 5 1.5337423 0.0007804 299 24 16792 11.700112 0.0239025
GOTERM_BP_DIRECT GO:0007088~regulation of mitotic nuclear division 5 1.5337423 0.0007804 299 24 16792 11.700112 0.0239025
GOTERM_BP_DIRECT GO:0006977~DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest 7 2.1472393 0.0007930 299 62 16792 6.340706 0.0239025
GOTERM_BP_DIRECT GO:0071897~DNA biosynthetic process 5 1.5337423 0.0010677 299 26 16792 10.800103 0.0316197
GOTERM_BP_DIRECT GO:0019886~antigen processing and presentation of exogenous peptide antigen via MHC class II 8 2.4539877 0.0012498 299 92 16792 4.883525 0.0363728
GOTERM_BP_DIRECT GO:0006312~mitotic recombination 4 1.2269939 0.0013868 299 13 16792 17.280165 0.0396762
GOTERM_BP_DIRECT GO:0031100~organ regeneration 6 1.8404908 0.0014187 299 47 16792 7.169430 0.0399120
GOTERM_BP_DIRECT GO:0071456~cellular response to hypoxia 8 2.4539877 0.0016014 299 96 16792 4.680045 0.0443155
GOTERM_BP_DIRECT GO:1901796~regulation of signal transduction by p53 class mediator 9 2.7607362 0.0016668 299 124 16792 4.076168 0.0453798
GOTERM_BP_DIRECT GO:0036297~interstrand cross-link repair 6 1.8404908 0.0017135 299 49 16792 6.876800 0.0459115
GOTERM_BP_DIRECT GO:0007131~reciprocal meiotic recombination 5 1.5337423 0.0018513 299 30 16792 9.360089 0.0488269
GOTERM_CC_DIRECT GO:0005654~nucleoplasm 117 35.8895706 0.0000000 313 2784 18224 2.446899 0.0000000
GOTERM_CC_DIRECT GO:0000777~condensed chromosome kinetochore 19 5.8282209 0.0000000 313 87 18224 12.715508 0.0000000
GOTERM_CC_DIRECT GO:0000776~kinetochore 18 5.5214724 0.0000000 313 81 18224 12.938587 0.0000000
GOTERM_CC_DIRECT GO:0000775~chromosome, centromeric region 15 4.6012270 0.0000000 313 57 18224 15.322011 0.0000000
GOTERM_CC_DIRECT GO:0030496~midbody 20 6.1349693 0.0000000 313 129 18224 9.026921 0.0000000
GOTERM_CC_DIRECT GO:0005819~spindle 18 5.5214724 0.0000000 313 121 18224 8.661368 0.0000000
GOTERM_CC_DIRECT GO:0005634~nucleus 147 45.0920245 0.0000000 313 5415 18224 1.580586 0.0000000
GOTERM_CC_DIRECT GO:0051233~spindle midzone 9 2.7607362 0.0000000 313 19 18224 27.579620 0.0000000
GOTERM_CC_DIRECT GO:0005874~microtubule 25 7.6687117 0.0000000 313 311 18224 4.680357 0.0000000
GOTERM_CC_DIRECT GO:0005876~spindle microtubule 11 3.3742331 0.0000000 313 44 18224 14.555910 0.0000001
GOTERM_CC_DIRECT GO:0000922~spindle pole 15 4.6012270 0.0000000 313 109 18224 8.012428 0.0000001
GOTERM_CC_DIRECT GO:0005871~kinesin complex 11 3.3742331 0.0000000 313 53 18224 12.084152 0.0000004
GOTERM_CC_DIRECT GO:0005829~cytosol 97 29.7546012 0.0000000 313 3315 18224 1.703678 0.0000008
GOTERM_CC_DIRECT GO:0005737~cytoplasm 132 40.4907975 0.0000003 313 5222 18224 1.471758 0.0000050
GOTERM_CC_DIRECT GO:0005694~chromosome 12 3.6809816 0.0000019 313 105 18224 6.654130 0.0000325
GOTERM_CC_DIRECT GO:0005730~nucleolus 34 10.4294479 0.0000121 313 857 18224 2.309923 0.0001992
GOTERM_CC_DIRECT GO:0031012~extracellular matrix 18 5.5214724 0.0000148 313 296 18224 3.540627 0.0002244
GOTERM_CC_DIRECT GO:0005813~centrosome 22 6.7484663 0.0000154 313 426 18224 3.006855 0.0002244
GOTERM_CC_DIRECT GO:0000942~condensed nuclear chromosome outer kinetochore 4 1.2269939 0.0000196 313 4 18224 58.223642 0.0002717
GOTERM_CC_DIRECT GO:0000785~chromatin 10 3.0674847 0.0000215 313 89 18224 6.541982 0.0002833
GOTERM_CC_DIRECT GO:0000796~condensin complex 4 1.2269939 0.0000485 313 5 18224 46.578914 0.0005792
GOTERM_CC_DIRECT GO:0032133~chromosome passenger complex 4 1.2269939 0.0000485 313 5 18224 46.578914 0.0005792
GOTERM_CC_DIRECT GO:0000793~condensed chromosome 6 1.8404908 0.0000571 313 25 18224 13.973674 0.0006531
GOTERM_CC_DIRECT GO:0072686~mitotic spindle 7 2.1472393 0.0000651 313 41 18224 9.940622 0.0007138
GOTERM_CC_DIRECT GO:0000784~nuclear chromosome, telomeric region 11 3.3742331 0.0000815 313 130 18224 4.926616 0.0008574
GOTERM_CC_DIRECT GO:0015630~microtubule cytoskeleton 11 3.3742331 0.0001263 313 137 18224 4.674891 0.0012776
GOTERM_CC_DIRECT GO:0031298~replication fork protection complex 4 1.2269939 0.0001653 313 7 18224 33.270653 0.0016102
GOTERM_CC_DIRECT GO:0031390~Ctf18 RFC-like complex 4 1.2269939 0.0002611 313 8 18224 29.111821 0.0023682
GOTERM_CC_DIRECT GO:0000940~condensed chromosome outer kinetochore 4 1.2269939 0.0002611 313 8 18224 29.111821 0.0023682
GOTERM_CC_DIRECT GO:0042555~MCM complex 4 1.2269939 0.0003867 313 9 18224 25.877174 0.0033904
GOTERM_CC_DIRECT GO:0000811~GINS complex 3 0.9202454 0.0008666 313 3 18224 58.223642 0.0073521
GOTERM_CC_DIRECT GO:0048471~perinuclear region of cytoplasm 23 7.0552147 0.0010977 313 621 18224 2.156431 0.0090214
GOTERM_CC_DIRECT GO:0005815~microtubule organizing center 10 3.0674847 0.0013040 313 153 18224 3.805467 0.0103922
GOTERM_CC_DIRECT GO:0031262~Ndc80 complex 3 0.9202454 0.0017136 313 4 18224 43.667732 0.0132550
GOTERM_CC_DIRECT GO:0016020~membrane 56 17.1779141 0.0024491 313 2200 18224 1.482056 0.0184030
GOTERM_CC_DIRECT GO:0000779~condensed chromosome, centromeric region 3 0.9202454 0.0057966 313 7 18224 24.952990 0.0423472
GOTERM_CC_DIRECT GO:0000790~nuclear chromatin 10 3.0674847 0.0061501 313 193 18224 3.016769 0.0437158
GOTERM_CC_DIRECT GO:0016363~nuclear matrix 7 2.1472393 0.0064495 313 97 18224 4.201706 0.0446374
GOTERM_CC_DIRECT GO:0005680~anaphase-promoting complex 4 1.2269939 0.0068287 313 23 18224 10.125851 0.0460497
GOTERM_MF_DIRECT GO:0005515~protein binding 212 65.0306748 0.0000000 295 8785 16881 1.380926 0.0000000
GOTERM_MF_DIRECT GO:0005524~ATP binding 62 19.0184049 0.0000000 295 1495 16881 2.373158 0.0000000
GOTERM_MF_DIRECT GO:0008017~microtubule binding 19 5.8282209 0.0000000 295 208 16881 5.227168 0.0000036
GOTERM_MF_DIRECT GO:0003777~microtubule motor activity 12 3.6809816 0.0000001 295 80 16881 8.583559 0.0000139
GOTERM_MF_DIRECT GO:0043142~single-stranded DNA-dependent ATPase activity 6 1.8404908 0.0000004 295 10 16881 34.334237 0.0000302
GOTERM_MF_DIRECT GO:0003682~chromatin binding 23 7.0552147 0.0000015 295 391 16881 3.366102 0.0001027
GOTERM_MF_DIRECT GO:0003697~single-stranded DNA binding 11 3.3742331 0.0000050 295 93 16881 6.768398 0.0002957
GOTERM_MF_DIRECT GO:0008574~ATP-dependent microtubule motor activity, plus-end-directed 6 1.8404908 0.0000081 295 17 16881 20.196610 0.0004197
GOTERM_MF_DIRECT GO:0019901~protein kinase binding 20 6.1349693 0.0000349 295 376 16881 3.043815 0.0016147
GOTERM_MF_DIRECT GO:0003678~DNA helicase activity 6 1.8404908 0.0000502 295 24 16881 14.305932 0.0020868
GOTERM_MF_DIRECT GO:0043138~3-5 DNA helicase activity 4 1.2269939 0.0001738 295 7 16881 32.699274 0.0065715
GOTERM_MF_DIRECT GO:0003689~DNA clamp loader activity 4 1.2269939 0.0002744 295 8 16881 28.611864 0.0095140
GOTERM_MF_DIRECT GO:0016887~ATPase activity 12 3.6809816 0.0003725 295 183 16881 3.752376 0.0119193
GOTERM_MF_DIRECT GO:0003688~DNA replication origin binding 4 1.2269939 0.0007778 295 11 16881 20.808629 0.0231122
GOTERM_MF_DIRECT GO:0003677~DNA binding 47 14.4171779 0.0012349 295 1674 16881 1.606640 0.0326577
GOTERM_MF_DIRECT GO:0017048~Rho GTPase binding 5 1.5337423 0.0013271 295 28 16881 10.218523 0.0326577
GOTERM_MF_DIRECT GO:0042393~histone binding 9 2.7607362 0.0013346 295 122 16881 4.221423 0.0326577

It looks as if these results replicate more or less perfectly.

Try to reproduce with corrected background gene list

As the RNA-seq data was on SRA (SRP158985), I was able to process it with DEE2 pipeline and find out which genes should be in the background list. The detection threshold was 10 reads per sample on average.

There were 16351 genes detected.

bge <- readLines("PMC6535219_bge.txt")
head(bge)
## [1] "ENSG00000227232" "ENSG00000233750" "ENSG00000268903" "ENSG00000269981"
## [5] "ENSG00000241860" "ENSG00000279457"
length(bge)
## [1] 16351

Then I ran DAVID again using the correct background. Here is the result of the upregulated genes.

repl2up <- read.table("PMC6535219_repl2_up.tsv",header=TRUE,sep="\t")

repl2up %>% kbl(caption="Upregulated GO terms obtained using article gene list with a background") %>% kable_paper("hover", full_width = F)
Upregulated GO terms obtained using article gene list with a background
Category Term Count X. PValue List.Total Pop.Hits Pop.Total Fold.Enrichment FDR
GOTERM_BP_DIRECT GO:0008544~epidermis development 25 5.387931 0.0000000 398 60 11485 12.023660 0.0000000
GOTERM_BP_DIRECT GO:0030216~keratinocyte differentiation 24 5.172414 0.0000000 398 55 11485 12.592051 0.0000000
GOTERM_BP_DIRECT GO:0031424~keratinization 17 3.663793 0.0000000 398 30 11485 16.352178 0.0000000
GOTERM_BP_DIRECT GO:0018149~peptide cross-linking 16 3.448276 0.0000000 398 28 11485 16.489591 0.0000000
GOTERM_BP_DIRECT GO:0060337~type I interferon signaling pathway 16 3.448276 0.0000000 398 47 11485 9.823586 0.0000000
GOTERM_BP_DIRECT GO:0051607~defense response to virus 20 4.310345 0.0000000 398 115 11485 5.018571 0.0000038
GOTERM_BP_DIRECT GO:0006334~nucleosome assembly 15 3.232759 0.0000000 398 63 11485 6.870663 0.0000056
GOTERM_BP_DIRECT GO:0045087~innate immune response 28 6.034483 0.0000000 398 232 11485 3.482715 0.0000068
GOTERM_BP_DIRECT GO:0009615~response to virus 16 3.448276 0.0000001 398 79 11485 5.844412 0.0000130
GOTERM_BP_DIRECT GO:0006955~immune response 24 5.172414 0.0000001 398 183 11485 3.784496 0.0000142
GOTERM_BP_DIRECT GO:0060333~interferon-gamma-mediated signaling pathway 13 2.801724 0.0000003 398 56 11485 6.698896 0.0000560
GOTERM_BP_DIRECT GO:0045071~negative regulation of viral genome replication 10 2.155172 0.0000016 398 34 11485 8.487289 0.0002317
GOTERM_BP_DIRECT GO:0002504~antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 6 1.293103 0.0000187 398 11 11485 15.740064 0.0023732
GOTERM_BP_DIRECT GO:0032200~telomere organization 6 1.293103 0.0000187 398 11 11485 15.740064 0.0023732
GOTERM_BP_DIRECT GO:0006508~proteolysis 25 5.387931 0.0000202 398 269 11485 2.681857 0.0023947
GOTERM_BP_DIRECT GO:0044267~cellular protein metabolic process 11 2.370690 0.0000219 398 57 11485 5.568853 0.0024349
GOTERM_BP_DIRECT GO:0044597~daunorubicin metabolic process 5 1.077586 0.0000453 398 7 11485 20.611988 0.0044683
GOTERM_BP_DIRECT GO:0044598~doxorubicin metabolic process 5 1.077586 0.0000453 398 7 11485 20.611988 0.0044683
GOTERM_BP_DIRECT GO:0010951~negative regulation of endopeptidase activity 11 2.370690 0.0000621 398 64 11485 4.959760 0.0057976
GOTERM_BP_DIRECT GO:0032496~response to lipopolysaccharide 14 3.017241 0.0000711 398 106 11485 3.811273 0.0063132
GOTERM_BP_DIRECT GO:0030855~epithelial cell differentiation 10 2.155172 0.0000999 398 55 11485 5.246688 0.0084399
GOTERM_BP_DIRECT GO:0050830~defense response to Gram-positive bacterium 9 1.939655 0.0001332 398 45 11485 5.771357 0.0107471
GOTERM_BP_DIRECT GO:0006335~DNA replication-dependent nucleosome assembly 6 1.293103 0.0001533 398 16 11485 10.821294 0.0118327
GOTERM_BP_DIRECT GO:0000183~chromatin silencing at rDNA 6 1.293103 0.0002840 398 18 11485 9.618928 0.0201662
GOTERM_BP_DIRECT GO:0061436~establishment of skin barrier 6 1.293103 0.0002840 398 18 11485 9.618928 0.0201662
GOTERM_BP_DIRECT GO:0051591~response to cAMP 7 1.508621 0.0003241 398 28 11485 7.214196 0.0221277
GOTERM_BP_DIRECT GO:0002227~innate immune response in mucosa 5 1.077586 0.0003825 398 11 11485 13.116720 0.0237776
GOTERM_BP_DIRECT GO:0042574~retinal metabolic process 5 1.077586 0.0003825 398 11 11485 13.116720 0.0237776
GOTERM_BP_DIRECT GO:0019882~antigen processing and presentation 8 1.724138 0.0003885 398 40 11485 5.771357 0.0237776
GOTERM_BP_DIRECT GO:0008202~steroid metabolic process 6 1.293103 0.0004854 398 20 11485 8.657035 0.0277950
GOTERM_BP_DIRECT GO:0019731~antibacterial humoral response 6 1.293103 0.0004854 398 20 11485 8.657035 0.0277950
GOTERM_BP_DIRECT GO:0007267~cell-cell signaling 13 2.801724 0.0005212 398 113 11485 3.319807 0.0289110
GOTERM_BP_DIRECT GO:0042448~progesterone metabolic process 4 0.862069 0.0007584 398 6 11485 19.237856 0.0406596
GOTERM_BP_DIRECT GO:0042572~retinol metabolic process 6 1.293103 0.0007788 398 22 11485 7.870032 0.0406596
GOTERM_BP_DIRECT GO:0001523~retinoid metabolic process 7 1.508621 0.0008234 398 33 11485 6.121136 0.0417600
GOTERM_BP_DIRECT GO:0030593~neutrophil chemotaxis 7 1.508621 0.0009712 398 34 11485 5.941103 0.0478840
GOTERM_CC_DIRECT GO:0001533~cornified envelope 19 4.094828 0.0000000 421 29 12206 18.995331 0.0000000
GOTERM_CC_DIRECT GO:0005615~extracellular space 73 15.732759 0.0000000 421 695 12206 3.045295 0.0000000
GOTERM_CC_DIRECT GO:0005576~extracellular region 66 14.224138 0.0000000 421 662 12206 2.890528 0.0000000
GOTERM_CC_DIRECT GO:0070062~extracellular exosome 132 28.448276 0.0000000 421 2119 12206 1.806069 0.0000000
GOTERM_CC_DIRECT GO:0000786~nucleosome 16 3.448276 0.0000000 421 43 12206 10.788046 0.0000000
GOTERM_CC_DIRECT GO:0000788~nuclear nucleosome 9 1.939655 0.0000002 421 20 12206 13.046793 0.0000060
GOTERM_CC_DIRECT GO:0005882~intermediate filament 12 2.586207 0.0000005 421 48 12206 7.248219 0.0000161
GOTERM_CC_DIRECT GO:0005886~plasma membrane 119 25.646552 0.0000028 421 2322 12206 1.485854 0.0000779
GOTERM_CC_DIRECT GO:0030057~desmosome 7 1.508621 0.0000412 421 20 12206 10.147506 0.0010247
GOTERM_CC_DIRECT GO:0042613~MHC class II protein complex 6 1.293103 0.0000729 421 14 12206 12.425517 0.0016332
GOTERM_CC_DIRECT GO:0031012~extracellular matrix 20 4.310345 0.0000849 421 205 12206 2.828573 0.0017279
GOTERM_CC_DIRECT GO:0030666~endocytic vesicle membrane 9 1.939655 0.0001097 421 44 12206 5.930361 0.0020472
GOTERM_CC_DIRECT GO:0030658~transport vesicle membrane 7 1.508621 0.0001272 421 24 12206 8.456255 0.0021915
GOTERM_CC_DIRECT GO:0097209~epidermal lamellar body 4 0.862069 0.0001577 421 4 12206 28.992874 0.0024271
GOTERM_CC_DIRECT GO:0045095~keratin filament 7 1.508621 0.0001625 421 25 12206 8.118005 0.0024271
GOTERM_CC_DIRECT GO:0030669~clathrin-coated endocytic vesicle membrane 7 1.508621 0.0003880 421 29 12206 6.998280 0.0054313
GOTERM_CC_DIRECT GO:0005887~integral component of plasma membrane 42 9.051724 0.0007463 421 709 12206 1.717490 0.0098337
GOTERM_CC_DIRECT GO:0071556~integral component of lumenal side of endoplasmic reticulum membrane 6 1.293103 0.0011648 421 24 12206 7.248219 0.0139197
GOTERM_CC_DIRECT GO:0031225~anchored component of membrane 8 1.724138 0.0011807 421 48 12206 4.832146 0.0139197
GOTERM_CC_DIRECT GO:0016021~integral component of membrane 128 27.586207 0.0022975 421 2951 12206 1.257570 0.0257318
GOTERM_CC_DIRECT GO:0005922~connexon complex 4 0.862069 0.0029103 421 9 12206 12.885722 0.0310436
GOTERM_MF_DIRECT GO:0005198~structural molecule activity 25 5.387931 0.0000000 398 142 11625 5.142349 0.0000000
GOTERM_MF_DIRECT GO:0004252~serine-type endopeptidase activity 19 4.094828 0.0000000 398 103 11625 5.387984 0.0000027
GOTERM_MF_DIRECT GO:0005509~calcium ion binding 37 7.974138 0.0000025 398 457 11625 2.364805 0.0004327
GOTERM_MF_DIRECT GO:0050786~RAGE receptor binding 6 1.293103 0.0000051 398 9 11625 19.472362 0.0006676
GOTERM_MF_DIRECT GO:0004867~serine-type endopeptidase inhibitor activity 10 2.155172 0.0000172 398 45 11625 6.490787 0.0015418
GOTERM_MF_DIRECT GO:0032395~MHC class II receptor activity 6 1.293103 0.0000177 398 11 11625 15.931932 0.0015418
GOTERM_MF_DIRECT GO:0008236~serine-type peptidase activity 8 1.724138 0.0001243 398 34 11625 6.872598 0.0093077
GOTERM_MF_DIRECT GO:0004745~retinol dehydrogenase activity 5 1.077586 0.0005332 398 12 11625 12.170226 0.0341224
GOTERM_MF_DIRECT GO:0042605~peptide antigen binding 6 1.293103 0.0005861 398 21 11625 8.345298 0.0341224
GOTERM_MF_DIRECT GO:0004032~alditol:NADP+ 1-oxidoreductase activity 4 0.862069 0.0007321 398 6 11625 19.472362 0.0371024
GOTERM_MF_DIRECT GO:0046982~protein heterodimerization activity 24 5.172414 0.0007789 398 325 11625 2.156938 0.0371024 
repl2dn <- read.table("PMC6535219_repl2_dn.tsv",header=TRUE,sep="\t")

repl2dn %>% kbl(caption="Downregulated GO terms obtained using article gene list with a background") %>% kable_paper("hover", full_width = F)
Downregulated GO terms obtained using article gene list with a background
Category Term Count X. PValue List.Total Pop.Hits Pop.Total Fold.Enrichment FDR
GOTERM_BP_DIRECT GO:0051301~cell division 53 16.2576687 0.0000000 299 350 16792 8.504310 0.0000000
GOTERM_BP_DIRECT GO:0007067~mitotic nuclear division 41 12.5766871 0.0000000 299 248 16792 9.284605 0.0000000
GOTERM_BP_DIRECT GO:0006260~DNA replication 30 9.2024540 0.0000000 299 155 16792 10.869781 0.0000000
GOTERM_BP_DIRECT GO:0007062~sister chromatid cohesion 24 7.3619632 0.0000000 299 103 16792 13.085950 0.0000000
GOTERM_BP_DIRECT GO:0000082~G1/S transition of mitotic cell cycle 21 6.4417178 0.0000000 299 102 16792 11.562463 0.0000000
GOTERM_BP_DIRECT GO:0000070~mitotic sister chromatid segregation 12 3.6809816 0.0000000 299 25 16792 26.957057 0.0000000
GOTERM_BP_DIRECT GO:0007059~chromosome segregation 16 4.9079755 0.0000000 299 68 16792 13.214244 0.0000000
GOTERM_BP_DIRECT GO:0008283~cell proliferation 29 8.8957055 0.0000000 299 366 16792 4.449878 0.0000000
GOTERM_BP_DIRECT GO:0006270~DNA replication initiation 11 3.3742331 0.0000000 299 32 16792 19.305184 0.0000000
GOTERM_BP_DIRECT GO:0000086~G2/M transition of mitotic cell cycle 17 5.2147239 0.0000000 299 137 16792 6.968826 0.0000005
GOTERM_BP_DIRECT GO:0006281~DNA repair 21 6.4417178 0.0000000 299 235 16792 5.018601 0.0000012
GOTERM_BP_DIRECT GO:0000281~mitotic cytokinesis 9 2.7607362 0.0000000 299 29 16792 17.429132 0.0000039
GOTERM_BP_DIRECT GO:0000083~regulation of transcription involved in G1/S transition of mitotic cell cycle 8 2.4539877 0.0000001 299 23 16792 19.534099 0.0000129
GOTERM_BP_DIRECT GO:0007018~microtubule-based movement 12 3.6809816 0.0000002 299 81 16792 8.320079 0.0000222
GOTERM_BP_DIRECT GO:0007080~mitotic metaphase plate congression 9 2.7607362 0.0000002 299 37 16792 13.660671 0.0000249
GOTERM_BP_DIRECT GO:0006268~DNA unwinding involved in DNA replication 6 1.8404908 0.0000004 299 10 16792 33.696321 0.0000396
GOTERM_BP_DIRECT GO:0007019~microtubule depolymerization 6 1.8404908 0.0000004 299 10 16792 33.696321 0.0000396
GOTERM_BP_DIRECT GO:0051310~metaphase plate congression 6 1.8404908 0.0000012 299 12 16792 28.080268 0.0001142
GOTERM_BP_DIRECT GO:0000910~cytokinesis 9 2.7607362 0.0000018 299 48 16792 10.530100 0.0001621
GOTERM_BP_DIRECT GO:0000731~DNA synthesis involved in DNA repair 8 2.4539877 0.0000023 299 35 16792 12.836694 0.0001915
GOTERM_BP_DIRECT GO:0090307~mitotic spindle assembly 8 2.4539877 0.0000028 299 36 16792 12.480119 0.0002230
GOTERM_BP_DIRECT GO:0007076~mitotic chromosome condensation 6 1.8404908 0.0000044 299 15 16792 22.464214 0.0003242
GOTERM_BP_DIRECT GO:0006271~DNA strand elongation involved in DNA replication 6 1.8404908 0.0000044 299 15 16792 22.464214 0.0003242
GOTERM_BP_DIRECT GO:0000732~strand displacement 7 2.1472393 0.0000051 299 26 16792 15.120144 0.0003567
GOTERM_BP_DIRECT GO:0000724~double-strand break repair via homologous recombination 10 3.0674847 0.0000062 299 74 16792 7.589262 0.0004111
GOTERM_BP_DIRECT GO:0007051~spindle organization 6 1.8404908 0.0000063 299 16 16792 21.060201 0.0004111
GOTERM_BP_DIRECT GO:0007049~cell cycle 16 4.9079755 0.0000080 299 217 16792 4.140869 0.0004985
GOTERM_BP_DIRECT GO:0034080~CENP-A containing nucleosome assembly 8 2.4539877 0.0000096 299 43 16792 10.448472 0.0005804
GOTERM_BP_DIRECT GO:0031145~anaphase-promoting complex-dependent catabolic process 10 3.0674847 0.0000107 299 79 16792 7.108929 0.0006217
GOTERM_BP_DIRECT GO:0032508~DNA duplex unwinding 8 2.4539877 0.0000113 299 44 16792 10.211006 0.0006217
GOTERM_BP_DIRECT GO:0030071~regulation of mitotic metaphase/anaphase transition 5 1.5337423 0.0000114 299 9 16792 31.200297 0.0006217
GOTERM_BP_DIRECT GO:0051726~regulation of cell cycle 12 3.6809816 0.0000131 299 124 16792 5.434890 0.0006893
GOTERM_BP_DIRECT GO:0006302~double-strand break repair 9 2.7607362 0.0000211 299 66 16792 7.658255 0.0010527
GOTERM_BP_DIRECT GO:0007094~mitotic spindle assembly checkpoint 6 1.8404908 0.0000212 299 20 16792 16.848160 0.0010527
GOTERM_BP_DIRECT GO:0051382~kinetochore assembly 5 1.5337423 0.0000430 299 12 16792 23.400223 0.0020740
GOTERM_BP_DIRECT GO:0000079~regulation of cyclin-dependent protein serine/threonine kinase activity 7 2.1472393 0.0000592 299 39 16792 10.080096 0.0027756
GOTERM_BP_DIRECT GO:0042787~protein ubiquitination involved in ubiquitin-dependent protein catabolic process 12 3.6809816 0.0000915 299 153 16792 4.404748 0.0041755
GOTERM_BP_DIRECT GO:0030335~positive regulation of cell migration 13 3.9877301 0.0001126 299 184 16792 3.967864 0.0050007
GOTERM_BP_DIRECT GO:0007052~mitotic spindle organization 6 1.8404908 0.0001685 299 30 16792 11.232107 0.0072941
GOTERM_BP_DIRECT GO:1900264~positive regulation of DNA-directed DNA polymerase activity 4 1.2269939 0.0001837 299 7 16792 32.091734 0.0077517
GOTERM_BP_DIRECT GO:0000722~telomere maintenance via recombination 6 1.8404908 0.0002313 299 32 16792 10.530100 0.0095242
GOTERM_BP_DIRECT GO:0085020~protein K6-linked ubiquitination 4 1.2269939 0.0002900 299 8 16792 28.080268 0.0113860
GOTERM_BP_DIRECT GO:0051983~regulation of chromosome segregation 4 1.2269939 0.0002900 299 8 16792 28.080268 0.0113860
GOTERM_BP_DIRECT GO:0051276~chromosome organization 5 1.5337423 0.0003053 299 19 16792 14.779088 0.0117106
GOTERM_BP_DIRECT GO:0006974~cellular response to DNA damage stimulus 13 3.9877301 0.0003512 299 208 16792 3.510033 0.0131735
GOTERM_BP_DIRECT GO:0031572~G2 DNA damage checkpoint 5 1.5337423 0.0003763 299 20 16792 14.040134 0.0138073
GOTERM_BP_DIRECT GO:1904668~positive regulation of ubiquitin protein ligase activity 4 1.2269939 0.0004294 299 9 16792 24.960238 0.0154204
GOTERM_BP_DIRECT GO:0032467~positive regulation of cytokinesis 6 1.8404908 0.0004658 299 37 16792 9.107114 0.0163793
GOTERM_BP_DIRECT GO:0042060~wound healing 8 2.4539877 0.0005427 299 80 16792 5.616053 0.0186950
GOTERM_BP_DIRECT GO:0034501~protein localization to kinetochore 4 1.2269939 0.0006053 299 10 16792 22.464214 0.0204358
GOTERM_BP_DIRECT GO:0051439~regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle 5 1.5337423 0.0006595 299 23 16792 12.208812 0.0218265
GOTERM_BP_DIRECT GO:0008284~positive regulation of cell proliferation 20 6.1349693 0.0006963 299 466 16792 2.410323 0.0226030
GOTERM_BP_DIRECT GO:0000278~mitotic cell cycle 6 1.8404908 0.0007557 299 41 16792 8.218615 0.0239025
GOTERM_BP_DIRECT GO:0007088~regulation of mitotic nuclear division 5 1.5337423 0.0007804 299 24 16792 11.700112 0.0239025
GOTERM_BP_DIRECT GO:0045737~positive regulation of cyclin-dependent protein serine/threonine kinase activity 5 1.5337423 0.0007804 299 24 16792 11.700112 0.0239025
GOTERM_BP_DIRECT GO:0006977~DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest 7 2.1472393 0.0007930 299 62 16792 6.340706 0.0239025
GOTERM_BP_DIRECT GO:0071897~DNA biosynthetic process 5 1.5337423 0.0010677 299 26 16792 10.800103 0.0316197
GOTERM_BP_DIRECT GO:0019886~antigen processing and presentation of exogenous peptide antigen via MHC class II 8 2.4539877 0.0012498 299 92 16792 4.883525 0.0363728
GOTERM_BP_DIRECT GO:0006312~mitotic recombination 4 1.2269939 0.0013868 299 13 16792 17.280165 0.0396762
GOTERM_BP_DIRECT GO:0031100~organ regeneration 6 1.8404908 0.0014187 299 47 16792 7.169430 0.0399120
GOTERM_BP_DIRECT GO:0071456~cellular response to hypoxia 8 2.4539877 0.0016014 299 96 16792 4.680045 0.0443155
GOTERM_BP_DIRECT GO:1901796~regulation of signal transduction by p53 class mediator 9 2.7607362 0.0016668 299 124 16792 4.076168 0.0453798
GOTERM_BP_DIRECT GO:0036297~interstrand cross-link repair 6 1.8404908 0.0017135 299 49 16792 6.876800 0.0459115
GOTERM_BP_DIRECT GO:0007131~reciprocal meiotic recombination 5 1.5337423 0.0018513 299 30 16792 9.360089 0.0488269
GOTERM_CC_DIRECT GO:0005654~nucleoplasm 117 35.8895706 0.0000000 313 2784 18224 2.446899 0.0000000
GOTERM_CC_DIRECT GO:0000777~condensed chromosome kinetochore 19 5.8282209 0.0000000 313 87 18224 12.715508 0.0000000
GOTERM_CC_DIRECT GO:0000776~kinetochore 18 5.5214724 0.0000000 313 81 18224 12.938587 0.0000000
GOTERM_CC_DIRECT GO:0000775~chromosome, centromeric region 15 4.6012270 0.0000000 313 57 18224 15.322011 0.0000000
GOTERM_CC_DIRECT GO:0030496~midbody 20 6.1349693 0.0000000 313 129 18224 9.026921 0.0000000
GOTERM_CC_DIRECT GO:0005819~spindle 18 5.5214724 0.0000000 313 121 18224 8.661368 0.0000000
GOTERM_CC_DIRECT GO:0005634~nucleus 147 45.0920245 0.0000000 313 5415 18224 1.580586 0.0000000
GOTERM_CC_DIRECT GO:0051233~spindle midzone 9 2.7607362 0.0000000 313 19 18224 27.579620 0.0000000
GOTERM_CC_DIRECT GO:0005874~microtubule 25 7.6687117 0.0000000 313 311 18224 4.680357 0.0000000
GOTERM_CC_DIRECT GO:0005876~spindle microtubule 11 3.3742331 0.0000000 313 44 18224 14.555910 0.0000001
GOTERM_CC_DIRECT GO:0000922~spindle pole 15 4.6012270 0.0000000 313 109 18224 8.012428 0.0000001
GOTERM_CC_DIRECT GO:0005871~kinesin complex 11 3.3742331 0.0000000 313 53 18224 12.084152 0.0000004
GOTERM_CC_DIRECT GO:0005829~cytosol 97 29.7546012 0.0000000 313 3315 18224 1.703678 0.0000008
GOTERM_CC_DIRECT GO:0005737~cytoplasm 132 40.4907975 0.0000003 313 5222 18224 1.471758 0.0000050
GOTERM_CC_DIRECT GO:0005694~chromosome 12 3.6809816 0.0000019 313 105 18224 6.654130 0.0000325
GOTERM_CC_DIRECT GO:0005730~nucleolus 34 10.4294479 0.0000121 313 857 18224 2.309923 0.0001992
GOTERM_CC_DIRECT GO:0031012~extracellular matrix 18 5.5214724 0.0000148 313 296 18224 3.540627 0.0002244
GOTERM_CC_DIRECT GO:0005813~centrosome 22 6.7484663 0.0000154 313 426 18224 3.006855 0.0002244
GOTERM_CC_DIRECT GO:0000942~condensed nuclear chromosome outer kinetochore 4 1.2269939 0.0000196 313 4 18224 58.223642 0.0002717
GOTERM_CC_DIRECT GO:0000785~chromatin 10 3.0674847 0.0000215 313 89 18224 6.541982 0.0002833
GOTERM_CC_DIRECT GO:0000796~condensin complex 4 1.2269939 0.0000485 313 5 18224 46.578914 0.0005792
GOTERM_CC_DIRECT GO:0032133~chromosome passenger complex 4 1.2269939 0.0000485 313 5 18224 46.578914 0.0005792
GOTERM_CC_DIRECT GO:0000793~condensed chromosome 6 1.8404908 0.0000571 313 25 18224 13.973674 0.0006531
GOTERM_CC_DIRECT GO:0072686~mitotic spindle 7 2.1472393 0.0000651 313 41 18224 9.940622 0.0007138
GOTERM_CC_DIRECT GO:0000784~nuclear chromosome, telomeric region 11 3.3742331 0.0000815 313 130 18224 4.926616 0.0008574
GOTERM_CC_DIRECT GO:0015630~microtubule cytoskeleton 11 3.3742331 0.0001263 313 137 18224 4.674891 0.0012776
GOTERM_CC_DIRECT GO:0031298~replication fork protection complex 4 1.2269939 0.0001653 313 7 18224 33.270653 0.0016102
GOTERM_CC_DIRECT GO:0031390~Ctf18 RFC-like complex 4 1.2269939 0.0002611 313 8 18224 29.111821 0.0023682
GOTERM_CC_DIRECT GO:0000940~condensed chromosome outer kinetochore 4 1.2269939 0.0002611 313 8 18224 29.111821 0.0023682
GOTERM_CC_DIRECT GO:0042555~MCM complex 4 1.2269939 0.0003867 313 9 18224 25.877174 0.0033904
GOTERM_CC_DIRECT GO:0000811~GINS complex 3 0.9202454 0.0008666 313 3 18224 58.223642 0.0073521
GOTERM_CC_DIRECT GO:0048471~perinuclear region of cytoplasm 23 7.0552147 0.0010977 313 621 18224 2.156431 0.0090214
GOTERM_CC_DIRECT GO:0005815~microtubule organizing center 10 3.0674847 0.0013040 313 153 18224 3.805467 0.0103922
GOTERM_CC_DIRECT GO:0031262~Ndc80 complex 3 0.9202454 0.0017136 313 4 18224 43.667732 0.0132550
GOTERM_CC_DIRECT GO:0016020~membrane 56 17.1779141 0.0024491 313 2200 18224 1.482056 0.0184030
GOTERM_CC_DIRECT GO:0000779~condensed chromosome, centromeric region 3 0.9202454 0.0057966 313 7 18224 24.952990 0.0423472
GOTERM_CC_DIRECT GO:0000790~nuclear chromatin 10 3.0674847 0.0061501 313 193 18224 3.016769 0.0437158
GOTERM_CC_DIRECT GO:0016363~nuclear matrix 7 2.1472393 0.0064495 313 97 18224 4.201706 0.0446374
GOTERM_CC_DIRECT GO:0005680~anaphase-promoting complex 4 1.2269939 0.0068287 313 23 18224 10.125851 0.0460497
GOTERM_MF_DIRECT GO:0005515~protein binding 212 65.0306748 0.0000000 295 8785 16881 1.380926 0.0000000
GOTERM_MF_DIRECT GO:0005524~ATP binding 62 19.0184049 0.0000000 295 1495 16881 2.373158 0.0000000
GOTERM_MF_DIRECT GO:0008017~microtubule binding 19 5.8282209 0.0000000 295 208 16881 5.227168 0.0000036
GOTERM_MF_DIRECT GO:0003777~microtubule motor activity 12 3.6809816 0.0000001 295 80 16881 8.583559 0.0000139
GOTERM_MF_DIRECT GO:0043142~single-stranded DNA-dependent ATPase activity 6 1.8404908 0.0000004 295 10 16881 34.334237 0.0000302
GOTERM_MF_DIRECT GO:0003682~chromatin binding 23 7.0552147 0.0000015 295 391 16881 3.366102 0.0001027
GOTERM_MF_DIRECT GO:0003697~single-stranded DNA binding 11 3.3742331 0.0000050 295 93 16881 6.768398 0.0002957
GOTERM_MF_DIRECT GO:0008574~ATP-dependent microtubule motor activity, plus-end-directed 6 1.8404908 0.0000081 295 17 16881 20.196610 0.0004197
GOTERM_MF_DIRECT GO:0019901~protein kinase binding 20 6.1349693 0.0000349 295 376 16881 3.043815 0.0016147
GOTERM_MF_DIRECT GO:0003678~DNA helicase activity 6 1.8404908 0.0000502 295 24 16881 14.305932 0.0020868
GOTERM_MF_DIRECT GO:0043138~3-5 DNA helicase activity 4 1.2269939 0.0001738 295 7 16881 32.699274 0.0065715
GOTERM_MF_DIRECT GO:0003689~DNA clamp loader activity 4 1.2269939 0.0002744 295 8 16881 28.611864 0.0095140
GOTERM_MF_DIRECT GO:0016887~ATPase activity 12 3.6809816 0.0003725 295 183 16881 3.752376 0.0119193
GOTERM_MF_DIRECT GO:0003688~DNA replication origin binding 4 1.2269939 0.0007778 295 11 16881 20.808629 0.0231122
GOTERM_MF_DIRECT GO:0003677~DNA binding 47 14.4171779 0.0012349 295 1674 16881 1.606640 0.0326577
GOTERM_MF_DIRECT GO:0017048~Rho GTPase binding 5 1.5337423 0.0013271 295 28 16881 10.218523 0.0326577
GOTERM_MF_DIRECT GO:0042393~histone binding 9 2.7607362 0.0013346 295 122 16881 4.221423 0.0326577

What about a replication using an R script

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.

# from supp table 2
upg <- readLines("PMC6535219_up.txt")
dng <- readLines("PMC6535219_dn.txt")
geneinfo <- read.table("http://dee2.io/data/hsapiens/hsa_gene_info.tsv",header=TRUE)
upe <- geneinfo[which(geneinfo$GeneSymbol %in% upg),"GeneID"]
dne <- geneinfo[which(geneinfo$GeneSymbol %in% dng),"GeneID"]

# up
go_up <- enrichGO(gene = upe,  keyType = "ENSEMBL", universe = bge,
    OrgDb = org.Hs.eg.db, ont = "ALL", pAdjustMethod = "BH", pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05, readable = TRUE)

go_up <- data.frame(go_up)
nrow(go_up)
## [1] 170
go_up[,c(1:8,10)] %>% kbl(caption="Upregulated GO terms obtained using clusterProfiler with the correct background") %>% kable_paper("hover", full_width = F)
Upregulated GO terms obtained using clusterProfiler with the correct background
ONTOLOGY ID Description GeneRatio BgRatio pvalue p.adjust qvalue Count
GO:0031424 BP GO:0031424 keratinization 43/434 88/12234 0.0000000 0.0000000 0.0000000 43
GO:0030216 BP GO:0030216 keratinocyte differentiation 53/434 159/12234 0.0000000 0.0000000 0.0000000 53
GO:0070268 BP GO:0070268 cornification 38/434 73/12234 0.0000000 0.0000000 0.0000000 38
GO:0009913 BP GO:0009913 epidermal cell differentiation 57/434 201/12234 0.0000000 0.0000000 0.0000000 57
GO:0008544 BP GO:0008544 epidermis development 65/434 288/12234 0.0000000 0.0000000 0.0000000 65
GO:0043588 BP GO:0043588 skin development 57/434 253/12234 0.0000000 0.0000000 0.0000000 57
GO:0030855 BP GO:0030855 epithelial cell differentiation 76/434 494/12234 0.0000000 0.0000000 0.0000000 76
GO:0019730 BP GO:0019730 antimicrobial humoral response 21/434 60/12234 0.0000000 0.0000000 0.0000000 21
GO:0006959 BP GO:0006959 humoral immune response 28/434 122/12234 0.0000000 0.0000000 0.0000000 28
GO:0042742 BP GO:0042742 defense response to bacterium 26/434 120/12234 0.0000000 0.0000000 0.0000000 26
GO:0061844 BP GO:0061844 antimicrobial humoral immune response mediated by antimicrobial peptide 15/434 35/12234 0.0000000 0.0000000 0.0000000 15
GO:0009617 BP GO:0009617 response to bacterium 42/434 365/12234 0.0000000 0.0000000 0.0000000 42
GO:0018149 BP GO:0018149 peptide cross-linking 11/434 23/12234 0.0000000 0.0000000 0.0000000 11
GO:0034308 BP GO:0034308 primary alcohol metabolic process 15/434 64/12234 0.0000000 0.0000012 0.0000011 15
GO:0060337 BP GO:0060337 type I interferon signaling pathway 16/434 75/12234 0.0000000 0.0000013 0.0000012 16
GO:0071357 BP GO:0071357 cellular response to type I interferon 16/434 75/12234 0.0000000 0.0000013 0.0000012 16
GO:0042572 BP GO:0042572 retinol metabolic process 11/434 32/12234 0.0000000 0.0000014 0.0000013 11
GO:0034340 BP GO:0034340 response to type I interferon 16/434 80/12234 0.0000000 0.0000032 0.0000030 16
GO:0019731 BP GO:0019731 antibacterial humoral response 10/434 28/12234 0.0000000 0.0000039 0.0000036 10
GO:0009615 BP GO:0009615 response to virus 30/434 267/12234 0.0000000 0.0000039 0.0000036 30
GO:0051607 BP GO:0051607 defense response to virus 25/434 195/12234 0.0000000 0.0000040 0.0000038 25
GO:0140546 BP GO:0140546 defense response to symbiont 25/434 195/12234 0.0000000 0.0000040 0.0000038 25
GO:0001523 BP GO:0001523 retinoid metabolic process 14/434 63/12234 0.0000000 0.0000048 0.0000045 14
GO:0034754 BP GO:0034754 cellular hormone metabolic process 16/434 86/12234 0.0000000 0.0000071 0.0000066 16
GO:0016101 BP GO:0016101 diterpenoid metabolic process 14/434 67/12234 0.0000001 0.0000102 0.0000095 14
GO:0071346 BP GO:0071346 cellular response to interferon-gamma 19/434 125/12234 0.0000001 0.0000110 0.0000103 19
GO:0034341 BP GO:0034341 response to interferon-gamma 20/434 140/12234 0.0000001 0.0000139 0.0000130 20
GO:0048525 BP GO:0048525 negative regulation of viral process 14/434 73/12234 0.0000002 0.0000274 0.0000255 14
GO:0060333 BP GO:0060333 interferon-gamma-mediated signaling pathway 14/434 73/12234 0.0000002 0.0000274 0.0000255 14
GO:0006721 BP GO:0006721 terpenoid metabolic process 14/434 74/12234 0.0000003 0.0000316 0.0000294 14
GO:1903900 BP GO:1903900 regulation of viral life cycle 18/434 122/12234 0.0000003 0.0000323 0.0000300 18
GO:0045071 BP GO:0045071 negative regulation of viral genome replication 11/434 45/12234 0.0000003 0.0000378 0.0000352 11
GO:0042445 BP GO:0042445 hormone metabolic process 19/434 137/12234 0.0000004 0.0000382 0.0000356 19
GO:0006720 BP GO:0006720 isoprenoid metabolic process 15/434 91/12234 0.0000006 0.0000681 0.0000634 15
GO:0052548 BP GO:0052548 regulation of endopeptidase activity 29/434 296/12234 0.0000007 0.0000717 0.0000667 29
GO:0120254 BP GO:0120254 olefinic compound metabolic process 14/434 80/12234 0.0000007 0.0000717 0.0000667 14
GO:0052547 BP GO:0052547 regulation of peptidase activity 30/434 319/12234 0.0000011 0.0001059 0.0000986 30
GO:0043903 BP GO:0043903 regulation of biological process involved in symbiotic interaction 20/434 165/12234 0.0000015 0.0001463 0.0001361 20
GO:0050792 BP GO:0050792 regulation of viral process 19/434 157/12234 0.0000029 0.0002665 0.0002480 19
GO:0010466 BP GO:0010466 negative regulation of peptidase activity 18/434 147/12234 0.0000045 0.0003874 0.0003606 18
GO:0042574 BP GO:0042574 retinal metabolic process 6/434 14/12234 0.0000045 0.0003874 0.0003606 6
GO:1902644 BP GO:1902644 tertiary alcohol metabolic process 6/434 14/12234 0.0000045 0.0003874 0.0003606 6
GO:0006334 BP GO:0006334 nucleosome assembly 14/434 93/12234 0.0000046 0.0003874 0.0003606 14
GO:0050830 BP GO:0050830 defense response to Gram-positive bacterium 10/434 50/12234 0.0000082 0.0006676 0.0006213 10
GO:0010951 BP GO:0010951 negative regulation of endopeptidase activity 17/434 142/12234 0.0000111 0.0008520 0.0007929 17
GO:0006335 BP GO:0006335 DNA replication-dependent nucleosome assembly 6/434 16/12234 0.0000114 0.0008520 0.0007929 6
GO:0016137 BP GO:0016137 glycoside metabolic process 6/434 16/12234 0.0000114 0.0008520 0.0007929 6
GO:0034723 BP GO:0034723 DNA replication-dependent nucleosome organization 6/434 16/12234 0.0000114 0.0008520 0.0007929 6
GO:0042448 BP GO:0042448 progesterone metabolic process 5/434 10/12234 0.0000119 0.0008748 0.0008141 5
GO:0001906 BP GO:0001906 cell killing 13/434 88/12234 0.0000125 0.0008995 0.0008371 13
GO:0008207 BP GO:0008207 C21-steroid hormone metabolic process 7/434 24/12234 0.0000138 0.0009716 0.0009043 7
GO:0002697 BP GO:0002697 regulation of immune effector process 24/434 260/12234 0.0000180 0.0012410 0.0011550 24
GO:0045109 BP GO:0045109 intermediate filament organization 6/434 18/12234 0.0000249 0.0016836 0.0015669 6
GO:1901615 BP GO:1901615 organic hydroxy compound metabolic process 31/434 396/12234 0.0000308 0.0020481 0.0019060 31
GO:0045069 BP GO:0045069 regulation of viral genome replication 11/434 72/12234 0.0000423 0.0027621 0.0025705 11
GO:0052372 BP GO:0052372 modulation by symbiont of entry into host 8/434 38/12234 0.0000451 0.0028881 0.0026878 8
GO:0045104 BP GO:0045104 intermediate filament cytoskeleton organization 8/434 39/12234 0.0000549 0.0034603 0.0032204 8
GO:0000183 BP GO:0000183 rDNA heterochromatin assembly 6/434 21/12234 0.0000664 0.0040113 0.0037332 6
GO:0045103 BP GO:0045103 intermediate filament-based process 8/434 40/12234 0.0000666 0.0040113 0.0037332 8
GO:0006066 BP GO:0006066 alcohol metabolic process 24/434 282/12234 0.0000670 0.0040113 0.0037332 24
GO:0002548 BP GO:0002548 monocyte chemotaxis 7/434 31/12234 0.0000846 0.0048966 0.0045570 7
GO:0046596 BP GO:0046596 regulation of viral entry into host cell 7/434 31/12234 0.0000846 0.0048966 0.0045570 7
GO:0071677 BP GO:0071677 positive regulation of mononuclear cell migration 8/434 42/12234 0.0000960 0.0054713 0.0050919 8
GO:0034728 BP GO:0034728 nucleosome organization 14/434 123/12234 0.0001146 0.0064188 0.0059737 14
GO:0031640 BP GO:0031640 killing of cells of other organism 6/434 23/12234 0.0001162 0.0064188 0.0059737 6
GO:0002698 BP GO:0002698 negative regulation of immune effector process 11/434 81/12234 0.0001275 0.0069337 0.0064529 11
GO:0061436 BP GO:0061436 establishment of skin barrier 6/434 24/12234 0.0001504 0.0080564 0.0074977 6
GO:0045814 BP GO:0045814 negative regulation of gene expression, epigenetic 11/434 83/12234 0.0001593 0.0084080 0.0078250 11
GO:0051346 BP GO:0051346 negative regulation of hydrolase activity 24/434 301/12234 0.0001837 0.0095570 0.0088943 24
GO:0019748 BP GO:0019748 secondary metabolic process 7/434 36/12234 0.0002303 0.0118115 0.0109924 7
GO:0033561 BP GO:0033561 regulation of water loss via skin 6/434 26/12234 0.0002422 0.0122442 0.0113951 6
GO:0002227 BP GO:0002227 innate immune response in mucosa 4/434 10/12234 0.0002767 0.0128995 0.0120050 4
GO:0045591 BP GO:0045591 positive regulation of regulatory T cell differentiation 4/434 10/12234 0.0002767 0.0128995 0.0120050 4
GO:0046598 BP GO:0046598 positive regulation of viral entry into host cell 4/434 10/12234 0.0002767 0.0128995 0.0120050 4
GO:0051238 BP GO:0051238 sequestering of metal ion 4/434 10/12234 0.0002767 0.0128995 0.0120050 4
GO:0075294 BP GO:0075294 positive regulation by symbiont of entry into host 4/434 10/12234 0.0002767 0.0128995 0.0120050 4
GO:0090713 BP GO:0090713 immunological memory process 4/434 10/12234 0.0002767 0.0128995 0.0120050 4
GO:0010817 BP GO:0010817 regulation of hormone levels 25/434 330/12234 0.0002983 0.0137301 0.0127780 25
GO:0042573 BP GO:0042573 retinoic acid metabolic process 5/434 18/12234 0.0003207 0.0145742 0.0135635 5
GO:0050777 BP GO:0050777 negative regulation of immune response 11/434 91/12234 0.0003622 0.0162541 0.0151270 11
GO:0006081 BP GO:0006081 cellular aldehyde metabolic process 8/434 51/12234 0.0003918 0.0173664 0.0161622 8
GO:0031497 BP GO:0031497 chromatin assembly 14/434 139/12234 0.0004160 0.0180151 0.0167658 14
GO:0019058 BP GO:0019058 viral life cycle 23/434 299/12234 0.0004165 0.0180151 0.0167658 23
GO:0006690 BP GO:0006690 icosanoid metabolic process 10/434 79/12234 0.0004586 0.0196017 0.0182424 10
GO:0019079 BP GO:0019079 viral genome replication 12/434 112/12234 0.0006081 0.0256814 0.0239005 12
GO:0070293 BP GO:0070293 renal absorption 4/434 12/12234 0.0006163 0.0257252 0.0239413 4
GO:0050891 BP GO:0050891 multicellular organismal water homeostasis 8/434 55/12234 0.0006621 0.0268810 0.0250170 8
GO:0030574 BP GO:0030574 collagen catabolic process 6/434 31/12234 0.0006664 0.0268810 0.0250170 6
GO:1901661 BP GO:1901661 quinone metabolic process 6/434 31/12234 0.0006664 0.0268810 0.0250170 6
GO:0097549 BP GO:0097549 chromatin organization involved in negative regulation of transcription 11/434 98/12234 0.0006870 0.0274029 0.0255027 11
GO:0034113 BP GO:0034113 heterotypic cell-cell adhesion 7/434 43/12234 0.0007179 0.0283198 0.0263560 7
GO:0022617 BP GO:0022617 extracellular matrix disassembly 8/434 56/12234 0.0007489 0.0292235 0.0271970 8
GO:0045861 BP GO:0045861 negative regulation of proteolysis 18/434 219/12234 0.0008089 0.0312254 0.0290601 18
GO:0042446 BP GO:0042446 hormone biosynthetic process 7/434 44/12234 0.0008280 0.0316238 0.0294308 7
GO:0016114 BP GO:0016114 terpenoid biosynthetic process 4/434 13/12234 0.0008653 0.0320268 0.0298059 4
GO:0050665 BP GO:0050665 hydrogen peroxide biosynthetic process 4/434 13/12234 0.0008653 0.0320268 0.0298059 4
GO:1903019 BP GO:1903019 negative regulation of glycoprotein metabolic process 4/434 13/12234 0.0008653 0.0320268 0.0298059 4
GO:0031347 BP GO:0031347 regulation of defense response 30/434 457/12234 0.0008753 0.0320655 0.0298419 30
GO:0030104 BP GO:0030104 water homeostasis 8/434 58/12234 0.0009501 0.0344516 0.0320625 8
GO:0051592 BP GO:0051592 response to calcium ion 11/434 104/12234 0.0011312 0.0406102 0.0377941 11
GO:0009636 BP GO:0009636 response to toxic substance 15/434 172/12234 0.0011934 0.0424180 0.0394765 15
GO:1901657 BP GO:1901657 glycosyl compound metabolic process 11/434 105/12234 0.0012243 0.0430899 0.0401019 11
GO:0030595 BP GO:0030595 leukocyte chemotaxis 13/434 138/12234 0.0012391 0.0431877 0.0401929 13
GO:0071466 BP GO:0071466 cellular response to xenobiotic stimulus 9/434 75/12234 0.0012909 0.0440379 0.0409841 9
GO:0071621 BP GO:0071621 granulocyte chemotaxis 9/434 75/12234 0.0012909 0.0440379 0.0409841 9
GO:0044409 BP GO:0044409 entry into host 12/434 122/12234 0.0013003 0.0440379 0.0409841 12
GO:0002286 BP GO:0002286 T cell activation involved in immune response 8/434 61/12234 0.0013306 0.0446450 0.0415491 8
GO:0071675 BP GO:0071675 regulation of mononuclear cell migration 9/434 76/12234 0.0014194 0.0471829 0.0439110 9
GO:0002920 BP GO:0002920 regulation of humoral immune response 6/434 36/12234 0.0015179 0.0499919 0.0465252 6
GO:0001533 CC GO:0001533 cornified envelope 21/441 35/12681 0.0000000 0.0000000 0.0000000 21
GO:0000786 CC GO:0000786 nucleosome 17/441 51/12681 0.0000000 0.0000000 0.0000000 17
GO:0044815 CC GO:0044815 DNA packaging complex 17/441 59/12681 0.0000000 0.0000000 0.0000000 17
GO:0005882 CC GO:0005882 intermediate filament 16/441 75/12681 0.0000000 0.0000003 0.0000003 16
GO:0045111 CC GO:0045111 intermediate filament cytoskeleton 18/441 111/12681 0.0000000 0.0000029 0.0000026 18
GO:0030057 CC GO:0030057 desmosome 8/441 21/12681 0.0000003 0.0000141 0.0000128 8
GO:0032993 CC GO:0032993 protein-DNA complex 19/441 139/12681 0.0000003 0.0000145 0.0000131 19
GO:0042613 CC GO:0042613 MHC class II protein complex 6/441 12/12681 0.0000013 0.0000509 0.0000461 6
GO:0045095 CC GO:0045095 keratin filament 7/441 25/12681 0.0000164 0.0005600 0.0005072 7
GO:0030669 CC GO:0030669 clathrin-coated endocytic vesicle membrane 7/441 27/12681 0.0000285 0.0008766 0.0007939 7
GO:0042599 CC GO:0042599 lamellar body 5/441 12/12681 0.0000322 0.0009007 0.0008157 5
GO:0042611 CC GO:0042611 MHC protein complex 6/441 20/12681 0.0000437 0.0011228 0.0010169 6
GO:0009986 CC GO:0009986 cell surface 33/441 462/12681 0.0000720 0.0017070 0.0015459 33
GO:0030312 CC GO:0030312 external encapsulating structure 25/441 316/12681 0.0001131 0.0023215 0.0021026 25
GO:0031012 CC GO:0031012 extracellular matrix 25/441 316/12681 0.0001131 0.0023215 0.0021026 25
GO:0071556 CC GO:0071556 integral component of lumenal side of endoplasmic reticulum membrane 6/441 24/12681 0.0001350 0.0024451 0.0022144 6
GO:0098553 CC GO:0098553 lumenal side of endoplasmic reticulum membrane 6/441 24/12681 0.0001350 0.0024451 0.0022144 6
GO:0062023 CC GO:0062023 collagen-containing extracellular matrix 20/441 240/12681 0.0002747 0.0047008 0.0042574 20
GO:0045334 CC GO:0045334 clathrin-coated endocytic vesicle 7/441 38/12681 0.0002906 0.0047101 0.0042658 7
GO:0098576 CC GO:0098576 lumenal side of membrane 6/441 30/12681 0.0004988 0.0076819 0.0069573 6
GO:0031225 CC GO:0031225 anchored component of membrane 10/441 90/12681 0.0011117 0.0163047 0.0147667 10
GO:0005921 CC GO:0005921 gap junction 4/441 17/12681 0.0023945 0.0335228 0.0303607 4
GO:0030665 CC GO:0030665 clathrin-coated vesicle membrane 9/441 88/12681 0.0034461 0.0461479 0.0417949 9
GO:0008106 MF GO:0008106 alcohol dehydrogenase (NADP+) activity 9/437 17/12535 0.0000000 0.0000007 0.0000007 9
GO:0004033 MF GO:0004033 aldo-keto reductase (NADP) activity 9/437 22/12535 0.0000000 0.0000049 0.0000044 9
GO:0004252 MF GO:0004252 serine-type endopeptidase activity 16/437 84/12535 0.0000000 0.0000049 0.0000044 16
GO:0008236 MF GO:0008236 serine-type peptidase activity 16/437 97/12535 0.0000002 0.0000279 0.0000252 16
GO:0017171 MF GO:0017171 serine hydrolase activity 16/437 98/12535 0.0000002 0.0000279 0.0000252 16
GO:0052650 MF GO:0052650 NADP-retinol dehydrogenase activity 6/437 11/12535 0.0000007 0.0000646 0.0000584 6
GO:0046982 MF GO:0046982 protein heterodimerization activity 24/437 232/12535 0.0000019 0.0001519 0.0001374 24
GO:0005509 MF GO:0005509 calcium ion binding 36/437 451/12535 0.0000031 0.0002081 0.0001882 36
GO:0004866 MF GO:0004866 endopeptidase inhibitor activity 14/437 92/12535 0.0000033 0.0002081 0.0001882 14
GO:0004867 MF GO:0004867 serine-type endopeptidase inhibitor activity 10/437 47/12535 0.0000039 0.0002184 0.0001975 10
GO:0030414 MF GO:0030414 peptidase inhibitor activity 14/437 94/12535 0.0000043 0.0002210 0.0001998 14
GO:0061135 MF GO:0061135 endopeptidase regulator activity 14/437 103/12535 0.0000129 0.0006009 0.0005434 14
GO:0004745 MF GO:0004745 retinol dehydrogenase activity 5/437 12/12535 0.0000325 0.0014044 0.0012701 5
GO:0048018 MF GO:0048018 receptor ligand activity 20/437 212/12535 0.0000520 0.0020839 0.0018847 20
GO:0042605 MF GO:0042605 peptide antigen binding 6/437 21/12535 0.0000603 0.0022496 0.0020345 6
GO:0061134 MF GO:0061134 peptidase regulator activity 15/437 134/12535 0.0000658 0.0022496 0.0020345 15
GO:0004857 MF GO:0004857 enzyme inhibitor activity 22/437 252/12535 0.0000720 0.0022496 0.0020345 22
GO:0030546 MF GO:0030546 signaling receptor activator activity 20/437 217/12535 0.0000722 0.0022496 0.0020345 20
GO:0016229 MF GO:0016229 steroid dehydrogenase activity 6/437 23/12535 0.0001056 0.0029401 0.0026590 6
GO:0048306 MF GO:0048306 calcium-dependent protein binding 9/437 55/12535 0.0001071 0.0029401 0.0026590 9
GO:0016616 MF GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 12/437 95/12535 0.0001101 0.0029401 0.0026590 12
GO:0004175 MF GO:0004175 endopeptidase activity 22/437 267/12535 0.0001675 0.0042716 0.0038632 22
GO:0030545 MF GO:0030545 receptor regulator activity 20/437 235/12535 0.0002143 0.0051046 0.0046166 20
GO:0016614 MF GO:0016614 oxidoreductase activity, acting on CH-OH group of donors 12/437 102/12535 0.0002184 0.0051046 0.0046166 12
GO:0033764 MF GO:0033764 steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 5/437 21/12535 0.0006447 0.0144675 0.0130844 5
GO:0016620 MF GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor 6/437 32/12535 0.0007270 0.0156855 0.0141860 6
GO:0008233 MF GO:0008233 peptidase activity 27/437 405/12535 0.0009732 0.0199793 0.0180693 27
GO:0003823 MF GO:0003823 antigen binding 6/437 34/12535 0.0010172 0.0199793 0.0180693 6
GO:0005125 MF GO:0005125 cytokine activity 11/437 105/12535 0.0010653 0.0199793 0.0180693 11
GO:0004303 MF GO:0004303 estradiol 17-beta-dehydrogenase activity 4/437 14/12535 0.0011040 0.0199793 0.0180693 4
GO:0038187 MF GO:0038187 pattern recognition receptor activity 4/437 14/12535 0.0011040 0.0199793 0.0180693 4
GO:0016628 MF GO:0016628 oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor 5/437 24/12535 0.0012354 0.0216584 0.0195879 5
GO:0005254 MF GO:0005254 chloride channel activity 6/437 38/12535 0.0018566 0.0304412 0.0275311 6
GO:0016903 MF GO:0016903 oxidoreductase activity, acting on the aldehyde or oxo group of donors 6/437 38/12535 0.0018566 0.0304412 0.0275311 6
GO:0022829 MF GO:0022829 wide pore channel activity 4/437 16/12535 0.0018992 0.0304412 0.0275311 4
GO:0004497 MF GO:0004497 monooxygenase activity 7/437 52/12535 0.0020554 0.0320297 0.0289676 7
GO:0005044 MF GO:0005044 scavenger receptor activity 5/437 29/12535 0.0029913 0.0441605 0.0399388 5
GO:0016709 MF GO:0016709 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen 5/437 29/12535 0.0029913 0.0441605 0.0399388 5 
# dn
go_dn <- enrichGO(gene = dne,  keyType = "ENSEMBL", universe = bge,
    OrgDb = org.Hs.eg.db, ont = "ALL", pAdjustMethod = "BH", pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05, readable = TRUE)

go_dn <- data.frame(go_dn)
nrow(go_dn)
## [1] 402
go_dn[,c(1:8,10)] %>% kbl(caption="Downregulated GO terms obtained using clusterProfiler with the correct background") %>% kable_paper("hover", full_width = F)
Downregulated GO terms obtained using clusterProfiler with the correct background
ONTOLOGY ID Description GeneRatio BgRatio pvalue p.adjust qvalue Count
GO:0000280 BP GO:0000280 nuclear division 66/298 361/12234 0.0000000 0.0000000 0.0000000 66
GO:0048285 BP GO:0048285 organelle fission 67/298 406/12234 0.0000000 0.0000000 0.0000000 67
GO:0140014 BP GO:0140014 mitotic nuclear division 56/298 273/12234 0.0000000 0.0000000 0.0000000 56
GO:0007059 BP GO:0007059 chromosome segregation 56/298 287/12234 0.0000000 0.0000000 0.0000000 56
GO:0000819 BP GO:0000819 sister chromatid segregation 43/298 180/12234 0.0000000 0.0000000 0.0000000 43
GO:0098813 BP GO:0098813 nuclear chromosome segregation 47/298 226/12234 0.0000000 0.0000000 0.0000000 47
GO:0000070 BP GO:0000070 mitotic sister chromatid segregation 40/298 154/12234 0.0000000 0.0000000 0.0000000 40
GO:0006260 BP GO:0006260 DNA replication 38/298 265/12234 0.0000000 0.0000000 0.0000000 38
GO:1901987 BP GO:1901987 regulation of cell cycle phase transition 46/298 416/12234 0.0000000 0.0000000 0.0000000 46
GO:0007091 BP GO:0007091 metaphase/anaphase transition of mitotic cell cycle 20/298 59/12234 0.0000000 0.0000000 0.0000000 20
GO:0010965 BP GO:0010965 regulation of mitotic sister chromatid separation 20/298 60/12234 0.0000000 0.0000000 0.0000000 20
GO:1901990 BP GO:1901990 regulation of mitotic cell cycle phase transition 44/298 386/12234 0.0000000 0.0000000 0.0000000 44
GO:0044784 BP GO:0044784 metaphase/anaphase transition of cell cycle 20/298 61/12234 0.0000000 0.0000000 0.0000000 20
GO:0051306 BP GO:0051306 mitotic sister chromatid separation 20/298 62/12234 0.0000000 0.0000000 0.0000000 20
GO:0051983 BP GO:0051983 regulation of chromosome segregation 22/298 80/12234 0.0000000 0.0000000 0.0000000 22
GO:0007088 BP GO:0007088 regulation of mitotic nuclear division 24/298 100/12234 0.0000000 0.0000000 0.0000000 24
GO:1902850 BP GO:1902850 microtubule cytoskeleton organization involved in mitosis 27/298 134/12234 0.0000000 0.0000000 0.0000000 27
GO:0071103 BP GO:0071103 DNA conformation change 37/298 278/12234 0.0000000 0.0000000 0.0000000 37
GO:0090068 BP GO:0090068 positive regulation of cell cycle process 35/298 250/12234 0.0000000 0.0000000 0.0000000 35
GO:0030071 BP GO:0030071 regulation of mitotic metaphase/anaphase transition 19/298 57/12234 0.0000000 0.0000000 0.0000000 19
GO:0051304 BP GO:0051304 chromosome separation 22/298 84/12234 0.0000000 0.0000000 0.0000000 22
GO:0033045 BP GO:0033045 regulation of sister chromatid segregation 20/298 66/12234 0.0000000 0.0000000 0.0000000 20
GO:1905818 BP GO:1905818 regulation of chromosome separation 20/298 66/12234 0.0000000 0.0000000 0.0000000 20
GO:0051783 BP GO:0051783 regulation of nuclear division 25/298 117/12234 0.0000000 0.0000000 0.0000000 25
GO:1902099 BP GO:1902099 regulation of metaphase/anaphase transition of cell cycle 19/298 59/12234 0.0000000 0.0000000 0.0000000 19
GO:0007051 BP GO:0007051 spindle organization 29/298 173/12234 0.0000000 0.0000000 0.0000000 29
GO:0051321 BP GO:0051321 meiotic cell cycle 29/298 177/12234 0.0000000 0.0000000 0.0000000 29
GO:0007093 BP GO:0007093 mitotic cell cycle checkpoint 27/298 151/12234 0.0000000 0.0000000 0.0000000 27
GO:0045787 BP GO:0045787 positive regulation of cell cycle 38/298 330/12234 0.0000000 0.0000000 0.0000000 38
GO:1903046 BP GO:1903046 meiotic cell cycle process 25/298 133/12234 0.0000000 0.0000000 0.0000000 25
GO:0007052 BP GO:0007052 mitotic spindle organization 23/298 112/12234 0.0000000 0.0000000 0.0000000 23
GO:0000075 BP GO:0000075 cell cycle checkpoint 29/298 196/12234 0.0000000 0.0000000 0.0000000 29
GO:0044843 BP GO:0044843 cell cycle G1/S phase transition 32/298 245/12234 0.0000000 0.0000000 0.0000000 32
GO:0051383 BP GO:0051383 kinetochore organization 12/298 22/12234 0.0000000 0.0000000 0.0000000 12
GO:0006261 BP GO:0006261 DNA-dependent DNA replication 25/298 151/12234 0.0000000 0.0000000 0.0000000 25
GO:0000082 BP GO:0000082 G1/S transition of mitotic cell cycle 30/298 228/12234 0.0000000 0.0000000 0.0000000 30
GO:0140013 BP GO:0140013 meiotic nuclear division 22/298 119/12234 0.0000000 0.0000000 0.0000000 22
GO:0051303 BP GO:0051303 establishment of chromosome localization 17/298 70/12234 0.0000000 0.0000000 0.0000000 17
GO:0050000 BP GO:0050000 chromosome localization 17/298 71/12234 0.0000000 0.0000000 0.0000000 17
GO:2001251 BP GO:2001251 negative regulation of chromosome organization 18/298 83/12234 0.0000000 0.0000000 0.0000000 18
GO:0051310 BP GO:0051310 metaphase plate congression 16/298 62/12234 0.0000000 0.0000000 0.0000000 16
GO:0007094 BP GO:0007094 mitotic spindle assembly checkpoint 13/298 36/12234 0.0000000 0.0000000 0.0000000 13
GO:0071173 BP GO:0071173 spindle assembly checkpoint 13/298 36/12234 0.0000000 0.0000000 0.0000000 13
GO:0071174 BP GO:0071174 mitotic spindle checkpoint 13/298 36/12234 0.0000000 0.0000000 0.0000000 13
GO:0031577 BP GO:0031577 spindle checkpoint 13/298 37/12234 0.0000000 0.0000000 0.0000000 13
GO:0045841 BP GO:0045841 negative regulation of mitotic metaphase/anaphase transition 13/298 38/12234 0.0000000 0.0000000 0.0000000 13
GO:0033044 BP GO:0033044 regulation of chromosome organization 29/298 252/12234 0.0000000 0.0000000 0.0000000 29
GO:0033046 BP GO:0033046 negative regulation of sister chromatid segregation 13/298 39/12234 0.0000000 0.0000000 0.0000000 13
GO:0033048 BP GO:0033048 negative regulation of mitotic sister chromatid segregation 13/298 39/12234 0.0000000 0.0000000 0.0000000 13
GO:1902100 BP GO:1902100 negative regulation of metaphase/anaphase transition of cell cycle 13/298 39/12234 0.0000000 0.0000000 0.0000000 13
GO:2000816 BP GO:2000816 negative regulation of mitotic sister chromatid separation 13/298 39/12234 0.0000000 0.0000000 0.0000000 13
GO:0051985 BP GO:0051985 negative regulation of chromosome segregation 13/298 40/12234 0.0000000 0.0000000 0.0000000 13
GO:1905819 BP GO:1905819 negative regulation of chromosome separation 13/298 40/12234 0.0000000 0.0000000 0.0000000 13
GO:0033047 BP GO:0033047 regulation of mitotic sister chromatid segregation 13/298 42/12234 0.0000000 0.0000000 0.0000000 13
GO:0032392 BP GO:0032392 DNA geometric change 19/298 108/12234 0.0000000 0.0000000 0.0000000 19
GO:1901988 BP GO:1901988 negative regulation of cell cycle phase transition 27/298 231/12234 0.0000000 0.0000000 0.0000000 27
GO:0061982 BP GO:0061982 meiosis I cell cycle process 17/298 84/12234 0.0000000 0.0000000 0.0000000 17
GO:1901991 BP GO:1901991 negative regulation of mitotic cell cycle phase transition 26/298 217/12234 0.0000000 0.0000000 0.0000000 26
GO:0010948 BP GO:0010948 negative regulation of cell cycle process 31/298 311/12234 0.0000000 0.0000000 0.0000000 31
GO:0044839 BP GO:0044839 cell cycle G2/M phase transition 28/298 258/12234 0.0000000 0.0000000 0.0000000 28
GO:0032508 BP GO:0032508 DNA duplex unwinding 18/298 101/12234 0.0000000 0.0000000 0.0000000 18
GO:0045839 BP GO:0045839 negative regulation of mitotic nuclear division 13/298 46/12234 0.0000000 0.0000000 0.0000000 13
GO:0006270 BP GO:0006270 DNA replication initiation 12/298 38/12234 0.0000000 0.0000000 0.0000000 12
GO:0006310 BP GO:0006310 DNA recombination 27/298 247/12234 0.0000000 0.0000000 0.0000000 27
GO:0065004 BP GO:0065004 protein-DNA complex assembly 23/298 183/12234 0.0000000 0.0000000 0.0000000 23
GO:0051225 BP GO:0051225 spindle assembly 18/298 108/12234 0.0000000 0.0000000 0.0000000 18
GO:0045930 BP GO:0045930 negative regulation of mitotic cell cycle 28/298 277/12234 0.0000000 0.0000000 0.0000000 28
GO:0006323 BP GO:0006323 DNA packaging 22/298 171/12234 0.0000000 0.0000000 0.0000000 22
GO:0000086 BP GO:0000086 G2/M transition of mitotic cell cycle 26/298 241/12234 0.0000000 0.0000000 0.0000000 26
GO:0006302 BP GO:0006302 double-strand break repair 26/298 241/12234 0.0000000 0.0000000 0.0000000 26
GO:0051784 BP GO:0051784 negative regulation of nuclear division 13/298 52/12234 0.0000000 0.0000000 0.0000000 13
GO:1901989 BP GO:1901989 positive regulation of cell cycle phase transition 16/298 89/12234 0.0000000 0.0000000 0.0000000 16
GO:0071824 BP GO:0071824 protein-DNA complex subunit organization 24/298 215/12234 0.0000000 0.0000000 0.0000000 24
GO:0007127 BP GO:0007127 meiosis I 15/298 79/12234 0.0000000 0.0000000 0.0000000 15
GO:0033260 BP GO:0033260 nuclear DNA replication 13/298 57/12234 0.0000000 0.0000000 0.0000000 13
GO:1902749 BP GO:1902749 regulation of cell cycle G2/M phase transition 23/298 206/12234 0.0000000 0.0000000 0.0000000 23
GO:0034508 BP GO:0034508 centromere complex assembly 12/298 48/12234 0.0000000 0.0000000 0.0000000 12
GO:0007080 BP GO:0007080 mitotic metaphase plate congression 12/298 49/12234 0.0000000 0.0000001 0.0000001 12
GO:0090307 BP GO:0090307 mitotic spindle assembly 13/298 61/12234 0.0000000 0.0000001 0.0000001 13
GO:0000724 BP GO:0000724 double-strand break repair via homologous recombination 18/298 129/12234 0.0000000 0.0000001 0.0000001 18
GO:0051382 BP GO:0051382 kinetochore assembly 8/298 17/12234 0.0000000 0.0000001 0.0000001 8
GO:0044786 BP GO:0044786 cell cycle DNA replication 13/298 62/12234 0.0000000 0.0000001 0.0000001 13
GO:0000725 BP GO:0000725 recombinational repair 18/298 131/12234 0.0000000 0.0000001 0.0000001 18
GO:0031570 BP GO:0031570 DNA integrity checkpoint 19/298 148/12234 0.0000000 0.0000001 0.0000001 19
GO:1901992 BP GO:1901992 positive regulation of mitotic cell cycle phase transition 14/298 76/12234 0.0000000 0.0000001 0.0000001 14
GO:0000727 BP GO:0000727 double-strand break repair via break-induced replication 7/298 12/12234 0.0000000 0.0000001 0.0000001 7
GO:0000079 BP GO:0000079 regulation of cyclin-dependent protein serine/threonine kinase activity 15/298 91/12234 0.0000000 0.0000002 0.0000002 15
GO:1904029 BP GO:1904029 regulation of cyclin-dependent protein kinase activity 15/298 94/12234 0.0000000 0.0000003 0.0000002 15
GO:0010389 BP GO:0010389 regulation of G2/M transition of mitotic cell cycle 21/298 191/12234 0.0000000 0.0000003 0.0000003 21
GO:0000910 BP GO:0000910 cytokinesis 18/298 144/12234 0.0000000 0.0000005 0.0000004 18
GO:0000281 BP GO:0000281 mitotic cytokinesis 12/298 66/12234 0.0000001 0.0000020 0.0000017 12
GO:0010639 BP GO:0010639 negative regulation of organelle organization 25/298 297/12234 0.0000001 0.0000025 0.0000021 25
GO:0045132 BP GO:0045132 meiotic chromosome segregation 11/298 56/12234 0.0000001 0.0000031 0.0000026 11
GO:0008608 BP GO:0008608 attachment of spindle microtubules to kinetochore 9/298 35/12234 0.0000001 0.0000039 0.0000033 9
GO:0044774 BP GO:0044774 mitotic DNA integrity checkpoint 14/298 102/12234 0.0000002 0.0000059 0.0000050 14
GO:0045931 BP GO:0045931 positive regulation of mitotic cell cycle 14/298 102/12234 0.0000002 0.0000059 0.0000050 14
GO:0061640 BP GO:0061640 cytoskeleton-dependent cytokinesis 13/298 87/12234 0.0000002 0.0000059 0.0000050 13
GO:0031055 BP GO:0031055 chromatin remodeling at centromere 9/298 39/12234 0.0000003 0.0000104 0.0000088 9
GO:0051302 BP GO:0051302 regulation of cell division 15/298 128/12234 0.0000005 0.0000170 0.0000144 15
GO:0000083 BP GO:0000083 regulation of transcription involved in G1/S transition of mitotic cell cycle 8/298 31/12234 0.0000005 0.0000186 0.0000158 8
GO:0007131 BP GO:0007131 reciprocal meiotic recombination 9/298 42/12234 0.0000006 0.0000197 0.0000167 9
GO:0140527 BP GO:0140527 reciprocal homologous recombination 9/298 42/12234 0.0000006 0.0000197 0.0000167 9
GO:0007076 BP GO:0007076 mitotic chromosome condensation 6/298 15/12234 0.0000008 0.0000271 0.0000229 6
GO:0051315 BP GO:0051315 attachment of mitotic spindle microtubules to kinetochore 6/298 15/12234 0.0000008 0.0000271 0.0000229 6
GO:0006336 BP GO:0006336 DNA replication-independent nucleosome assembly 9/298 44/12234 0.0000009 0.0000288 0.0000244 9
GO:0035825 BP GO:0035825 homologous recombination 9/298 44/12234 0.0000009 0.0000288 0.0000244 9
GO:0032465 BP GO:0032465 regulation of cytokinesis 11/298 71/12234 0.0000010 0.0000331 0.0000280 11
GO:0034724 BP GO:0034724 DNA replication-independent nucleosome organization 9/298 45/12234 0.0000011 0.0000346 0.0000293 9
GO:0071897 BP GO:0071897 DNA biosynthetic process 17/298 174/12234 0.0000012 0.0000364 0.0000308 17
GO:0000076 BP GO:0000076 DNA replication checkpoint 6/298 16/12234 0.0000013 0.0000398 0.0000337 6
GO:0006268 BP GO:0006268 DNA unwinding involved in DNA replication 6/298 16/12234 0.0000013 0.0000398 0.0000337 6
GO:0030261 BP GO:0030261 chromosome condensation 8/298 35/12234 0.0000015 0.0000448 0.0000379 8
GO:0034080 BP GO:0034080 CENP-A containing nucleosome assembly 8/298 35/12234 0.0000015 0.0000448 0.0000379 8
GO:0061641 BP GO:0061641 CENP-A containing chromatin organization 8/298 35/12234 0.0000015 0.0000448 0.0000379 8
GO:0071459 BP GO:0071459 protein localization to chromosome, centromeric region 7/298 25/12234 0.0000016 0.0000461 0.0000390 7
GO:0000077 BP GO:0000077 DNA damage checkpoint 15/298 140/12234 0.0000016 0.0000461 0.0000390 15
GO:0030335 BP GO:0030335 positive regulation of cell migration 27/298 403/12234 0.0000019 0.0000556 0.0000470 27
GO:0051272 BP GO:0051272 positive regulation of cellular component movement 28/298 428/12234 0.0000019 0.0000562 0.0000476 28
GO:0022616 BP GO:0022616 DNA strand elongation 7/298 26/12234 0.0000021 0.0000600 0.0000508 7
GO:0006334 BP GO:0006334 nucleosome assembly 12/298 93/12234 0.0000025 0.0000711 0.0000602 12
GO:0007077 BP GO:0007077 mitotic nuclear envelope disassembly 5/298 11/12234 0.0000034 0.0000957 0.0000810 5
GO:2000147 BP GO:2000147 positive regulation of cell motility 27/298 418/12234 0.0000038 0.0001062 0.0000899 27
GO:0007062 BP GO:0007062 sister chromatid cohesion 9/298 52/12234 0.0000039 0.0001087 0.0000920 9
GO:0006271 BP GO:0006271 DNA strand elongation involved in DNA replication 6/298 19/12234 0.0000041 0.0001134 0.0000960 6
GO:0044773 BP GO:0044773 mitotic DNA damage checkpoint 12/298 98/12234 0.0000044 0.0001193 0.0001010 12
GO:0048514 BP GO:0048514 blood vessel morphogenesis 28/298 448/12234 0.0000047 0.0001270 0.0001075 28
GO:0051052 BP GO:0051052 regulation of DNA metabolic process 22/298 303/12234 0.0000049 0.0001325 0.0001122 22
GO:0040017 BP GO:0040017 positive regulation of locomotion 27/298 428/12234 0.0000059 0.0001570 0.0001330 27
GO:0072401 BP GO:0072401 signal transduction involved in DNA integrity checkpoint 10/298 70/12234 0.0000069 0.0001806 0.0001529 10
GO:0072422 BP GO:0072422 signal transduction involved in DNA damage checkpoint 10/298 70/12234 0.0000069 0.0001806 0.0001529 10
GO:0031497 BP GO:0031497 chromatin assembly 14/298 139/12234 0.0000073 0.0001891 0.0001601 14
GO:0001667 BP GO:0001667 ameboidal-type cell migration 23/298 335/12234 0.0000076 0.0001961 0.0001660 23
GO:0072395 BP GO:0072395 signal transduction involved in cell cycle checkpoint 10/298 72/12234 0.0000089 0.0002285 0.0001935 10
GO:0034502 BP GO:0034502 protein localization to chromosome 11/298 88/12234 0.0000090 0.0002288 0.0001937 11
GO:0034728 BP GO:0034728 nucleosome organization 13/298 123/12234 0.0000091 0.0002303 0.0001950 13
GO:0043486 BP GO:0043486 histone exchange 8/298 44/12234 0.0000093 0.0002337 0.0001978 8
GO:0007143 BP GO:0007143 female meiotic nuclear division 6/298 22/12234 0.0000107 0.0002653 0.0002246 6
GO:0051785 BP GO:0051785 positive regulation of nuclear division 8/298 45/12234 0.0000111 0.0002742 0.0002321 8
GO:0030397 BP GO:0030397 membrane disassembly 5/298 14/12234 0.0000139 0.0003374 0.0002856 5
GO:0051081 BP GO:0051081 nuclear envelope disassembly 5/298 14/12234 0.0000139 0.0003374 0.0002856 5
GO:0031572 BP GO:0031572 G2 DNA damage checkpoint 7/298 34/12234 0.0000145 0.0003504 0.0002967 7
GO:0044818 BP GO:0044818 mitotic G2/M transition checkpoint 7/298 35/12234 0.0000177 0.0004230 0.0003581 7
GO:0045840 BP GO:0045840 positive regulation of mitotic nuclear division 7/298 35/12234 0.0000177 0.0004230 0.0003581 7
GO:0031145 BP GO:0031145 anaphase-promoting complex-dependent catabolic process 10/298 78/12234 0.0000184 0.0004355 0.0003687 10
GO:1902806 BP GO:1902806 regulation of cell cycle G1/S phase transition 14/298 152/12234 0.0000203 0.0004776 0.0004044 14
GO:0007019 BP GO:0007019 microtubule depolymerization 7/298 36/12234 0.0000216 0.0005037 0.0004264 7
GO:0032467 BP GO:0032467 positive regulation of cytokinesis 6/298 25/12234 0.0000238 0.0005518 0.0004671 6
GO:0006275 BP GO:0006275 regulation of DNA replication 11/298 98/12234 0.0000254 0.0005845 0.0004949 11
GO:0051054 BP GO:0051054 positive regulation of DNA metabolic process 15/298 177/12234 0.0000278 0.0006366 0.0005390 15
GO:1902969 BP GO:1902969 mitotic DNA replication 5/298 16/12234 0.0000290 0.0006600 0.0005588 5
GO:2000045 BP GO:2000045 regulation of G1/S transition of mitotic cell cycle 13/298 137/12234 0.0000293 0.0006610 0.0005596 13
GO:1902750 BP GO:1902750 negative regulation of cell cycle G2/M phase transition 11/298 102/12234 0.0000370 0.0008302 0.0007029 11
GO:0006333 BP GO:0006333 chromatin assembly or disassembly 14/298 161/12234 0.0000387 0.0008625 0.0007302 14
GO:1904738 BP GO:1904738 vascular associated smooth muscle cell migration 5/298 17/12234 0.0000403 0.0008869 0.0007508 5
GO:1904752 BP GO:1904752 regulation of vascular associated smooth muscle cell migration 5/298 17/12234 0.0000403 0.0008869 0.0007508 5
GO:0071900 BP GO:0071900 regulation of protein serine/threonine kinase activity 24/298 398/12234 0.0000411 0.0008973 0.0007596 24
GO:0051656 BP GO:0051656 establishment of organelle localization 23/298 373/12234 0.0000422 0.0009168 0.0007762 23
GO:0051493 BP GO:0051493 regulation of cytoskeleton organization 25/298 426/12234 0.0000443 0.0009503 0.0008045 25
GO:0070192 BP GO:0070192 chromosome organization involved in meiotic cell cycle 7/298 40/12234 0.0000443 0.0009503 0.0008045 7
GO:0045737 BP GO:0045737 positive regulation of cyclin-dependent protein serine/threonine kinase activity 6/298 28/12234 0.0000476 0.0010140 0.0008585 6
GO:0042770 BP GO:0042770 signal transduction in response to DNA damage 12/298 124/12234 0.0000488 0.0010340 0.0008754 12
GO:0051781 BP GO:0051781 positive regulation of cell division 8/298 56/12234 0.0000580 0.0012203 0.0010331 8
GO:0001525 BP GO:0001525 angiogenesis 23/298 381/12234 0.0000586 0.0012220 0.0010346 23
GO:1902751 BP GO:1902751 positive regulation of cell cycle G2/M phase transition 6/298 29/12234 0.0000588 0.0012220 0.0010346 6
GO:0000723 BP GO:0000723 telomere maintenance 13/298 147/12234 0.0000614 0.0012677 0.0010733 13
GO:0051255 BP GO:0051255 spindle midzone assembly 4/298 10/12234 0.0000645 0.0013247 0.0011215 4
GO:0040001 BP GO:0040001 establishment of mitotic spindle localization 6/298 30/12234 0.0000720 0.0014697 0.0012442 6
GO:0034501 BP GO:0034501 protein localization to kinetochore 5/298 19/12234 0.0000728 0.0014772 0.0012506 5
GO:0009611 BP GO:0009611 response to wounding 26/298 468/12234 0.0000777 0.0015664 0.0013261 26
GO:1904031 BP GO:1904031 positive regulation of cyclin-dependent protein kinase activity 6/298 31/12234 0.0000875 0.0017539 0.0014849 6
GO:0032200 BP GO:0032200 telomere organization 13/298 153/12234 0.0000927 0.0018467 0.0015635 13
GO:0051653 BP GO:0051653 spindle localization 7/298 45/12234 0.0000972 0.0019155 0.0016217 7
GO:0090329 BP GO:0090329 regulation of DNA-dependent DNA replication 7/298 45/12234 0.0000972 0.0019155 0.0016217 7
GO:0030198 BP GO:0030198 extracellular matrix organization 18/298 271/12234 0.0001152 0.0022559 0.0019099 18
GO:0072331 BP GO:0072331 signal transduction by p53 class mediator 17/298 247/12234 0.0001158 0.0022559 0.0019099 17
GO:0043062 BP GO:0043062 extracellular structure organization 18/298 272/12234 0.0001207 0.0023366 0.0019782 18
GO:1904666 BP GO:1904666 regulation of ubiquitin protein ligase activity 5/298 21/12234 0.0001224 0.0023574 0.0019958 5
GO:0045229 BP GO:0045229 external encapsulating structure organization 18/298 273/12234 0.0001264 0.0024199 0.0020487 18
GO:1904668 BP GO:1904668 positive regulation of ubiquitin protein ligase activity 4/298 12/12234 0.0001463 0.0027861 0.0023587 4
GO:0042060 BP GO:0042060 wound healing 22/298 379/12234 0.0001498 0.0028363 0.0024012 22
GO:0014032 BP GO:0014032 neural crest cell development 8/298 64/12234 0.0001527 0.0028755 0.0024344 8
GO:0007050 BP GO:0007050 cell cycle arrest 15/298 206/12234 0.0001572 0.0029434 0.0024919 15
GO:0051445 BP GO:0051445 regulation of meiotic cell cycle 6/298 35/12234 0.0001777 0.0033096 0.0028019 6
GO:0048864 BP GO:0048864 stem cell development 8/298 66/12234 0.0001900 0.0035193 0.0029795 8
GO:0048609 BP GO:0048609 multicellular organismal reproductive process 26/298 496/12234 0.0001979 0.0036456 0.0030864 26
GO:0030330 BP GO:0030330 DNA damage response, signal transduction by p53 class mediator 10/298 103/12234 0.0002020 0.0037005 0.0031329 10
GO:0051984 BP GO:0051984 positive regulation of chromosome segregation 4/298 13/12234 0.0002073 0.0037385 0.0031651 4
GO:0051988 BP GO:0051988 regulation of attachment of spindle microtubules to kinetochore 4/298 13/12234 0.0002073 0.0037385 0.0031651 4
GO:1904754 BP GO:1904754 positive regulation of vascular associated smooth muscle cell migration 4/298 13/12234 0.0002073 0.0037385 0.0031651 4
GO:0048146 BP GO:0048146 positive regulation of fibroblast proliferation 6/298 36/12234 0.0002089 0.0037478 0.0031729 6
GO:0014031 BP GO:0014031 mesenchymal cell development 8/298 67/12234 0.0002113 0.0037502 0.0031750 8
GO:0048661 BP GO:0048661 positive regulation of smooth muscle cell proliferation 8/298 67/12234 0.0002113 0.0037502 0.0031750 8
GO:0045214 BP GO:0045214 sarcomere organization 5/298 24/12234 0.0002409 0.0042530 0.0036007 5
GO:0071294 BP GO:0071294 cellular response to zinc ion 4/298 14/12234 0.0002847 0.0049255 0.0041700 4
GO:0090231 BP GO:0090231 regulation of spindle checkpoint 4/298 14/12234 0.0002847 0.0049255 0.0041700 4
GO:0090266 BP GO:0090266 regulation of mitotic cell cycle spindle assembly checkpoint 4/298 14/12234 0.0002847 0.0049255 0.0041700 4
GO:1903504 BP GO:1903504 regulation of mitotic spindle checkpoint 4/298 14/12234 0.0002847 0.0049255 0.0041700 4
GO:0014033 BP GO:0014033 neural crest cell differentiation 8/298 70/12234 0.0002871 0.0049419 0.0041839 8
GO:0002504 BP GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 9/298 89/12234 0.0003084 0.0052820 0.0044718 9
GO:0036297 BP GO:0036297 interstrand cross-link repair 7/298 54/12234 0.0003148 0.0053634 0.0045407 7
GO:0090092 BP GO:0090092 regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 13/298 174/12234 0.0003339 0.0056608 0.0047925 13
GO:0006977 BP GO:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest 7/298 55/12234 0.0003532 0.0059597 0.0050456 7
GO:0010971 BP GO:0010971 positive regulation of G2/M transition of mitotic cell cycle 5/298 26/12234 0.0003582 0.0060130 0.0050907 5
GO:0007292 BP GO:0007292 female gamete generation 9/298 91/12234 0.0003645 0.0060601 0.0051305 9
GO:0010972 BP GO:0010972 negative regulation of G2/M transition of mitotic cell cycle 9/298 91/12234 0.0003645 0.0060601 0.0051305 9
GO:0043044 BP GO:0043044 ATP-dependent chromatin remodeling 8/298 73/12234 0.0003839 0.0063507 0.0053766 8
GO:0048762 BP GO:0048762 mesenchymal cell differentiation 13/298 177/12234 0.0003939 0.0064479 0.0054589 13
GO:0072431 BP GO:0072431 signal transduction involved in mitotic G1 DNA damage checkpoint 7/298 56/12234 0.0003954 0.0064479 0.0054589 7
GO:1902400 BP GO:1902400 intracellular signal transduction involved in G1 DNA damage checkpoint 7/298 56/12234 0.0003954 0.0064479 0.0054589 7
GO:0071158 BP GO:0071158 positive regulation of cell cycle arrest 8/298 74/12234 0.0004215 0.0068397 0.0057906 8
GO:0032201 BP GO:0032201 telomere maintenance via semi-conservative replication 5/298 27/12234 0.0004309 0.0069596 0.0058921 5
GO:0051293 BP GO:0051293 establishment of spindle localization 6/298 41/12234 0.0004355 0.0070013 0.0059274 6
GO:1902402 BP GO:1902402 signal transduction involved in mitotic DNA damage checkpoint 7/298 57/12234 0.0004415 0.0070315 0.0059530 7
GO:1902403 BP GO:1902403 signal transduction involved in mitotic DNA integrity checkpoint 7/298 57/12234 0.0004415 0.0070315 0.0059530 7
GO:0071156 BP GO:0071156 regulation of cell cycle arrest 9/298 94/12234 0.0004643 0.0073591 0.0062303 9
GO:0010035 BP GO:0010035 response to inorganic substance 21/298 384/12234 0.0004706 0.0074244 0.0062856 21
GO:0033002 BP GO:0033002 muscle cell proliferation 11/298 136/12234 0.0004872 0.0076512 0.0064776 11
GO:0072413 BP GO:0072413 signal transduction involved in mitotic cell cycle checkpoint 7/298 59/12234 0.0005466 0.0085346 0.0072255 7
GO:0060485 BP GO:0060485 mesenchyme development 14/298 207/12234 0.0005484 0.0085346 0.0072255 14
GO:0021700 BP GO:0021700 developmental maturation 13/298 184/12234 0.0005704 0.0088366 0.0074812 13
GO:0048660 BP GO:0048660 regulation of smooth muscle cell proliferation 9/298 97/12234 0.0005854 0.0090274 0.0076427 9
GO:2000278 BP GO:2000278 regulation of DNA biosynthetic process 9/298 98/12234 0.0006311 0.0096883 0.0082023 9
GO:0031571 BP GO:0031571 mitotic G1 DNA damage checkpoint 7/298 61/12234 0.0006707 0.0102035 0.0086384 7
GO:0044819 BP GO:0044819 mitotic G1/S transition checkpoint 7/298 61/12234 0.0006707 0.0102035 0.0086384 7
GO:0048659 BP GO:0048659 smooth muscle cell proliferation 9/298 99/12234 0.0006797 0.0102950 0.0087159 9
GO:0007098 BP GO:0007098 centrosome cycle 10/298 120/12234 0.0006914 0.0104257 0.0088266 10
GO:0031109 BP GO:0031109 microtubule polymerization or depolymerization 9/298 100/12234 0.0007313 0.0109789 0.0092949 9
GO:0044783 BP GO:0044783 G1 DNA damage checkpoint 7/298 62/12234 0.0007405 0.0110689 0.0093711 7
GO:1904019 BP GO:1904019 epithelial cell apoptotic process 8/298 81/12234 0.0007767 0.0115589 0.0097859 8
GO:0051307 BP GO:0051307 meiotic chromosome separation 4/298 18/12234 0.0008059 0.0119411 0.0101095 4
GO:0032886 BP GO:0032886 regulation of microtubule-based process 13/298 191/12234 0.0008098 0.0119470 0.0101145 13
GO:2000573 BP GO:2000573 positive regulation of DNA biosynthetic process 7/298 63/12234 0.0008160 0.0119872 0.0101485 7
GO:0031032 BP GO:0031032 actomyosin structure organization 11/298 145/12234 0.0008347 0.0122087 0.0103361 11
GO:0030193 BP GO:0030193 regulation of blood coagulation 6/298 47/12234 0.0009204 0.0133479 0.0113005 6
GO:1900046 BP GO:1900046 regulation of hemostasis 6/298 47/12234 0.0009204 0.0133479 0.0113005 6
GO:0070507 BP GO:0070507 regulation of microtubule cytoskeleton organization 10/298 125/12234 0.0009498 0.0137162 0.0116123 10
GO:0001935 BP GO:0001935 endothelial cell proliferation 9/298 104/12234 0.0009706 0.0139572 0.0118164 9
GO:0010631 BP GO:0010631 epithelial cell migration 15/298 246/12234 0.0010281 0.0147219 0.0124638 15
GO:0019886 BP GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II 8/298 85/12234 0.0010688 0.0152092 0.0128763 8
GO:0090132 BP GO:0090132 epithelium migration 15/298 247/12234 0.0010711 0.0152092 0.0128763 15
GO:0071363 BP GO:0071363 cellular response to growth factor stimulus 24/298 496/12234 0.0010799 0.0152715 0.0129291 24
GO:0061448 BP GO:0061448 connective tissue development 12/298 174/12234 0.0011380 0.0160257 0.0135676 12
GO:0090130 BP GO:0090130 tissue migration 15/298 249/12234 0.0011615 0.0162901 0.0137915 15
GO:0051216 BP GO:0051216 cartilage development 10/298 129/12234 0.0012095 0.0168929 0.0143018 10
GO:0006936 BP GO:0006936 muscle contraction 13/298 200/12234 0.0012367 0.0172029 0.0145642 13
GO:0050818 BP GO:0050818 regulation of coagulation 6/298 50/12234 0.0012815 0.0176268 0.0149231 6
GO:0010212 BP GO:0010212 response to ionizing radiation 10/298 130/12234 0.0012827 0.0176268 0.0149231 10
GO:0031023 BP GO:0031023 microtubule organizing center organization 10/298 130/12234 0.0012827 0.0176268 0.0149231 10
GO:0042493 BP GO:0042493 response to drug 15/298 252/12234 0.0013093 0.0179195 0.0151709 15
GO:0002495 BP GO:0002495 antigen processing and presentation of peptide antigen via MHC class II 8/298 88/12234 0.0013407 0.0182765 0.0154732 8
GO:0007063 BP GO:0007063 regulation of sister chromatid cohesion 4/298 21/12234 0.0014880 0.0202039 0.0171050 4
GO:0000212 BP GO:0000212 meiotic spindle organization 3/298 10/12234 0.0015120 0.0202072 0.0171078 3
GO:0032060 BP GO:0032060 bleb assembly 3/298 10/12234 0.0015120 0.0202072 0.0171078 3
GO:0051798 BP GO:0051798 positive regulation of hair follicle development 3/298 10/12234 0.0015120 0.0202072 0.0171078 3
GO:0090280 BP GO:0090280 positive regulation of calcium ion import 3/298 10/12234 0.0015120 0.0202072 0.0171078 3
GO:0060537 BP GO:0060537 muscle tissue development 15/298 257/12234 0.0015905 0.0211738 0.0179260 15
GO:0043277 BP GO:0043277 apoptotic cell clearance 5/298 36/12234 0.0016825 0.0223115 0.0188893 5
GO:0001936 BP GO:0001936 regulation of endothelial cell proliferation 8/298 92/12234 0.0017859 0.0235905 0.0199721 8
GO:0051928 BP GO:0051928 positive regulation of calcium ion transport 7/298 72/12234 0.0018042 0.0237402 0.0200988 7
GO:0016572 BP GO:0016572 histone phosphorylation 5/298 37/12234 0.0019072 0.0249039 0.0210840 5
GO:0030239 BP GO:0030239 myofibril assembly 5/298 37/12234 0.0019072 0.0249039 0.0210840 5
GO:0045785 BP GO:0045785 positive regulation of cell adhesion 17/298 317/12234 0.0019818 0.0257790 0.0218249 17
GO:0035404 BP GO:0035404 histone-serine phosphorylation 3/298 11/12234 0.0020417 0.0264565 0.0223985 3
GO:0071560 BP GO:0071560 cellular response to transforming growth factor beta stimulus 12/298 187/12234 0.0021006 0.0268440 0.0227265 12
GO:0031100 BP GO:0031100 animal organ regeneration 6/298 55/12234 0.0021124 0.0268440 0.0227265 6
GO:0031099 BP GO:0031099 regeneration 10/298 139/12234 0.0021186 0.0268440 0.0227265 10
GO:0007095 BP GO:0007095 mitotic G2 DNA damage checkpoint 4/298 23/12234 0.0021189 0.0268440 0.0227265 4
GO:0016339 BP GO:0016339 calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules 4/298 23/12234 0.0021189 0.0268440 0.0227265 4
GO:0042634 BP GO:0042634 regulation of hair cycle 4/298 23/12234 0.0021189 0.0268440 0.0227265 4
GO:0032506 BP GO:0032506 cytokinetic process 5/298 38/12234 0.0021532 0.0271776 0.0230089 5
GO:2000134 BP GO:2000134 negative regulation of G1/S transition of mitotic cell cycle 8/298 95/12234 0.0021906 0.0275488 0.0233232 8
GO:0050918 BP GO:0050918 positive chemotaxis 5/298 39/12234 0.0024214 0.0303385 0.0256850 5
GO:0014706 BP GO:0014706 striated muscle tissue development 14/298 242/12234 0.0024468 0.0305445 0.0258594 14
GO:0006882 BP GO:0006882 cellular zinc ion homeostasis 4/298 24/12234 0.0024944 0.0309600 0.0262112 4
GO:1902807 BP GO:1902807 negative regulation of cell cycle G1/S phase transition 8/298 97/12234 0.0024982 0.0309600 0.0262112 8
GO:0071559 BP GO:0071559 response to transforming growth factor beta 12/298 192/12234 0.0026149 0.0322881 0.0273356 12
GO:0007100 BP GO:0007100 mitotic centrosome separation 3/298 12/12234 0.0026735 0.0328923 0.0278471 3
GO:0086003 BP GO:0086003 cardiac muscle cell contraction 5/298 40/12234 0.0027131 0.0332597 0.0281582 5
GO:0048608 BP GO:0048608 reproductive structure development 16/298 300/12234 0.0028137 0.0343699 0.0290981 16
GO:0007276 BP GO:0007276 gamete generation 20/298 414/12234 0.0028268 0.0344063 0.0291289 20
GO:0000132 BP GO:0000132 establishment of mitotic spindle orientation 4/298 25/12234 0.0029134 0.0350840 0.0297026 4
GO:0014911 BP GO:0014911 positive regulation of smooth muscle cell migration 4/298 25/12234 0.0029134 0.0350840 0.0297026 4
GO:0055069 BP GO:0055069 zinc ion homeostasis 4/298 25/12234 0.0029134 0.0350840 0.0297026 4
GO:0060249 BP GO:0060249 anatomical structure homeostasis 18/298 358/12234 0.0029756 0.0357074 0.0302304 18
GO:2000241 BP GO:2000241 regulation of reproductive process 8/298 100/12234 0.0030219 0.0360988 0.0305618 8
GO:1902808 BP GO:1902808 positive regulation of cell cycle G1/S phase transition 5/298 41/12234 0.0030294 0.0360988 0.0305618 5
GO:0061458 BP GO:0061458 reproductive system development 16/298 303/12234 0.0031039 0.0368575 0.0312041 16
GO:0001706 BP GO:0001706 endoderm formation 5/298 42/12234 0.0033715 0.0391668 0.0331592 5
GO:1904705 BP GO:1904705 regulation of vascular associated smooth muscle cell proliferation 5/298 42/12234 0.0033715 0.0391668 0.0331592 5
GO:1990874 BP GO:1990874 vascular associated smooth muscle cell proliferation 5/298 42/12234 0.0033715 0.0391668 0.0331592 5
GO:0010458 BP GO:0010458 exit from mitosis 4/298 26/12234 0.0033780 0.0391668 0.0331592 4
GO:0071353 BP GO:0071353 cellular response to interleukin-4 4/298 26/12234 0.0033780 0.0391668 0.0331592 4
GO:0031935 BP GO:0031935 regulation of chromatin silencing 3/298 13/12234 0.0034133 0.0391668 0.0331592 3
GO:0035791 BP GO:0035791 platelet-derived growth factor receptor-beta signaling pathway 3/298 13/12234 0.0034133 0.0391668 0.0331592 3
GO:0051299 BP GO:0051299 centrosome separation 3/298 13/12234 0.0034133 0.0391668 0.0331592 3
GO:0072425 BP GO:0072425 signal transduction involved in G2 DNA damage checkpoint 3/298 13/12234 0.0034133 0.0391668 0.0331592 3
GO:1905168 BP GO:1905168 positive regulation of double-strand break repair via homologous recombination 3/298 13/12234 0.0034133 0.0391668 0.0331592 3
GO:0060415 BP GO:0060415 muscle tissue morphogenesis 5/298 43/12234 0.0037405 0.0427778 0.0362163 5
GO:0006890 BP GO:0006890 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum 7/298 82/12234 0.0037902 0.0432010 0.0365746 7
GO:0050920 BP GO:0050920 regulation of chemotaxis 10/298 151/12234 0.0038630 0.0437583 0.0370464 10
GO:0050673 BP GO:0050673 epithelial cell proliferation 15/298 282/12234 0.0038662 0.0437583 0.0370464 15
GO:0070670 BP GO:0070670 response to interleukin-4 4/298 27/12234 0.0038905 0.0437583 0.0370464 4
GO:1904707 BP GO:1904707 positive regulation of vascular associated smooth muscle cell proliferation 4/298 27/12234 0.0038905 0.0437583 0.0370464 4
GO:0007178 BP GO:0007178 transmembrane receptor protein serine/threonine kinase signaling pathway 14/298 255/12234 0.0039217 0.0439638 0.0372204 14
GO:0061061 BP GO:0061061 muscle structure development 20/298 428/12234 0.0041107 0.0459315 0.0388863 20
GO:0001701 BP GO:0001701 in utero embryonic development 15/298 284/12234 0.0041276 0.0459319 0.0388866 15
GO:0014910 BP GO:0014910 regulation of smooth muscle cell migration 5/298 44/12234 0.0041376 0.0459319 0.0388866 5
GO:0048145 BP GO:0048145 regulation of fibroblast proliferation 6/298 63/12234 0.0042114 0.0463071 0.0392043 6
GO:0007096 BP GO:0007096 regulation of exit from mitosis 3/298 14/12234 0.0042666 0.0463071 0.0392043 3
GO:0045842 BP GO:0045842 positive regulation of mitotic metaphase/anaphase transition 3/298 14/12234 0.0042666 0.0463071 0.0392043 3
GO:0051767 BP GO:0051767 nitric-oxide synthase biosynthetic process 3/298 14/12234 0.0042666 0.0463071 0.0392043 3
GO:0051769 BP GO:0051769 regulation of nitric-oxide synthase biosynthetic process 3/298 14/12234 0.0042666 0.0463071 0.0392043 3
GO:0098801 BP GO:0098801 regulation of renal system process 3/298 14/12234 0.0042666 0.0463071 0.0392043 3
GO:1901970 BP GO:1901970 positive regulation of mitotic sister chromatid separation 3/298 14/12234 0.0042666 0.0463071 0.0392043 3
GO:0001937 BP GO:0001937 negative regulation of endothelial cell proliferation 4/298 28/12234 0.0044532 0.0480269 0.0406603 4
GO:0060969 BP GO:0060969 negative regulation of gene silencing 4/298 28/12234 0.0044532 0.0480269 0.0406603 4
GO:0048144 BP GO:0048144 fibroblast proliferation 6/298 64/12234 0.0045542 0.0484546 0.0410224 6
GO:0070252 BP GO:0070252 actin-mediated cell contraction 6/298 64/12234 0.0045542 0.0484546 0.0410224 6
GO:0010569 BP GO:0010569 regulation of double-strand break repair via homologous recombination 5/298 45/12234 0.0045639 0.0484546 0.0410224 5
GO:0061035 BP GO:0061035 regulation of cartilage development 5/298 45/12234 0.0045639 0.0484546 0.0410224 5
GO:1901379 BP GO:1901379 regulation of potassium ion transmembrane transport 5/298 45/12234 0.0045639 0.0484546 0.0410224 5
GO:0043542 BP GO:0043542 endothelial cell migration 11/298 180/12234 0.0046078 0.0487681 0.0412878 11
GO:0098687 CC GO:0098687 chromosomal region 51/306 315/12681 0.0000000 0.0000000 0.0000000 51
GO:0000775 CC GO:0000775 chromosome, centromeric region 38/306 188/12681 0.0000000 0.0000000 0.0000000 38
GO:0000793 CC GO:0000793 condensed chromosome 35/306 185/12681 0.0000000 0.0000000 0.0000000 35
GO:0000779 CC GO:0000779 condensed chromosome, centromeric region 28/306 113/12681 0.0000000 0.0000000 0.0000000 28
GO:0000776 CC GO:0000776 kinetochore 29/306 134/12681 0.0000000 0.0000000 0.0000000 29
GO:0005819 CC GO:0005819 spindle 43/306 354/12681 0.0000000 0.0000000 0.0000000 43
GO:0000777 CC GO:0000777 condensed chromosome kinetochore 25/306 103/12681 0.0000000 0.0000000 0.0000000 25
GO:0072686 CC GO:0072686 mitotic spindle 24/306 142/12681 0.0000000 0.0000000 0.0000000 24
GO:0000228 CC GO:0000228 nuclear chromosome 26/306 203/12681 0.0000000 0.0000000 0.0000000 26
GO:0051233 CC GO:0051233 spindle midzone 12/306 33/12681 0.0000000 0.0000000 0.0000000 12
GO:0000922 CC GO:0000922 spindle pole 22/306 156/12681 0.0000000 0.0000000 0.0000000 22
GO:0031261 CC GO:0031261 DNA replication preinitiation complex 8/306 12/12681 0.0000000 0.0000000 0.0000000 8
GO:0005874 CC GO:0005874 microtubule 32/306 366/12681 0.0000000 0.0000000 0.0000000 32
GO:0071162 CC GO:0071162 CMG complex 7/306 10/12681 0.0000000 0.0000000 0.0000000 7
GO:0000778 CC GO:0000778 condensed nuclear chromosome kinetochore 8/306 17/12681 0.0000000 0.0000000 0.0000000 8
GO:0000940 CC GO:0000940 condensed chromosome outer kinetochore 7/306 13/12681 0.0000000 0.0000001 0.0000001 7
GO:0030496 CC GO:0030496 midbody 20/306 182/12681 0.0000000 0.0000003 0.0000002 20
GO:0000794 CC GO:0000794 condensed nuclear chromosome 12/306 63/12681 0.0000000 0.0000005 0.0000004 12
GO:0005876 CC GO:0005876 spindle microtubule 12/306 67/12681 0.0000001 0.0000009 0.0000007 12
GO:1990023 CC GO:1990023 mitotic spindle midzone 6/306 11/12681 0.0000001 0.0000012 0.0000009 6
GO:0005871 CC GO:0005871 kinesin complex 10/306 45/12681 0.0000001 0.0000013 0.0000010 10
GO:0062023 CC GO:0062023 collagen-containing extracellular matrix 21/306 240/12681 0.0000004 0.0000050 0.0000039 21
GO:0005875 CC GO:0005875 microtubule associated complex 15/306 132/12681 0.0000007 0.0000087 0.0000068 15
GO:0030312 CC GO:0030312 external encapsulating structure 24/306 316/12681 0.0000007 0.0000087 0.0000068 24
GO:0031012 CC GO:0031012 extracellular matrix 24/306 316/12681 0.0000007 0.0000087 0.0000068 24
GO:0032993 CC GO:0032993 protein-DNA complex 14/306 139/12681 0.0000066 0.0000784 0.0000612 14
GO:0097431 CC GO:0097431 mitotic spindle pole 7/306 32/12681 0.0000089 0.0001023 0.0000799 7
GO:0000781 CC GO:0000781 chromosome, telomeric region 13/306 139/12681 0.0000311 0.0003448 0.0002693 13
GO:0000307 CC GO:0000307 cyclin-dependent protein kinase holoenzyme complex 7/306 40/12681 0.0000418 0.0004473 0.0003493 7
GO:0005788 CC GO:0005788 endoplasmic reticulum lumen 16/306 218/12681 0.0000783 0.0008090 0.0006318 16
GO:0005657 CC GO:0005657 replication fork 8/306 63/12681 0.0001282 0.0012819 0.0010012 8
GO:0042555 CC GO:0042555 MCM complex 4/306 12/12681 0.0001412 0.0013679 0.0010683 4
GO:0045171 CC GO:0045171 intercellular bridge 8/306 69/12681 0.0002442 0.0022943 0.0017918 8
GO:0000152 CC GO:0000152 nuclear ubiquitin ligase complex 6/306 42/12681 0.0004743 0.0043244 0.0033773 6
GO:0016342 CC GO:0016342 catenin complex 4/306 18/12681 0.0007785 0.0068950 0.0053849 4
GO:0000795 CC GO:0000795 synaptonemal complex 4/306 20/12681 0.0011865 0.0099414 0.0077640 4
GO:0099086 CC GO:0099086 synaptonemal structure 4/306 20/12681 0.0011865 0.0099414 0.0077640 4
GO:0000792 CC GO:0000792 heterochromatin 7/306 68/12681 0.0012232 0.0099790 0.0077934 7
GO:0005680 CC GO:0005680 anaphase-promoting complex 4/306 21/12681 0.0014381 0.0111302 0.0086925 4
GO:0045120 CC GO:0045120 pronucleus 3/306 10/12681 0.0014721 0.0111302 0.0086925 3
GO:0070938 CC GO:0070938 contractile ring 3/306 10/12681 0.0014721 0.0111302 0.0086925 3
GO:0044815 CC GO:0044815 DNA packaging complex 6/306 59/12681 0.0028933 0.0213552 0.0166781 6
GO:1902554 CC GO:1902554 serine/threonine protein kinase complex 7/306 81/12681 0.0033647 0.0242569 0.0189443 7
GO:0005581 CC GO:0005581 collagen trimer 5/306 43/12681 0.0035963 0.0253375 0.0197882 5
GO:0010369 CC GO:0010369 chromocenter 3/306 14/12681 0.0041566 0.0286345 0.0223631 3
GO:0031616 CC GO:0031616 spindle pole centrosome 3/306 15/12681 0.0051039 0.0343956 0.0268624 3
GO:1990752 CC GO:1990752 microtubule end 4/306 31/12681 0.0062578 0.0407032 0.0317885 4
GO:0005604 CC GO:0005604 basement membrane 6/306 69/12681 0.0063024 0.0407032 0.0317885 6
GO:1902911 CC GO:1902911 protein kinase complex 7/306 93/12681 0.0071835 0.0454467 0.0354932 7
GO:0005884 CC GO:0005884 actin filament 7/306 94/12681 0.0076058 0.0462313 0.0361059 7
GO:0031674 CC GO:0031674 I band 7/306 94/12681 0.0076058 0.0462313 0.0361059 7
GO:0034451 CC GO:0034451 centriolar satellite 7/306 95/12681 0.0080461 0.0479674 0.0374618 7
GO:0017116 MF GO:0017116 single-stranded DNA helicase activity 11/295 19/12535 0.0000000 0.0000000 0.0000000 11
GO:0008017 MF GO:0008017 microtubule binding 26/295 236/12535 0.0000000 0.0000000 0.0000000 26
GO:0003678 MF GO:0003678 DNA helicase activity 15/295 70/12535 0.0000000 0.0000000 0.0000000 15
GO:0016887 MF GO:0016887 ATPase activity 34/295 409/12535 0.0000000 0.0000000 0.0000000 34
GO:0015631 MF GO:0015631 tubulin binding 29/295 314/12535 0.0000000 0.0000000 0.0000000 29
GO:0140097 MF GO:0140097 catalytic activity, acting on DNA 22/295 184/12535 0.0000000 0.0000000 0.0000000 22
GO:0003777 MF GO:0003777 microtubule motor activity 12/295 58/12535 0.0000000 0.0000005 0.0000004 12
GO:0008094 MF GO:0008094 DNA-dependent ATPase activity 11/295 49/12535 0.0000000 0.0000008 0.0000007 11
GO:0003688 MF GO:0003688 DNA replication origin binding 8/295 23/12535 0.0000000 0.0000015 0.0000013 8
GO:0004386 MF GO:0004386 helicase activity 16/295 147/12535 0.0000004 0.0000161 0.0000141 16
GO:0008574 MF GO:0008574 ATP-dependent microtubule motor activity, plus-end-directed 6/295 15/12535 0.0000007 0.0000275 0.0000241 6
GO:0003774 MF GO:0003774 motor activity 12/295 101/12535 0.0000042 0.0001585 0.0001389 12
GO:0003697 MF GO:0003697 single-stranded DNA binding 12/295 108/12535 0.0000086 0.0002957 0.0002591 12
GO:0030545 MF GO:0030545 receptor regulator activity 18/295 235/12535 0.0000112 0.0003467 0.0003039 18
GO:0000217 MF GO:0000217 DNA secondary structure binding 7/295 34/12535 0.0000116 0.0003467 0.0003039 7
GO:0043138 MF GO:0043138 3’-5’ DNA helicase activity 5/295 17/12535 0.0000342 0.0009584 0.0008399 5
GO:0048018 MF GO:0048018 receptor ligand activity 16/295 212/12535 0.0000415 0.0010935 0.0009584 16
GO:1990939 MF GO:1990939 ATP-dependent microtubule motor activity 6/295 29/12535 0.0000486 0.0012093 0.0010598 6
GO:0030546 MF GO:0030546 signaling receptor activator activity 16/295 217/12535 0.0000550 0.0012961 0.0011359 16
GO:0005201 MF GO:0005201 extracellular matrix structural constituent 10/295 93/12535 0.0000644 0.0014436 0.0012652 10
GO:0003682 MF GO:0003682 chromatin binding 25/295 466/12535 0.0001083 0.0023098 0.0020243 25
GO:0050839 MF GO:0050839 cell adhesion molecule binding 23/295 444/12535 0.0003383 0.0068884 0.0060371 23
GO:0003779 MF GO:0003779 actin binding 19/295 345/12535 0.0005302 0.0103276 0.0090512 19
GO:0016538 MF GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity 6/295 45/12535 0.0006075 0.0113405 0.0099389 6
GO:0005179 MF GO:0005179 hormone activity 5/295 31/12535 0.0007174 0.0128562 0.0112673 5
GO:0019894 MF GO:0019894 kinesin binding 5/295 36/12535 0.0014462 0.0249189 0.0218392 5
GO:1990825 MF GO:1990825 sequence-specific mRNA binding 3/295 11/12535 0.0018503 0.0307015 0.0269071 3
GO:0051015 MF GO:0051015 actin filament binding 11/295 172/12535 0.0025119 0.0401906 0.0352234 11

Are the conclusions of the study supported?

Session information

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] MASS_7.3-54            gtools_3.9.2           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