categoryCompare2: visNetwork • categoryCompare2

categoryCompare2: Alternative Visualization

Authored by: Robert M Flight <rflight79@gmail.com> on 2026-05-04 15:59:38.973338

Introduction

Current high-throughput molecular biology experiments are generating larger and larger amounts of data. Although there are many different methods to analyze individual experiments, methods that allow the comparison of different data sets are sorely lacking. This is important due to the number of experiments that have been carried out on biological systems that may be amenable to either fusion or comparison. Most of the current tools available focus on finding those genes in experiments that are listed as the same, or that can be shown statistically that it is significant that the gene was listed in the results of both experiments.

However, what many of these tools do not do is consider the similarities (and just as importantly, the differences) between experimental results at the categorical level. Categoical data includes any gene annotation, such as Gene Ontologies, KEGG pathways, chromosome location, etc. categoryCompare has been developed to allow the comparison of high-throughput experiments at a categorical level, and to explore those results in an intuitive fashion.

Sample Data

To make the concept more concrete, we will examine data from the microarray data set estrogen available from Bioconductor. This data set contains 8 samples, with 2 levels of estrogen therapy (present vs absent), and two time points (10 and 48 hours). A pre-processed version of the data is available with this package, the commands used to generate it are below. Note: the preprocessed one keeps only the top 100 genes, if you use it the results will be slightly different than those shown in the vignette.

library("affy")
library("hgu95av2.db")
library("genefilter")
library("estrogen")
library("limma")

datadir <- system.file("extdata", package = "estrogen")
pd <- read.AnnotatedDataFrame(
  file.path(datadir, "estrogen.txt"),
  header = TRUE,
  sep = "",
  row.names = 1
)
pData(pd)

Here you can see the descriptions for each of the arrays. First, we will read in the cel files, and then normalize the data using RMA.

currDir <- getwd()
setwd(datadir)
a <- ReadAffy(filenames = rownames(pData(pd)), phenoData = pd, verbose = TRUE)
setwd(currDir)

eData <- rma(a)

To make it easier to conceptualize, we will split the data up into two eSet objects by time, and perform all of the manipulations for calculating significantly differentially expressed genes on each eSet object.

So for the 10 hour samples:

e_file <- system.file(
  "extdata/test_data/estrogen_edata.rds",
  package = "categoryCompare2"
)
eData <- readRDS(e_file)
e10 <- eData[, eData$time.h == 10]
e10 <- nsFilter(
  e10,
  remove.dupEntrez = TRUE,
  var.filter = FALSE,
  feature.exclude = "^AFFX"
)$eset

e10$estrogen <- factor(e10$estrogen)
d10 <- model.matrix(~ 0 + e10$estrogen)
colnames(d10) <- unique(e10$estrogen)
fit10 <- lmFit(e10, d10)
c10 <- makeContrasts(present - absent, levels = d10)
fit10_2 <- contrasts.fit(fit10, c10)
eB10 <- eBayes(fit10_2)
table10 <- topTable(eB10, number = nrow(e10), p.value = 1, adjust.method = "BH")
table10$Entrez <- unlist(mget(
  rownames(table10),
  hgu95av2ENTREZID,
  ifnotfound = NA
))

And the 48 hour samples we do the same thing:

e48 <- eData[, eData$time.h == 48]
e48 <- nsFilter(
  e48,
  remove.dupEntrez = TRUE,
  var.filter = FALSE,
  feature.exclude = "^AFFX"
)$eset

e48$estrogen <- factor(e48$estrogen)
d48 <- model.matrix(~ 0 + e48$estrogen)
colnames(d48) <- unique(e48$estrogen)
fit48 <- lmFit(e48, d48)
c48 <- makeContrasts(present - absent, levels = d48)
fit48_2 <- contrasts.fit(fit48, c48)
eB48 <- eBayes(fit48_2)
table48 <- topTable(eB48, number = nrow(e48), p.value = 1, adjust.method = "BH")
table48$Entrez <- unlist(mget(
  rownames(table48),
  hgu95av2ENTREZID,
  ifnotfound = NA
))

And grab all the genes on the array to have a background set.

gUniverse <- unique(union(table10$Entrez, table48$Entrez))

For both time points we have generated a list of genes that are differentially expressed in the present vs absent samples. To compare the time-points, we could find the common and discordant genes from both experiments, and then try to interpret those lists. This is commonly done in many meta-analysis studies that attempt to combine the results of many different experiments.

An alternative approach, used in categoryCompare, would be to compare the significantly enriched categories from the two gene lists. Currently the package supports two category classes, Gene Ontology, and KEGG pathways. Both are used below.

Note 1: I am not proposing that this is the best way to analyse this particular data, it is a sample data set that merely serves to illustrate the functionality of this package. However, there are many different experiments where this type of approach is definitely appropriate, and it is up to the user to determine if their data fits the analytical paradigm advocated here.

Create Gene List

library("categoryCompare2")
library("GO.db")
library("org.Hs.eg.db")

g10 <- unique(table10$Entrez[table10$adj.P.Val < 0.05])
g48 <- unique(table48$Entrez[table48$adj.P.Val < 0.05])

Create GO Annotation Object

Before we can do our analysis, we need to define the annotation object, which maps the annotations to the features (genes in this case). For a Gene Ontology (GO) based analysis, this would be all the genes annotated to a particular GO term based on inheritance in the GO DAG. We can generate this list using the GOALL column of the org.Hs.eg.db, and then filter to the terms of interest, or use them all.

go_all_gene <- AnnotationDbi::select(
  org.Hs.eg.db,
  keys = gUniverse,
  columns = c("GOALL", "ONTOLOGYALL")
)

## 'select()' returned 1:many mapping between keys and columns

go_all_gene <- go_all_gene[go_all_gene$ONTOLOGYALL == "BP", ]
bp_2_gene <- split(go_all_gene$ENTREZID, go_all_gene$GOALL)

bp_2_gene <- lapply(bp_2_gene, unique)
bp_desc <- AnnotationDbi::select(
  GO.db,
  keys = names(bp_2_gene),
  columns = "TERM",
  keytype = "GOID"
)$TERM

## 'select()' returned 1:1 mapping between keys and columns

names(bp_desc) <- names(bp_2_gene)

bp_annotation <- categoryCompare2::annotation(
  annotation_features = bp_2_gene,
  description = bp_desc,
  annotation_type = "GO.BP"
)

Do Enrichment

Now we can do hypergeometric enrichment with each of the gene lists.

g10_enrich <- hypergeometric_feature_enrichment(
  new(
    "hypergeometric_features",
    significant = g10,
    universe = gUniverse,
    annotation = bp_annotation
  ),
  p_adjust = "BH"
)

g48_enrich <- hypergeometric_feature_enrichment(
  new(
    "hypergeometric_features",
    significant = g48,
    universe = gUniverse,
    annotation = bp_annotation
  ),
  p_adjust = "BH"
)

Combine and Find Significant

bp_combined <- combine_enrichments(g10 = g10_enrich, g48 = g48_enrich)

bp_sig <- get_significant_annotations(
  bp_combined,
  padjust <= 0.001,
  counts >= 2
)
bp_sig@statistics@significant

## Signficance Cutoffs:
##   ~padjust <= 0.001
##   ~counts >= 2
## 
## Counts:
##    g10 g48 counts
## G1   1   1     60
## G2   1   0     38
## G3   0   1     49
## G4   0   0  13764

Generate Graph

bp_graph <- generate_annotation_graph(bp_sig)
bp_graph

## A cc_graph with
## Number of Nodes = 123 
## Number of Edges = 6793 
##    g10 g48 counts
## G1   1   1     53
## G2   1   0     24
## G3   0   1     46

bp_graph <- remove_edges(bp_graph, 0.8)

## Removed 6593 edges from graph

bp_graph

## A cc_graph with
## Number of Nodes = 123 
## Number of Edges = 200 
##    g10 g48 counts
## G1   1   1     53
## G2   1   0     24
## G3   0   1     46

bp_assign <- annotation_combinations(bp_graph)
bp_assign <- assign_colors(bp_assign)

visNetwork Visualization

We can use the DiagrammeR and visNetwork html widgets to create interactive visualizations either in the RStudio viewer, or as panes in the html report.

Find Communities

It is useful to define the annotations in terms of their communities. To do this we run methods that find and then label the communities, before generating the visualization and table.

bp_communities <- assign_communities(bp_graph)
bp_comm_labels <- label_communities(bp_communities, bp_annotation)

Create Stats Table

To provide a list of which GO terms are in each of the communities we found, lets generate a table, with the community labels so it makes it easier to find them in the graph if desired.

bp_table <- table_from_graph(bp_graph, bp_assign, bp_comm_labels)
knitr::kable(bp_table)

name	description	sig_group	g10.p	g10.odds	g10.expected	g10.counts	g10.padjust	g10.significant	g48.p	g48.odds	g48.expected	g48.counts	g48.padjust	g48.significant	group
	spindle organization		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	1
GO:0007051	spindle organization	g10,g48	0.0000070	3.027139	10.2303351	26	0.0009908	687	0.0000000	11.185374	1.4593491	13	0.0000005	98	1
GO:0007052	mitotic spindle organization	g48	0.0000397	3.314717	6.9302270	19	0.0040651	687	0.0000000	12.523034	0.9885913	10	0.0000084	98	1
GO:0051225	spindle assembly	g48	0.0017651	2.642299	6.5177135	15	0.0919640	687	0.0000003	11.786677	0.9297466	9	0.0000510	98	1
GO:1902850	microtubule cytoskeleton organization involved in mitosis	g48	0.0000356	3.012121	8.6627837	22	0.0037207	687	0.0000000	12.207052	1.2357392	12	0.0000007	98	1
	cell cycle phase transition		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	2
GO:0007346	regulation of mitotic cell cycle	g10,g48	0.0000000	2.727088	26.3183620	60	0.0000002	687	0.0000000	6.356582	3.7542933	19	0.0000010	98	2
GO:0044770	cell cycle phase transition	g10,g48	0.0000000	3.059389	27.8859133	69	0.0000000	687	0.0000000	8.175245	3.9779032	24	0.0000000	98	2
GO:0044772	mitotic cell cycle phase transition	g10,g48	0.0000000	3.184457	22.5232377	58	0.0000000	687	0.0000000	9.787573	3.2129218	23	0.0000000	98	2
GO:1901987	regulation of cell cycle phase transition	g10,g48	0.0000000	3.281417	21.6157079	57	0.0000000	687	0.0000000	7.363217	3.0834634	18	0.0000003	98	2
GO:1901990	regulation of mitotic cell cycle phase transition	g10,g48	0.0000000	3.488421	16.5005404	46	0.0000000	687	0.0000000	9.227687	2.3537889	17	0.0000001	98	2
	chromosome segregation		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	3
GO:0000070	mitotic sister chromatid segregation	g10,g48	0.0000000	4.107415	9.4053080	30	0.0000019	687	0.0000000	16.189149	1.3416597	16	0.0000000	98	3
GO:0000819	sister chromatid segregation	g10,g48	0.0000000	3.692304	11.2203675	33	0.0000028	687	0.0000000	15.465890	1.6005764	18	0.0000000	98	3
GO:0007059	chromosome segregation	g10,g48	0.0000000	2.872291	18.7281134	45	0.0000050	687	0.0000000	10.621801	2.6715504	21	0.0000000	98	3
GO:0098813	nuclear chromosome segregation	g10,g48	0.0000000	3.314335	13.6954485	37	0.0000039	687	0.0000000	15.205016	1.9536448	21	0.0000000	98	3
	cell cycle checkpoint signaling		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	4
GO:0000077	DNA damage checkpoint signaling	g10	0.0000000	5.718374	5.6926864	23	0.0000009	687	0.0012628	6.859039	0.8120572	5	0.0825711	98	4
GO:0031570	DNA integrity checkpoint signaling	g10	0.0000000	6.337570	6.2702054	27	0.0000000	687	0.0002563	7.601553	0.8944398	6	0.0227078	98	4
GO:0000075	cell cycle checkpoint signaling	g10,g48	0.0000000	6.701797	8.8277891	39	0.0000000	687	0.0000000	14.580645	1.2592771	14	0.0000000	98	4
GO:0007093	mitotic cell cycle checkpoint signaling	g10,g48	0.0000000	7.975779	6.2702054	31	0.0000000	687	0.0000000	19.824090	0.8944398	13	0.0000000	98	4
	meiotic cell cycle		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	5
GO:0051321	meiotic cell cycle	g10,g48	0.0000010	3.097207	11.6328810	30	0.0001882	687	0.0000000	9.679504	1.6594212	13	0.0000020	98	5
GO:0007127	meiosis I	g48	0.0001608	3.675248	4.7026540	14	0.0127789	687	0.0000003	14.839002	0.6708298	8	0.0000477	98	5
GO:0061982	meiosis I cell cycle process	g48	0.0000085	4.188773	5.1976702	17	0.0011615	687	0.0000000	15.308989	0.7414435	9	0.0000083	98	5
GO:0140013	meiotic nuclear division	g48	0.0009529	2.630117	7.4252432	17	0.0554642	687	0.0000010	10.172285	1.0592050	9	0.0001437	98	5
GO:1903046	meiotic cell cycle process	g48	0.0000079	3.273343	8.4977783	23	0.0010902	687	0.0000003	9.941349	1.2122013	10	0.0000506	98	5
	negative regulation of cell cycle		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	6
GO:0010948	negative regulation of cell cycle process	g10,g48	0.0000000	4.177036	14.7679837	47	0.0000000	687	0.0000000	8.887379	2.1066410	15	0.0000005	98	6
GO:0045786	negative regulation of cell cycle	g10,g48	0.0000000	3.213583	19.5531404	51	0.0000000	687	0.0000001	6.518235	2.7892398	15	0.0000173	98	6
GO:1901988	negative regulation of cell cycle phase transition	g10,g48	0.0000000	4.838270	12.1278972	43	0.0000000	687	0.0000000	10.145363	1.7300348	14	0.0000004	98	6
	negative regulation of mitotic cell cycle		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	7
GO:0045930	negative regulation of mitotic cell cycle	g10,g48	0.0000000	4.426503	11.0553621	37	0.0000000	687	0.0000000	10.248323	1.5770385	13	0.0000011	98	7
GO:1901991	negative regulation of mitotic cell cycle phase transition	g10,g48	0.0000000	5.110409	8.3327729	31	0.0000000	687	0.0000000	14.148797	1.1886634	13	0.0000001	98	7
	organelle fission		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	8
GO:0000280	nuclear division	g10,g48	0.0000000	2.823351	20.2956647	48	0.0000030	687	0.0000000	9.701818	2.8951603	21	0.0000000	98	8
GO:0048285	organelle fission	g10,g48	0.0000000	2.717261	22.2757296	51	0.0000032	687	0.0000000	8.740416	3.1776150	21	0.0000000	98	8
GO:0140014	mitotic nuclear division	g10,g48	0.0000002	3.006211	14.3554702	36	0.0000378	687	0.0000000	11.643750	2.0477963	18	0.0000000	98	8
	negative regulation of cell cycle G2/M phase transition		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	9
GO:0010972	negative regulation of G2/M transition of mitotic cell cycle	g10,g48	0.0000013	6.336404	3.2176054	14	0.0002276	687	0.0000003	19.704327	0.4589888	7	0.0000477	98	9
GO:0044818	mitotic G2/M transition checkpoint	g10,g48	0.0000044	6.773333	2.6400865	12	0.0007044	687	0.0000016	20.576087	0.3766062	6	0.0002288	98	9
GO:1902750	negative regulation of cell cycle G2/M phase transition	g10,g48	0.0000026	5.865500	3.3826108	14	0.0004436	687	0.0000004	18.540724	0.4825267	7	0.0000653	98	9
	chromosome localization		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	10
GO:0007080	mitotic metaphase chromosome alignment	g48	0.0003750	4.499261	2.8875946	10	0.0251998	687	0.0000001	22.530220	0.4119131	7	0.0000237	98	10
GO:0050000	chromosome localization	g48	0.0003400	3.195334	5.6101837	15	0.0233007	687	0.0000011	12.102222	0.8002882	8	0.0001670	98	10
GO:0051310	metaphase chromosome alignment	g48	0.0000317	4.137086	4.6201513	15	0.0034137	687	0.0000002	15.150000	0.6590609	8	0.0000428	98	10
	cell cycle G2/M phase transition		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	11
GO:0000086	G2/M transition of mitotic cell cycle	g10,g48	0.0000002	4.091578	7.5077459	24	0.0000413	687	0.0000000	17.645022	1.0709739	14	0.0000000	98	11
GO:0010389	regulation of G2/M transition of mitotic cell cycle	g10,g48	0.0000001	5.060803	5.3626756	20	0.0000295	687	0.0000000	16.888430	0.7649814	10	0.0000008	98	11
GO:0044839	cell cycle G2/M phase transition	g10,g48	0.0000001	3.914802	8.4152756	26	0.0000292	687	0.0000000	16.913170	1.2004323	15	0.0000000	98	11
GO:1902749	regulation of cell cycle G2/M phase transition	g10,g48	0.0000008	4.375505	5.9401945	20	0.0001587	687	0.0000000	14.968842	0.8473640	10	0.0000022	98	11
	chromosome separation		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	12
GO:0007094	mitotic spindle assembly checkpoint signaling	g10,g48	0.0000065	7.296641	2.3100757	11	0.0009293	687	0.0000000	36.484444	0.3295304	8	0.0000002	98	12
GO:0010965	regulation of mitotic sister chromatid separation	g10,g48	0.0000041	6.120673	3.0526000	13	0.0006714	687	0.0000000	34.520202	0.4354509	10	0.0000000	98	12
GO:0031577	spindle checkpoint signaling	g10,g48	0.0000065	7.296641	2.3100757	11	0.0009293	687	0.0000000	36.484444	0.3295304	8	0.0000002	98	12
GO:0051784	negative regulation of nuclear division	g10,g48	0.0000057	5.875074	3.1351027	13	0.0008622	687	0.0000000	24.293333	0.4472199	8	0.0000023	98	12
GO:0071173	spindle assembly checkpoint signaling	g10,g48	0.0000065	7.296641	2.3100757	11	0.0009293	687	0.0000000	36.484444	0.3295304	8	0.0000002	98	12
GO:0071174	mitotic spindle checkpoint signaling	g10,g48	0.0000065	7.296641	2.3100757	11	0.0009293	687	0.0000000	36.484444	0.3295304	8	0.0000002	98	12
GO:0033046	negative regulation of sister chromatid segregation	g48	0.0000097	6.890368	2.3925784	11	0.0012689	687	0.0000000	34.742857	0.3412994	8	0.0000003	98	12
GO:0033047	regulation of mitotic sister chromatid segregation	g48	0.0000128	5.887536	2.8875946	12	0.0016295	687	0.0000000	31.904494	0.4119131	9	0.0000001	98	12
GO:0033048	negative regulation of mitotic sister chromatid segregation	g48	0.0000097	6.890368	2.3925784	11	0.0012689	687	0.0000000	34.742857	0.3412994	8	0.0000003	98	12
GO:0045839	negative regulation of mitotic nuclear division	g48	0.0000128	5.887536	2.8875946	12	0.0016295	687	0.0000000	27.002469	0.4119131	8	0.0000012	98	12
GO:0045841	negative regulation of mitotic metaphase/anaphase transition	g48	0.0000097	6.890368	2.3925784	11	0.0012689	687	0.0000000	34.742857	0.3412994	8	0.0000003	98	12
GO:0051304	chromosome separation	g48	0.0000430	4.274607	4.2076378	14	0.0043659	687	0.0000000	22.694013	0.6002162	10	0.0000001	98	12
GO:0051306	mitotic sister chromatid separation	g48	0.0000079	5.648368	3.2176054	13	0.0010902	687	0.0000000	32.131661	0.4589888	10	0.0000000	98	12
GO:0051985	negative regulation of chromosome segregation	g48	0.0000141	6.526861	2.4750811	11	0.0017406	687	0.0000000	33.159596	0.3530683	8	0.0000004	98	12
GO:1902100	negative regulation of metaphase/anaphase transition of cell cycle	g48	0.0000141	6.526861	2.4750811	11	0.0017406	687	0.0000000	33.159596	0.3530683	8	0.0000004	98	12
GO:1905818	regulation of chromosome separation	g48	0.0000203	4.653614	3.9601297	14	0.0023476	687	0.0000000	24.494617	0.5649093	10	0.0000001	98	12
GO:1905819	negative regulation of chromosome separation	g48	0.0000141	6.526861	2.4750811	11	0.0017406	687	0.0000000	33.159596	0.3530683	8	0.0000004	98	12
GO:2000816	negative regulation of mitotic sister chromatid separation	g48	0.0000097	6.890368	2.3925784	11	0.0012689	687	0.0000000	34.742857	0.3412994	8	0.0000003	98	12
	regulation of chromosome segregation		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	13
GO:0007091	metaphase/anaphase transition of mitotic cell cycle	g48	0.0000397	4.038053	4.7026540	15	0.0040651	687	0.0000000	22.492004	0.6708298	11	0.0000000	98	13
GO:0030071	regulation of mitotic metaphase/anaphase transition	g48	0.0000317	4.137086	4.6201513	15	0.0034137	687	0.0000000	22.994636	0.6590609	11	0.0000000	98	13
GO:0033045	regulation of sister chromatid segregation	g48	0.0000440	3.771485	5.2801729	16	0.0044352	687	0.0000000	21.941861	0.7532124	12	0.0000000	98	13
GO:0044784	metaphase/anaphase transition of cell cycle	g48	0.0000496	3.943625	4.7851567	15	0.0047576	687	0.0000000	22.010761	0.6825988	11	0.0000000	98	13
GO:0051983	regulation of chromosome segregation	g48	0.0001630	3.152508	6.4352108	17	0.0128811	687	0.0000000	19.209412	0.9179777	13	0.0000000	98	13
GO:1902099	regulation of metaphase/anaphase transition of cell cycle	g48	0.0000397	4.038053	4.7026540	15	0.0040651	687	0.0000000	22.492004	0.6708298	11	0.0000000	98	13
	regulation of DNA biosynthetic process		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	14
GO:2000278	regulation of DNA biosynthetic process	g10	0.0000002	5.271688	4.9501621	19	0.0000360	687	0.0053152	6.210486	0.7061367	4	0.2464644	98	14
GO:2000573	positive regulation of DNA biosynthetic process	g10	0.0000000	9.084948	2.9700973	16	0.0000018	687	0.0667043	5.021446	0.4236820	2	1.0000000	98	14
	positive regulation of chromosome separation		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	15
GO:1901970	positive regulation of mitotic sister chromatid separation	g48	0.0179681	4.965674	1.0725351	4	0.4679284	687	0.0000002	55.248656	0.1529963	5	0.0000428	98	15
GO:1905820	positive regulation of chromosome separation	g48	0.0252188	3.493402	1.7325567	5	0.5672621	687	0.0000036	27.597446	0.2471478	5	0.0004870	98	15
	recombinational repair		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	16
GO:0000724	double-strand break repair via homologous recombination	g10,g48	0.0000000	4.484967	8.8277891	30	0.0000004	687	0.0000004	9.526710	1.2592771	10	0.0000693	98	16
GO:0000725	recombinational repair	g10,g48	0.0000000	4.581418	8.9927945	31	0.0000002	687	0.0000005	9.331956	1.2828149	10	0.0000797	98	16
	DNA replication		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	17
GO:0006260	DNA replication	g10,g48	0.0000000	6.904838	14.5204756	64	0.0000000	687	0.0000000	10.652225	2.0713342	17	0.0000000	98	17
GO:0006261	DNA-templated DNA replication	g10,g48	0.0000000	9.333025	8.9927945	48	0.0000000	687	0.0000001	10.490382	1.2828149	11	0.0000097	98	17
	regulation of nuclear division		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	18
GO:0007088	regulation of mitotic nuclear division	g48	0.0002256	3.051623	6.6002162	17	0.0168703	687	0.0000000	14.952524	0.9415156	11	0.0000005	98	18
GO:0051783	regulation of nuclear division	g48	0.0008491	2.575126	8.0027621	18	0.0496320	687	0.0000000	11.971799	1.1415876	11	0.0000032	98	18
	regulation of DNA metabolic process		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	19
GO:0051054	positive regulation of DNA metabolic process	g10	0.0000000	3.413823	15.2629999	42	0.0000003	687	0.0060259	3.479257	2.1772547	7	0.2636052	98	19
GO:0051052	regulation of DNA metabolic process	g10,g48	0.0000000	2.876259	25.2458268	60	0.0000001	687	0.0000005	5.341632	3.6012970	16	0.0000723	98	19
	positive regulation of ubiquitin-protein transferase activity		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	20
GO:0051443	positive regulation of ubiquitin-protein transferase activity	g48	0.1365378	3.714842	0.6600216	2	1.0000000	687	0.0000012	87.500000	0.0941516	4	0.0001747	98	20
GO:1904668	positive regulation of ubiquitin protein ligase activity	g48	0.0815704	5.573723	0.4950162	2	0.9188912	687	0.0000003	175.042553	0.0706137	4	0.0000456	98	20
	meiotic chromosome segregation		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	21
GO:0045132	meiotic chromosome segregation	g48	0.0044778	3.258207	3.3001081	9	0.1837478	687	0.0000003	19.104895	0.4707578	7	0.0000553	98	21
GO:0045143	homologous chromosome segregation	g48	0.0114429	3.730788	1.9800648	6	0.3553170	687	0.0000073	23.231466	0.2824547	5	0.0009257	98	21
	telomere organization		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	22
GO:0000723	telomere maintenance	g10	0.0000000	5.283315	8.4152756	32	0.0000000	687	0.0069056	4.507261	1.2004323	5	0.2946732	98	22
GO:0032200	telomere organization	g10	0.0000000	5.503759	9.2403026	36	0.0000000	687	0.0019975	4.997744	1.3181218	6	0.1129586	98	22
	mitotic DNA integrity checkpoint signaling		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	23
GO:0044773	mitotic DNA damage checkpoint signaling	g10	0.0000001	7.263189	3.3826108	16	0.0000137	687	0.0013084	9.421507	0.4825267	4	0.0825711	98	23
GO:0044774	mitotic DNA integrity checkpoint signaling	g10	0.0000000	7.154284	3.6301189	17	0.0000065	687	0.0001538	11.290323	0.5178336	5	0.0144605	98	23
	positive regulation of chromosome organization		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	24
GO:0032206	positive regulation of telomere maintenance	g10	0.0000053	4.993435	4.0426324	15	0.0008188	687	0.4411013	1.757088	0.5766783	1	1.0000000	98	24
GO:2001252	positive regulation of chromosome organization	g10	0.0000008	4.375505	5.9401945	20	0.0001587	687	0.0526481	3.734554	0.8473640	3	0.9611395	98	24
	cell cycle DNA replication		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	25
GO:0033260	nuclear DNA replication	g10,g48	0.0000000	10.636161	2.5575838	15	0.0000013	687	0.0000000	37.723698	0.3648373	9	0.0000000	98	25
GO:0044786	cell cycle DNA replication	g10,g48	0.0000000	10.009191	2.6400865	15	0.0000021	687	0.0000000	36.079140	0.3766062	9	0.0000000	98	25
	DNA-templated DNA replication maintenance of fidelity		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	26
GO:0031297	replication fork processing	g10	0.0000000	10.177298	2.9700973	17	0.0000002	687	0.0007960	10.900266	0.4236820	4	0.0577893	98	26
GO:0045005	DNA-templated DNA replication maintenance of fidelity	g10	0.0000000	10.319433	3.3001081	19	0.0000000	687	0.0011914	9.684397	0.4707578	4	0.0789242	98	26
	other		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	27
GO:0000082	G1/S transition of mitotic cell cycle	g10	0.0000045	2.837466	12.4579080	30	0.0007149	687	0.0000102	6.518375	1.7771106	10	0.0012229	98	27
GO:0000731	DNA synthesis involved in DNA repair	g10	0.0000003	11.285503	1.8150594	11	0.0000691	687	0.0271782	8.551042	0.2589168	2	0.6703483	98	27
GO:0006270	DNA replication initiation	g10	0.0000000	14.188988	2.2275730	15	0.0000001	687	0.0000134	20.056207	0.3177615	5	0.0015661	98	27
GO:0006271	DNA strand elongation involved in DNA replication	g10	0.0000000	73.660237	1.2375405	13	0.0000000	687	0.0006491	21.623684	0.1765342	3	0.0493398	98	27
GO:0006298	mismatch repair	g10	0.0000008	8.471111	2.3100757	12	0.0001566	687	0.0425010	6.572917	0.3295304	2	0.8519193	98	27
GO:0006301	postreplication repair	g10	0.0000041	11.255162	1.4850486	9	0.0006778	687	0.0185565	10.694010	0.2118410	2	0.5551394	98	27
GO:0022616	DNA strand elongation	g10	0.0000000	18.193741	2.1450703	16	0.0000000	687	0.0033770	11.266819	0.3059926	3	0.1702075	98	27
GO:0042770	signal transduction in response to DNA damage	g10	0.0000012	3.132506	11.1378648	29	0.0002256	687	0.0050543	4.095046	1.5888075	6	0.2359415	98	27
GO:0071897	DNA biosynthetic process	g10	0.0000000	6.618081	8.6627837	38	0.0000000	687	0.0000301	7.452005	1.2357392	8	0.0031727	98	27
GO:1901293	nucleoside phosphate biosynthetic process	g10	0.0000049	2.468761	17.7380809	38	0.0007709	687	0.0408801	2.502600	2.5303230	6	0.8306317	98	27
GO:1901976	regulation of cell cycle checkpoint	g10	0.0000013	7.971765	2.3925784	12	0.0002276	687	0.0000193	18.380376	0.3412994	5	0.0021355	98	27
GO:0000727	double-strand break repair via break-induced replication	g10,g48	0.0000002	78.636765	0.6600216	7	0.0000402	687	0.0000012	87.500000	0.0941516	4	0.0001747	98	27
GO:0006275	regulation of DNA replication	g10,g48	0.0000013	4.212338	6.1052000	20	0.0002363	687	0.0000000	14.497514	0.8709019	10	0.0000028	98	27
GO:0006281	DNA repair	g10,g48	0.0000000	3.767273	29.7834754	85	0.0000000	687	0.0000000	5.546413	4.2485889	19	0.0000061	98	27
GO:0006302	double-strand break repair	g10,g48	0.0000000	3.576974	15.0979945	43	0.0000001	687	0.0000002	7.250311	2.1537168	13	0.0000346	98	27
GO:0006310	DNA recombination	g10,g48	0.0000000	3.607890	16.0880269	46	0.0000000	687	0.0000001	7.410681	2.2949442	14	0.0000104	98	27
GO:0010564	regulation of cell cycle process	g10,g48	0.0000000	2.293814	36.5486970	72	0.0000029	687	0.0000000	5.045454	5.2136424	21	0.0000062	98	27
GO:0030174	regulation of DNA-templated DNA replication initiation	g10,g48	0.0000003	29.993127	0.9075297	8	0.0000565	687	0.0000056	49.981763	0.1294584	4	0.0007475	98	27
GO:0033044	regulation of chromosome organization	g10,g48	0.0000000	3.555713	12.6229134	36	0.0000016	687	0.0000000	8.836723	1.8006485	13	0.0000049	98	27
GO:0051276	chromosome organization	g10,g48	0.0000000	3.786010	27.0608863	78	0.0000000	687	0.0000000	8.958362	3.8602138	25	0.0000000	98	27
GO:0051301	cell division	g10,g48	0.0000000	2.312187	32.0935511	64	0.0000112	687	0.0000000	7.825069	4.5781194	26	0.0000000	98	27
GO:1902969	mitotic DNA replication	g10,g48	0.0000000	20.703649	1.4025459	11	0.0000025	687	0.0000000	48.723320	0.2000721	6	0.0000053	98	27
GO:1903047	mitotic cell cycle process	g10,g48	0.0000000	3.103393	39.2712862	96	0.0000000	687	0.0000000	9.359375	5.6020175	34	0.0000000	98	27
GO:0000226	microtubule cytoskeleton organization	g48	0.0000656	1.933876	28.7109403	50	0.0060068	687	0.0000005	5.007870	4.0955927	17	0.0000785	98	27
GO:0000910	cytokinesis	g48	0.2568559	1.292354	8.7452864	11	1.0000000	687	0.0000038	8.477702	1.2475081	9	0.0005168	98	27
GO:0010639	negative regulation of organelle organization	g48	0.0007806	1.936907	19.3056323	34	0.0470060	687	0.0000032	5.541868	2.7539330	13	0.0004389	98	27
GO:0051338	regulation of transferase activity	g48	0.0005224	2.036351	17.4080701	32	0.0339590	687	0.0000010	6.203387	2.4832473	13	0.0001462	98	27
GO:0051984	positive regulation of chromosome segregation	g48	0.0165229	3.993507	1.5675513	5	0.4560508	687	0.0000021	31.547619	0.2236099	5	0.0002921	98	27
GO:0090068	positive regulation of cell cycle process	g48	0.0004205	2.223913	13.6129458	27	0.0277249	687	0.0000033	6.629721	1.9418758	11	0.0004613	98	27
GO:0090231	regulation of spindle checkpoint	g48	0.0000278	13.097549	1.0725351	7	0.0031241	687	0.0000002	55.248656	0.1529963	5	0.0000428	98	27
GO:0090307	mitotic spindle assembly	g48	0.0086364	2.884324	3.6301189	9	0.3057009	687	0.0000007	17.031185	0.5178336	7	0.0001023	98	27
GO:1901992	positive regulation of mitotic cell cycle phase transition	g48	0.0000931	3.684977	5.0326648	15	0.0080440	687	0.0000065	11.645299	0.7179056	7	0.0008425	98	27
GO:2001251	negative regulation of chromosome organization	g48	0.0002380	3.510979	4.8676594	14	0.0175183	687	0.0000000	16.541798	0.6943677	9	0.0000049	98	27

Actually Visualize It!

bp_network <- graph_to_visnetwork(bp_graph, bp_assign, bp_comm_labels)

vis_visnetwork(bp_network)

annotation_table <- annotation_gene_table(
  bp_combined,
  graph::nodes(bp_graph),
  use_db = org.Hs.eg.db
)

We will show the table that is generated here for the first 3 GO terms.

This one is not run, below you find the table.

kable_annotation_table(annotation_table, header = 4)
csv_annotation_table(annotation_table, out_file = "bp_annotations.csv")

GO:0000070 - mitotic sister chromatid segregation

ENTREZID	SYMBOL	GENENAME	significant
3832	KIF11	kinesin family member 11	g10
10615	SPAG5	sperm associated antigen 5	g10
701	BUB1B	BUB1 mitotic checkpoint serine/threonine kinase B	g10
7283	TUBG1	tubulin gamma 1	g10
81620	CDT1	chromatin licensing and DNA replication factor 1	g10
5901	RAN	RAN, member RAS oncogene family	g10
4085	MAD2L1	mitotic arrest deficient 2 like 1	g10
57405	SPC25	SPC25 component of NDC80 kinetochore complex	g10
7517	XRCC3	X-ray repair cross complementing 3	g10
9735	KNTC1	kinetochore associated 1	g10
26065	LSM14A	LSM14A mRNA processing body assembly factor	g10
10403	NDC80	NDC80 kinetochore complex component	g10
10726	NUDC	nuclear distribution C, dynein complex regulator	g10
3835	KIF22	kinesin family member 22	g10
2801	GOLGA2	golgin A2	g10
23636	NUP62	nucleoporin 62	g10
8243	SMC1A	structural maintenance of chromosomes 1A	g10
23212	RRS1	regulator of ribosome synthesis 1	g10
23310	NCAPD3	non-SMC condensin II complex subunit D3	g10
126353	MISP	mitotic spindle positioning	g10
4605	MYBL2	MYB proto-oncogene like 2	g10,g48
11130	ZWINT	ZW10 interacting kinetochore protein	g10,g48
9319	TRIP13	thyroid hormone receptor interactor 13	g10,g48
332	BIRC5	baculoviral IAP repeat containing 5	g10,g48
983	CDK1	cyclin dependent kinase 1	g10,g48
3833	KIFC1	kinesin family member C1	g10,g48
9212	AURKB	aurora kinase B	g10,g48
11065	UBE2C	ubiquitin conjugating enzyme E2 C	g10,g48
9700	ESPL1	extra spindle pole bodies like 1, separase	g10,g48
1843	DUSP1	dual specificity phosphatase 1	g10,g48
991	CDC20	cell division cycle 20	g48
22974	TPX2	TPX2 microtubule nucleation factor	g48
891	CCNB1	cyclin B1	g48
9928	KIF14	kinesin family member 14	g48
11004	KIF2C	kinesin family member 2C	g48
5347	PLK1	polo like kinase 1	g48

GO:0000070 - mitotic sister chromatid segregation

ENTREZID	SYMBOL	GENENAME	significant
3832	KIF11	kinesin family member 11	g10
10615	SPAG5	sperm associated antigen 5	g10
701	BUB1B	BUB1 mitotic checkpoint serine/threonine kinase B	g10
7283	TUBG1	tubulin gamma 1	g10
81620	CDT1	chromatin licensing and DNA replication factor 1	g10
5901	RAN	RAN, member RAS oncogene family	g10
4085	MAD2L1	mitotic arrest deficient 2 like 1	g10
57405	SPC25	SPC25 component of NDC80 kinetochore complex	g10
7517	XRCC3	X-ray repair cross complementing 3	g10
9735	KNTC1	kinetochore associated 1	g10
26065	LSM14A	LSM14A mRNA processing body assembly factor	g10
10403	NDC80	NDC80 kinetochore complex component	g10
10726	NUDC	nuclear distribution C, dynein complex regulator	g10
3835	KIF22	kinesin family member 22	g10
2801	GOLGA2	golgin A2	g10
23636	NUP62	nucleoporin 62	g10
8243	SMC1A	structural maintenance of chromosomes 1A	g10
23212	RRS1	regulator of ribosome synthesis 1	g10
23310	NCAPD3	non-SMC condensin II complex subunit D3	g10
126353	MISP	mitotic spindle positioning	g10
4605	MYBL2	MYB proto-oncogene like 2	g10,g48
11130	ZWINT	ZW10 interacting kinetochore protein	g10,g48
9319	TRIP13	thyroid hormone receptor interactor 13	g10,g48
332	BIRC5	baculoviral IAP repeat containing 5	g10,g48
983	CDK1	cyclin dependent kinase 1	g10,g48
3833	KIFC1	kinesin family member C1	g10,g48
9212	AURKB	aurora kinase B	g10,g48
11065	UBE2C	ubiquitin conjugating enzyme E2 C	g10,g48
9700	ESPL1	extra spindle pole bodies like 1, separase	g10,g48
1843	DUSP1	dual specificity phosphatase 1	g10,g48
991	CDC20	cell division cycle 20	g48
22974	TPX2	TPX2 microtubule nucleation factor	g48
891	CCNB1	cyclin B1	g48
9928	KIF14	kinesin family member 14	g48
11004	KIF2C	kinesin family member 2C	g48
5347	PLK1	polo like kinase 1	g48

GO:0000070 - mitotic sister chromatid segregation

ENTREZID	SYMBOL	GENENAME	significant
3832	KIF11	kinesin family member 11	g10
10615	SPAG5	sperm associated antigen 5	g10
701	BUB1B	BUB1 mitotic checkpoint serine/threonine kinase B	g10
7283	TUBG1	tubulin gamma 1	g10
81620	CDT1	chromatin licensing and DNA replication factor 1	g10
5901	RAN	RAN, member RAS oncogene family	g10
4085	MAD2L1	mitotic arrest deficient 2 like 1	g10
57405	SPC25	SPC25 component of NDC80 kinetochore complex	g10
7517	XRCC3	X-ray repair cross complementing 3	g10
9735	KNTC1	kinetochore associated 1	g10
26065	LSM14A	LSM14A mRNA processing body assembly factor	g10
10403	NDC80	NDC80 kinetochore complex component	g10
10726	NUDC	nuclear distribution C, dynein complex regulator	g10
3835	KIF22	kinesin family member 22	g10
2801	GOLGA2	golgin A2	g10
23636	NUP62	nucleoporin 62	g10
8243	SMC1A	structural maintenance of chromosomes 1A	g10
23212	RRS1	regulator of ribosome synthesis 1	g10
23310	NCAPD3	non-SMC condensin II complex subunit D3	g10
126353	MISP	mitotic spindle positioning	g10
4605	MYBL2	MYB proto-oncogene like 2	g10,g48
11130	ZWINT	ZW10 interacting kinetochore protein	g10,g48
9319	TRIP13	thyroid hormone receptor interactor 13	g10,g48
332	BIRC5	baculoviral IAP repeat containing 5	g10,g48
983	CDK1	cyclin dependent kinase 1	g10,g48
3833	KIFC1	kinesin family member C1	g10,g48
9212	AURKB	aurora kinase B	g10,g48
11065	UBE2C	ubiquitin conjugating enzyme E2 C	g10,g48
9700	ESPL1	extra spindle pole bodies like 1, separase	g10,g48
1843	DUSP1	dual specificity phosphatase 1	g10,g48
991	CDC20	cell division cycle 20	g48
22974	TPX2	TPX2 microtubule nucleation factor	g48
891	CCNB1	cyclin B1	g48
9928	KIF14	kinesin family member 14	g48
11004	KIF2C	kinesin family member 2C	g48
5347	PLK1	polo like kinase 1	g48