categoryCompare2: visNetwork • categoryCompare2

categoryCompare2: Alternative Visualization

Authored by: Robert M Flight <rflight79@gmail.com> on 2025-09-08 19:34:47.943478

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     72
## G2   1   0     53
## G3   0   1     48
## G4   0   0  14118

Generate Graph

bp_graph <- generate_annotation_graph(bp_sig)
bp_graph

## A cc_graph with
## Number of Nodes = 135 
## Number of Edges = 7740 
##    g10 g48 counts
## G1   1   1     64
## G2   1   0     26
## G3   0   1     45

bp_graph <- remove_edges(bp_graph, 0.8)

## Removed 7530 edges from graph

bp_graph

## A cc_graph with
## Number of Nodes = 135 
## Number of Edges = 210 
##    g10 g48 counts
## G1   1   1     64
## G2   1   0     26
## G3   0   1     45

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	0.0000029	3.207006	9.7765269	26	0.0004061	686	0.0000000	11.753385	1.3966467	13	0.0000003	98	1
GO:0007052	mitotic spindle organization	g48	0.0000261	3.436829	6.7367665	19	0.0023784	686	0.0000000	12.910353	0.9623952	10	0.0000067	98	1
GO:0051225	spindle assembly	g48	0.0009736	2.833085	6.1616766	15	0.0476519	686	0.0000002	12.542390	0.8802395	9	0.0000349	98	1
GO:1902850	microtubule cytoskeleton organization involved in mitosis	g48	0.0000207	3.140964	8.3798802	22	0.0020126	686	0.0000000	12.654264	1.1971257	12	0.0000005	98	1
	cell cycle checkpoint signaling		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	2
GO:0000077	DNA damage checkpoint signaling	g10	0.0000000	5.178452	6.0795210	23	0.0000027	686	0.0017076	6.376032	0.8685030	5	0.1065655	98	2
GO:0031570	DNA integrity checkpoint signaling	g10	0.0000000	5.773900	6.6546108	27	0.0000000	686	0.0003576	7.110435	0.9506587	6	0.0309761	98	2
GO:0044773	mitotic DNA damage checkpoint signaling	g10	0.0000013	5.359087	4.1077844	16	0.0001887	686	0.0027179	7.591119	0.5868263	4	0.1526879	98	2
GO:0044774	mitotic DNA integrity checkpoint signaling	g10	0.0000006	5.384322	4.3542515	17	0.0000912	686	0.0003693	9.189068	0.6220359	5	0.0314121	98	2
GO:0000075	cell cycle checkpoint signaling	g10,g48	0.0000000	6.446372	9.0371257	39	0.0000000	686	0.0000000	14.159722	1.2910180	14	0.0000000	98	2
GO:0007093	mitotic cell cycle checkpoint signaling	g10,g48	0.0000000	6.694418	6.7367665	30	0.0000000	686	0.0000000	18.137937	0.9623952	13	0.0000000	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	4.335366	9.0371257	30	0.0000006	686	0.0000000	16.934094	1.2910180	16	0.0000000	98	3
GO:0000819	sister chromatid segregation	g10,g48	0.0000000	3.861664	10.8445509	33	0.0000011	686	0.0000000	16.061842	1.5492216	18	0.0000000	98	3
GO:0007059	chromosome segregation	g10,g48	0.0000000	3.004279	18.0742515	45	0.0000016	686	0.0000000	11.036546	2.5820359	21	0.0000000	98	3
GO:0098813	nuclear chromosome segregation	g10,g48	0.0000000	3.438435	13.3092216	37	0.0000016	686	0.0000000	15.688588	1.9013174	21	0.0000000	98	3
	cell cycle phase transition		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	4
GO:0007346	regulation of mitotic cell cycle	g10,g48	0.0000000	2.773562	25.9611976	60	0.0000001	686	0.0000000	6.441845	3.7087425	19	0.0000008	98	4
GO:0044770	cell cycle phase transition	g10,g48	0.0000000	3.070092	26.9470659	67	0.0000000	686	0.0000000	7.990426	3.8495808	23	0.0000000	98	4
GO:0044772	mitotic cell cycle phase transition	g10,g48	0.0000000	3.065021	22.3463473	56	0.0000000	686	0.0000000	9.265474	3.1923353	22	0.0000000	98	4
GO:1901987	regulation of cell cycle phase transition	g10,g48	0.0000000	3.334450	20.9497006	56	0.0000000	686	0.0000000	7.609177	2.9928144	18	0.0000002	98	4
GO:1901990	regulation of mitotic cell cycle phase transition	g10,g48	0.0000000	3.313661	16.7597605	45	0.0000002	686	0.0000000	9.051627	2.3942515	17	0.0000001	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	0.0000007	3.169753	11.4196407	30	0.0001044	686	0.0000000	9.863492	1.6313772	13	0.0000015	98	5
GO:0061982	meiosis I cell cycle process	g10,g48	0.0000064	4.302375	5.0936527	17	0.0007571	686	0.0000000	15.643629	0.7276647	9	0.0000070	98	5
GO:1903046	meiotic cell cycle process	g10,g48	0.0000052	3.373903	8.2977246	23	0.0006592	686	0.0000002	10.191059	1.1853892	10	0.0000416	98	5
GO:0007127	meiosis I	g48	0.0001538	3.692345	4.6828743	14	0.0108774	686	0.0000003	14.880726	0.6689820	8	0.0000461	98	5
GO:0140013	meiotic nuclear division	g48	0.0007968	2.679455	7.3118563	17	0.0398172	686	0.0000009	10.329775	1.0445509	9	0.0001326	98	5
	negative regulation of mitotic cell cycle		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	6
GO:0045930	negative regulation of mitotic cell cycle	g10,g48	0.0000000	4.347555	11.5017964	38	0.0000000	686	0.0000000	10.748677	1.6431138	14	0.0000002	98	6
GO:1901991	negative regulation of mitotic cell cycle phase transition	g10,g48	0.0000000	4.506058	8.7906587	30	0.0000003	686	0.0000000	13.273342	1.2558084	13	0.0000001	98	6
	organelle fission		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	7
GO:0000280	nuclear division	g10,g48	0.0000000	2.927900	19.7173653	48	0.0000011	686	0.0000000	10.003736	2.8167665	21	0.0000000	98	7
GO:0048285	organelle fission	g10,g48	0.0000000	2.823147	21.6069461	51	0.0000011	686	0.0000000	9.027047	3.0867066	21	0.0000000	98	7
GO:0140014	mitotic nuclear division	g10,g48	0.0000001	3.136102	13.8843114	36	0.0000136	686	0.0000000	12.071027	1.9834731	18	0.0000000	98	7
	establishment of chromosome localization		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	8
GO:0007080	mitotic metaphase chromosome alignment	g48	0.0010316	4.231905	2.7111377	9	0.0498075	686	0.0000019	19.867150	0.3873054	6	0.0002745	98	8
GO:0051303	establishment of chromosome localization	g48	0.0002278	3.527315	4.8471856	14	0.0150013	686	0.0000051	12.130178	0.6924551	7	0.0006653	98	8
GO:0051310	metaphase chromosome alignment	g48	0.0000817	3.970833	4.4364072	14	0.0061796	686	0.0000028	13.428805	0.6337725	7	0.0003795	98	8
	DNA biosynthetic process		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	9
GO:0071897	DNA biosynthetic process	g10	0.0000000	5.521034	10.2694611	40	0.0000000	686	0.0006377	5.302477	1.4670659	7	0.0481780	98	9
GO:2000278	regulation of DNA biosynthetic process	g10	0.0000005	4.129617	6.8189222	22	0.0000880	686	0.0161796	4.402370	0.9741317	4	0.5231269	98	9
GO:2000573	positive regulation of DNA biosynthetic process	g10	0.0000000	6.545688	4.5185629	20	0.0000013	686	0.0264931	4.979757	0.6455090	3	0.6799512	98	9
	chromosome separation		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	10
GO:0007094	mitotic spindle assembly checkpoint signaling	g10,g48	0.0000041	7.789630	2.2182036	11	0.0005330	686	0.0000000	38.516959	0.3168862	8	0.0000002	98	10
GO:0010965	regulation of mitotic sister chromatid separation	g10,g48	0.0000027	6.417275	2.9576048	13	0.0003836	686	0.0000000	35.952797	0.4225150	10	0.0000000	98	10
GO:0031577	spindle checkpoint signaling	g10,g48	0.0000041	7.789630	2.2182036	11	0.0005330	686	0.0000000	38.516959	0.3168862	8	0.0000002	98	10
GO:0033046	negative regulation of sister chromatid segregation	g10,g48	0.0000062	7.330457	2.3003593	11	0.0007471	686	0.0000000	36.586667	0.3286228	8	0.0000002	98	10
GO:0033047	regulation of mitotic sister chromatid segregation	g10,g48	0.0000087	6.184516	2.7932934	12	0.0009923	686	0.0000000	33.277753	0.3990419	9	0.0000001	98	10
GO:0033048	negative regulation of mitotic sister chromatid segregation	g10,g48	0.0000062	7.330457	2.3003593	11	0.0007471	686	0.0000000	36.586667	0.3286228	8	0.0000002	98	10
GO:0045839	negative regulation of mitotic nuclear division	g10,g48	0.0000087	6.184516	2.7932934	12	0.0009923	686	0.0000000	28.123077	0.3990419	8	0.0000009	98	10
GO:0045841	negative regulation of mitotic metaphase/anaphase transition	g10,g48	0.0000062	7.330457	2.3003593	11	0.0007471	686	0.0000000	36.586667	0.3286228	8	0.0000002	98	10
GO:0051306	mitotic sister chromatid separation	g10,g48	0.0000054	5.902348	3.1219162	13	0.0006764	686	0.0000000	33.376623	0.4459880	10	0.0000000	98	10
GO:0051784	negative regulation of nuclear division	g10,g48	0.0000039	6.149084	3.0397605	13	0.0005330	686	0.0000000	25.204598	0.4342515	8	0.0000017	98	10
GO:0071173	spindle assembly checkpoint signaling	g10,g48	0.0000041	7.789630	2.2182036	11	0.0005330	686	0.0000000	38.516959	0.3168862	8	0.0000002	98	10
GO:0071174	mitotic spindle checkpoint signaling	g10,g48	0.0000041	7.789630	2.2182036	11	0.0005330	686	0.0000000	38.516959	0.3168862	8	0.0000002	98	10
GO:2000816	negative regulation of mitotic sister chromatid separation	g10,g48	0.0000062	7.330457	2.3003593	11	0.0007471	686	0.0000000	36.586667	0.3286228	8	0.0000002	98	10
GO:0051304	chromosome separation	g48	0.0000322	4.414352	4.1077844	14	0.0027860	686	0.0000000	23.329545	0.5868263	10	0.0000001	98	10
GO:0051985	negative regulation of chromosome segregation	g48	0.0000093	6.922305	2.3825150	11	0.0010208	686	0.0000000	34.840212	0.3403593	8	0.0000003	98	10
GO:1902100	negative regulation of metaphase/anaphase transition of cell cycle	g48	0.0000093	6.922305	2.3825150	11	0.0010208	686	0.0000000	34.840212	0.3403593	8	0.0000003	98	10
GO:1905818	regulation of chromosome separation	g48	0.0000148	4.817551	3.8613174	14	0.0015304	686	0.0000000	25.230344	0.5516168	10	0.0000001	98	10
GO:1905819	negative regulation of chromosome separation	g48	0.0000093	6.922305	2.3825150	11	0.0010208	686	0.0000000	34.840212	0.3403593	8	0.0000003	98	10
	negative regulation of cell cycle		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	11
GO:0010948	negative regulation of cell cycle process	g10,g48	0.0000000	4.102046	14.9523353	47	0.0000000	686	0.0000000	8.749369	2.1360479	15	0.0000006	98	11
GO:0045786	negative regulation of cell cycle	g10,g48	0.0000000	3.311475	19.8816766	53	0.0000000	686	0.0000000	6.929419	2.8402395	16	0.0000035	98	11
GO:1901988	negative regulation of cell cycle phase transition	g10,g48	0.0000000	4.723056	12.3233533	43	0.0000000	686	0.0000000	9.946078	1.7604790	14	0.0000005	98	11
	regulation of chromosome segregation		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	12
GO:0007091	metaphase/anaphase transition of mitotic cell cycle	g48	0.0000301	4.156338	4.6007186	15	0.0026255	686	0.0000000	23.059259	0.6572455	11	0.0000000	98	12
GO:0030071	regulation of mitotic metaphase/anaphase transition	g48	0.0000238	4.260805	4.5185629	15	0.0022562	686	0.0000000	23.586207	0.6455090	11	0.0000000	98	12
GO:0033045	regulation of sister chromatid segregation	g48	0.0000339	3.870181	5.1758084	16	0.0028999	686	0.0000000	22.437756	0.7394012	12	0.0000000	98	12
GO:0044784	metaphase/anaphase transition of cell cycle	g48	0.0000378	4.056845	4.6828743	15	0.0031623	686	0.0000000	22.555222	0.6689820	11	0.0000000	98	12
GO:0051983	regulation of chromosome segregation	g48	0.0000374	3.473308	6.3259880	18	0.0031614	686	0.0000000	19.566912	0.9037126	13	0.0000000	98	12
GO:1902099	regulation of metaphase/anaphase transition of cell cycle	g48	0.0000301	4.156338	4.6007186	15	0.0026255	686	0.0000000	23.059259	0.6572455	11	0.0000000	98	12
	cell cycle G2/M phase transition		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	13
GO:0000086	G2/M transition of mitotic cell cycle	g10,g48	0.0000013	3.873448	7.1475449	22	0.0001912	686	0.0000000	15.213023	1.0210778	12	0.0000001	98	13
GO:0010389	regulation of G2/M transition of mitotic cell cycle	g10,g48	0.0000005	4.822955	5.2579641	19	0.0000798	686	0.0000000	17.251683	0.7511377	10	0.0000007	98	13
GO:0044839	cell cycle G2/M phase transition	g10,g48	0.0000007	3.769896	7.9691018	24	0.0001039	686	0.0000000	14.871709	1.1384431	13	0.0000000	98	13
GO:1902749	regulation of cell cycle G2/M phase transition	g10,g48	0.0000022	4.252197	5.7508982	19	0.0003114	686	0.0000000	15.515151	0.8215569	10	0.0000015	98	13
	negative regulation of cell cycle G2/M phase transition		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	14
GO:0010972	negative regulation of G2/M transition of mitotic cell cycle	g10,g48	0.0000054	5.902348	3.1219162	13	0.0006764	686	0.0000002	20.399504	0.4459880	7	0.0000399	98	14
GO:0044818	mitotic G2/M transition checkpoint	g48	0.0000275	5.931076	2.6289820	11	0.0024601	686	0.0000016	20.633779	0.3755689	6	0.0002290	98	14
GO:1902750	negative regulation of cell cycle G2/M phase transition	g48	0.0000104	5.463706	3.2862275	13	0.0011223	686	0.0000003	19.158508	0.4694611	7	0.0000545	98	14
	DNA conformation change		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	15
GO:0032508	DNA duplex unwinding	g10	0.0000000	7.162162	4.2720958	20	0.0000005	686	0.0000295	11.634215	0.6102994	6	0.0031932	98	15
GO:0032392	DNA geometric change	g10,g48	0.0000000	6.691228	4.6828743	21	0.0000005	686	0.0000040	12.618462	0.6689820	7	0.0005454	98	15
GO:0071103	DNA conformation change	g10,g48	0.0000000	5.730827	5.1758084	21	0.0000028	686	0.0000080	11.258242	0.7394012	7	0.0009519	98	15
	regulation of spindle checkpoint		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	16
GO:0090231	regulation of spindle checkpoint	g48	0.0000135	15.791753	0.9858683	7	0.0014139	686	0.0000001	63.325653	0.1408383	5	0.0000277	98	16
GO:0090266	regulation of mitotic cell cycle spindle assembly checkpoint	g48	0.0000970	13.515882	0.9037126	6	0.0071487	686	0.0000055	50.121581	0.1291018	4	0.0006991	98	16
GO:1903504	regulation of mitotic spindle checkpoint	g48	0.0000970	13.515882	0.9037126	6	0.0071487	686	0.0000055	50.121581	0.1291018	4	0.0006991	98	16
	regulation of nuclear division		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	17
GO:0007088	regulation of mitotic nuclear division	g48	0.0001549	3.167218	6.4081437	17	0.0109028	686	0.0000000	15.446046	0.9154491	11	0.0000004	98	17
GO:0051783	regulation of nuclear division	g48	0.0006249	2.655067	7.8047904	18	0.0339568	686	0.0000000	12.294472	1.1149701	11	0.0000024	98	17
	positive regulation of chromosome separation		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	18
GO:1901970	positive regulation of mitotic sister chromatid separation	g48	0.0130991	5.612903	0.9858683	4	0.3579328	686	0.0000001	63.325653	0.1408383	5	0.0000277	98	18
GO:1905820	positive regulation of chromosome separation	g48	0.0202334	3.744004	1.6431138	5	0.4518054	686	0.0000027	29.523298	0.2347305	5	0.0003724	98	18
	meiotic chromosome segregation		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	19
GO:0045132	meiotic chromosome segregation	g48	0.0043544	3.273312	3.2862275	9	0.1620543	686	0.0000003	19.158508	0.4694611	7	0.0000545	98	19
GO:0045143	homologous chromosome segregation	g48	0.0112189	3.748039	1.9717365	6	0.3162607	686	0.0000072	23.296548	0.2816766	5	0.0008596	98	19
	DNA-templated DNA replication maintenance of fidelity		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	20
GO:0031297	replication fork processing	g10	0.0000000	10.555084	2.2182036	13	0.0000095	686	0.0037380	10.826316	0.3168862	3	0.1935512	98	20
GO:0045005	DNA-templated DNA replication maintenance of fidelity	g10	0.0000000	11.414925	2.6289820	16	0.0000002	686	0.0060761	8.954265	0.3755689	3	0.2810139	98	20
	telomere organization		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	21
GO:0000723	telomere maintenance	g10	0.0000000	5.286843	8.1334132	31	0.0000000	686	0.0060263	4.665980	1.1619162	5	0.2805285	98	21
GO:0032200	telomere organization	g10	0.0000000	5.768731	9.2014371	37	0.0000000	686	0.0019702	5.011895	1.3144910	6	0.1181049	98	21
	recombinational repair		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	22
GO:0000724	double-strand break repair via homologous recombination	g10,g48	0.0000000	4.865326	7.4761677	27	0.0000006	686	0.0000010	10.075363	1.0680240	9	0.0001586	98	22
GO:0000725	recombinational repair	g10,g48	0.0000000	4.974795	7.6404790	28	0.0000002	686	0.0000012	9.833066	1.0914970	9	0.0001831	98	22
	regulation of cyclin-dependent protein kinase activity		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	23
GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity	g48	0.0003254	3.591454	4.4364072	13	0.0200435	686	0.0000002	15.857005	0.6337725	8	0.0000330	98	23
GO:1904029	regulation of cyclin-dependent protein kinase activity	g48	0.0003947	3.505484	4.5185629	13	0.0233513	686	0.0000002	15.517731	0.6455090	8	0.0000368	98	23
	microtubule-based process		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	24
GO:0000226	microtubule cytoskeleton organization	g48	0.0000108	2.096531	26.8649102	50	0.0011654	686	0.0000002	5.376902	3.8378443	17	0.0000360	98	24
GO:0007017	microtubule-based process	g48	0.0001646	1.749803	37.6273054	60	0.0115335	686	0.0000050	3.994773	5.3753293	18	0.0006576	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	10.623611	2.3825150	14	0.0000031	686	0.0000000	34.840212	0.3403593	8	0.0000003	98	25
GO:0044786	cell cycle DNA replication	g10,g48	0.0000000	9.958333	2.4646707	14	0.0000050	686	0.0000000	33.252525	0.3520958	8	0.0000003	98	25
	regulation of DNA metabolic process		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	26
GO:0051054	positive regulation of DNA metabolic process	g10	0.0000000	3.342234	16.2668263	44	0.0000002	686	0.0022034	3.771696	2.3238323	8	0.1290505	98	26
GO:0051052	regulation of DNA metabolic process	g10,g48	0.0000000	2.707851	26.4541317	60	0.0000003	686	0.0000045	4.677014	3.7791617	15	0.0005989	98	26
	other		NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	27
GO:0000731	DNA synthesis involved in DNA repair	g10	0.0000002	12.473185	1.7252695	11	0.0000312	686	0.0247685	9.027412	0.2464671	2	0.6459254	98	27
GO:0006270	DNA replication initiation	g10	0.0000000	14.254843	2.2182036	15	0.0000001	686	0.0000132	20.112414	0.3168862	5	0.0014995	98	27
GO:0006271	DNA strand elongation involved in DNA replication	g10	0.0000000	74.001486	1.2323353	13	0.0000000	686	0.0006439	21.684210	0.1760479	3	0.0481780	98	27
GO:0006284	base-excision repair	g10	0.0000042	6.804748	2.6289820	12	0.0005366	686	0.0004986	12.498480	0.3755689	4	0.0393665	98	27
GO:0006298	mismatch repair	g10	0.0000005	9.078932	2.2182036	12	0.0000798	686	0.0395659	6.855833	0.3168862	2	0.8451971	98	27
GO:0006301	postreplication repair	g10	0.0000040	11.307238	1.4788024	9	0.0005330	686	0.0184606	10.723958	0.2112575	2	0.5710414	98	27
GO:0006325	chromatin organization	g10	0.0000054	1.952228	37.3808383	65	0.0006764	686	0.0854652	1.769890	5.3401198	9	1.0000000	98	27
GO:0009411	response to UV	g10	0.0000084	3.157412	9.1192814	24	0.0009772	686	0.0018822	5.060248	1.3027545	6	0.1169500	98	27
GO:0022616	DNA strand elongation	g10	0.0000000	18.278209	2.1360479	16	0.0000000	686	0.0033510	11.298398	0.3051497	3	0.1820863	98	27
GO:0034502	protein localization to chromosome	g10	0.0000000	4.712993	6.4902994	23	0.0000091	686	0.0137047	4.639433	0.9271856	4	0.4608316	98	27
GO:0042770	signal transduction in response to DNA damage	g10	0.0000007	3.319588	10.2694611	28	0.0001099	686	0.0034199	4.457253	1.4670659	6	0.1830496	98	27
GO:1901293	nucleoside phosphate biosynthetic process	g10	0.0000066	2.537702	15.9382036	35	0.0007776	686	0.0262784	2.797410	2.2768862	6	0.6791041	98	27
GO:1901976	regulation of cell cycle checkpoint	g10	0.0000003	9.728699	2.1360479	12	0.0000487	686	0.0000109	21.072709	0.3051497	5	0.0012601	98	27
GO:0000727	double-strand break repair via break-induced replication	g10,g48	0.0000002	79.000000	0.6572455	7	0.0000322	686	0.0000012	87.744681	0.0938922	4	0.0001794	98	27
GO:0006260	DNA replication	g10,g48	0.0000000	7.141972	13.9664671	63	0.0000000	686	0.0000000	11.109739	1.9952096	17	0.0000000	98	27
GO:0006261	DNA-templated DNA replication	g10,g48	0.0000000	10.562406	8.2155689	47	0.0000000	686	0.0000002	10.305556	1.1736527	10	0.0000393	98	27
GO:0006268	DNA unwinding involved in DNA replication	g10,g48	0.0000000	27.272404	1.3966467	12	0.0000001	686	0.0000011	36.917563	0.1995210	5	0.0001673	98	27
GO:0006275	regulation of DNA replication	g10,g48	0.0000000	5.047509	6.7367665	25	0.0000011	686	0.0000000	14.568723	0.9623952	11	0.0000006	98	27
GO:0006281	DNA repair	g10,g48	0.0000000	3.835524	28.2615569	82	0.0000000	686	0.0000000	5.866134	4.0373653	19	0.0000027	98	27
GO:0006302	double-strand break repair	g10,g48	0.0000000	3.674703	13.7200000	40	0.0000001	686	0.0000001	8.042322	1.9600000	13	0.0000124	98	27
GO:0006310	DNA recombination	g10,g48	0.0000000	3.729589	14.6237126	43	0.0000000	686	0.0000001	7.495971	2.0891018	13	0.0000256	98	27
GO:0010564	regulation of cell cycle process	g10,g48	0.0000000	2.356025	35.2447904	71	0.0000013	686	0.0000000	5.243315	5.0349701	21	0.0000035	98	27
GO:0030174	regulation of DNA-templated DNA replication initiation	g10,g48	0.0000003	30.131760	0.9037126	8	0.0000459	686	0.0000055	50.121581	0.1291018	4	0.0006991	98	27
GO:0033044	regulation of chromosome organization	g10,g48	0.0000001	3.306310	12.5698204	34	0.0000110	686	0.0000000	9.727818	1.7956886	14	0.0000006	98	27
GO:0051276	chromosome organization	g10,g48	0.0000000	4.344828	29.5760479	93	0.0000000	686	0.0000000	10.057752	4.2251497	29	0.0000000	98	27
GO:0051301	cell division	g10,g48	0.0000000	2.376914	31.3834731	64	0.0000041	686	0.0000000	7.573577	4.4833533	25	0.0000000	98	27
GO:0090329	regulation of DNA-templated DNA replication	g10,g48	0.0000000	11.399404	2.4646707	15	0.0000006	686	0.0000011	22.358696	0.3520958	6	0.0001610	98	27
GO:1902969	mitotic DNA replication	g10,g48	0.0000000	22.659763	1.2323353	10	0.0000057	686	0.0000005	44.311828	0.1760479	5	0.0000864	98	27
GO:1903047	mitotic cell cycle process	g10,g48	0.0000000	3.148061	37.9559281	94	0.0000000	686	0.0000000	9.257988	5.4222754	33	0.0000000	98	27
GO:0000910	cytokinesis	g48	0.1173880	1.532776	8.2155689	12	1.0000000	686	0.0000023	9.068897	1.1736527	9	0.0003187	98	27
GO:0007143	female meiotic nuclear division	g48	0.0423042	2.954247	1.9717365	5	0.7235861	686	0.0000072	23.296548	0.2816766	5	0.0008596	98	27
GO:0010639	negative regulation of organelle organization	g48	0.0006199	1.966320	19.0601198	34	0.0338113	686	0.0000005	6.142202	2.7228743	14	0.0000728	98	27
GO:0031100	animal organ regeneration	g48	0.0000301	4.156338	4.6007186	15	0.0026255	686	0.0000000	20.271739	0.6572455	10	0.0000002	98	27
GO:0051338	regulation of transferase activity	g48	0.0002615	1.722460	37.4629940	59	0.0168343	686	0.0000047	4.014041	5.3518563	18	0.0006242	98	27
GO:0051984	positive regulation of chromosome segregation	g48	0.0128177	4.321134	1.4788024	5	0.3536241	686	0.0000015	34.073615	0.2112575	5	0.0002225	98	27
GO:0090068	positive regulation of cell cycle process	g48	0.0000760	2.466121	12.9805988	28	0.0057751	686	0.0000021	6.971225	1.8543713	11	0.0003011	98	27
GO:0090307	mitotic spindle assembly	g48	0.0061271	3.074124	3.4505389	9	0.2099832	686	0.0000005	18.059341	0.4929341	7	0.0000757	98	27
GO:0097421	liver regeneration	g48	0.0024515	4.637356	1.9717365	7	0.1015479	686	0.0000072	23.296548	0.2816766	5	0.0008596	98	27
GO:1904668	positive regulation of ubiquitin protein ligase activity	g48	0.1652168	3.198413	0.7394012	2	1.0000000	686	0.0000021	70.187234	0.1056287	4	0.0003011	98	27
GO:2001251	negative regulation of chromosome organization	g48	0.0000378	4.056845	4.6828743	15	0.0031623	686	0.0000000	19.838008	0.6689820	10	0.0000003	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	ribosome biogenesis regulator 1 homolog	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	ribosome biogenesis regulator 1 homolog	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	ribosome biogenesis regulator 1 homolog	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