Cormotifcluster

Last updated: 2023-04-16

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Knit directory: Cardiotoxicity/

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/Cormotifcluster_analysis.Rmd) and HTML (docs/Cormotifcluster_analysis.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	6d925a2	reneeisnowhere	2023-04-16	updating cormotif with updated RNAseq counts
Rmd	4e52216	reneeisnowhere	2023-03-31	End of week updates
Rmd	c365253	reneeisnowhere	2023-03-22	updated code and plots
Rmd	3a26d52	reneeisnowhere	2023-03-22	Wed poster analysis changes
Rmd	a150323	reneeisnowhere	2023-03-20	addingcormotif analysis and go on DEGs

library(tidyverse)
library(gprofiler2)
library(readr)
library(BiocGenerics)
library(gridExtra)
library(VennDiagram)
library(kableExtra)
library(scales)
library(ggVennDiagram)

##motif No response genes

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0034645	cellular macromolecule biosynthetic process	615	1040	3.41e-07
GO:BP	GO:0002181	cytoplasmic translation	115	155	7.89e-07
GO:BP	GO:1901564	organonitrogen compound metabolic process	2727	5164	7.89e-07
GO:BP	GO:0009060	aerobic respiration	129	181	2.98e-06
GO:BP	GO:0045333	cellular respiration	154	223	2.98e-06
GO:BP	GO:0006518	peptide metabolic process	474	795	2.98e-06
GO:BP	GO:0006119	oxidative phosphorylation	100	134	3.00e-06
GO:BP	GO:1901566	organonitrogen compound biosynthetic process	860	1524	3.73e-06
GO:BP	GO:0022904	respiratory electron transport chain	80	103	4.08e-06
GO:BP	GO:0019646	aerobic electron transport chain	61	74	4.13e-06
GO:BP	GO:0019538	protein metabolic process	2311	4367	6.77e-06
GO:BP	GO:0043603	amide metabolic process	585	1009	6.86e-06
GO:BP	GO:0042775	mitochondrial ATP synthesis coupled electron transport	65	82	1.89e-05
GO:BP	GO:0042773	ATP synthesis coupled electron transport	65	82	1.89e-05
GO:BP	GO:0006412	translation	386	645	2.15e-05
GO:BP	GO:0015980	energy derivation by oxidation of organic compounds	192	299	8.81e-05
GO:BP	GO:0043043	peptide biosynthetic process	393	665	1.03e-04
GO:BP	GO:0009100	glycoprotein metabolic process	207	327	1.21e-04
GO:BP	GO:0008150	biological_process	6280	12534	1.21e-04
GO:BP	GO:0043604	amide biosynthetic process	449	772	1.59e-04
GO:BP	GO:0006091	generation of precursor metabolites and energy	267	437	1.99e-04
GO:BP	GO:0022900	electron transport chain	99	142	3.38e-04
GO:BP	GO:0022613	ribonucleoprotein complex biogenesis	274	454	5.69e-04
GO:BP	GO:0043413	macromolecule glycosylation	128	193	5.91e-04
GO:BP	GO:0006486	protein glycosylation	128	193	5.91e-04
GO:BP	GO:0070085	glycosylation	137	209	6.57e-04
GO:BP	GO:0033108	mitochondrial respiratory chain complex assembly	68	94	2.08e-03
GO:BP	GO:0015986	proton motive force-driven ATP synthesis	50	66	4.43e-03
GO:BP	GO:0008152	metabolic process	4446	8768	6.16e-03
GO:BP	GO:0009101	glycoprotein biosynthetic process	163	262	6.43e-03
GO:BP	GO:1901135	carbohydrate derivative metabolic process	517	926	9.56e-03
GO:BP	GO:0006396	RNA processing	527	946	1.06e-02
GO:BP	GO:0042254	ribosome biogenesis	184	303	1.38e-02
GO:BP	GO:0006754	ATP biosynthetic process	62	88	1.65e-02
GO:BP	GO:0006487	protein N-linked glycosylation	48	65	1.69e-02
GO:BP	GO:0042776	proton motive force-driven mitochondrial ATP synthesis	43	57	1.72e-02
GO:BP	GO:0046034	ATP metabolic process	119	187	1.72e-02
GO:BP	GO:0019081	viral translation	17	18	1.91e-02
GO:BP	GO:0042273	ribosomal large subunit biogenesis	53	74	2.51e-02
GO:BP	GO:0009987	cellular process	5967	11931	2.64e-02
GO:BP	GO:0006807	nitrogen compound metabolic process	3909	7699	2.67e-02
GO:BP	GO:0016072	rRNA metabolic process	159	261	2.84e-02
GO:BP	GO:0030199	collagen fibril organization	43	58	2.92e-02
GO:BP	GO:0010257	NADH dehydrogenase complex assembly	41	55	3.29e-02
GO:BP	GO:0032981	mitochondrial respiratory chain complex I assembly	41	55	3.29e-02
GO:BP	GO:0009199	ribonucleoside triphosphate metabolic process	133	215	3.57e-02
GO:BP	GO:0009205	purine ribonucleoside triphosphate metabolic process	129	208	3.72e-02
GO:BP	GO:0044260	cellular macromolecule metabolic process	1476	2817	3.73e-02
GO:BP	GO:0006457	protein folding	120	192	3.77e-02
GO:BP	GO:1901137	carbohydrate derivative biosynthetic process	326	575	4.43e-02
GO:BP	GO:0071704	organic substance metabolic process	4251	8408	4.86e-02
GO:BP	GO:0006122	mitochondrial electron transport, ubiquinol to cytochrome c	12	12	4.98e-02
KEGG	KEGG:05171	Coronavirus disease - COVID-19	122	167	5.05e-08
KEGG	KEGG:03010	Ribosome	98	128	5.05e-08
KEGG	KEGG:04510	Focal adhesion	125	177	6.88e-07
KEGG	KEGG:05208	Chemical carcinogenesis - reactive oxygen species	131	188	8.66e-07
KEGG	KEGG:05012	Parkinson disease	151	227	6.98e-06
KEGG	KEGG:00190	Oxidative phosphorylation	79	107	1.09e-05
KEGG	KEGG:05020	Prion disease	146	221	1.53e-05
KEGG	KEGG:05415	Diabetic cardiomyopathy	116	170	1.76e-05
KEGG	KEGG:04714	Thermogenesis	132	199	3.09e-05
KEGG	KEGG:04141	Protein processing in endoplasmic reticulum	110	162	4.07e-05
KEGG	KEGG:04512	ECM-receptor interaction	55	72	7.18e-05
KEGG	KEGG:05010	Alzheimer disease	195	319	3.27e-04
KEGG	KEGG:00531	Glycosaminoglycan degradation	16	16	3.27e-04
KEGG	KEGG:05016	Huntington disease	162	260	3.60e-04
KEGG	KEGG:04142	Lysosome	80	120	2.03e-03
KEGG	KEGG:04932	Non-alcoholic fatty liver disease	86	131	2.43e-03
KEGG	KEGG:03040	Spliceosome	86	133	5.00e-03
KEGG	KEGG:00000	KEGG root term	2926	5730	6.08e-03
KEGG	KEGG:04810	Regulation of actin cytoskeleton	113	182	6.08e-03
KEGG	KEGG:01200	Carbon metabolism	65	99	1.22e-02
KEGG	KEGG:05022	Pathways of neurodegeneration - multiple diseases	226	394	1.22e-02
KEGG	KEGG:04151	PI3K-Akt signaling pathway	155	262	1.25e-02
KEGG	KEGG:05014	Amyotrophic lateral sclerosis	179	308	1.63e-02
KEGG	KEGG:04066	HIF-1 signaling pathway	59	90	1.95e-02
KEGG	KEGG:00513	Various types of N-glycan biosynthesis	27	36	2.10e-02
KEGG	KEGG:00510	N-Glycan biosynthesis	34	48	2.73e-02
KEGG	KEGG:01100	Metabolic pathways	628	1181	4.00e-02
KEGG	KEGG:00010	Glycolysis / Gluconeogenesis	31	44	4.53e-02

motif Late response Top2inhibitors

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0007049	cell cycle	637	1550	2.05e-09
GO:BP	GO:0022402	cell cycle process	462	1091	1.91e-08
GO:BP	GO:0007059	chromosome segregation	189	383	2.71e-08
GO:BP	GO:0000278	mitotic cell cycle	364	845	1.89e-07
GO:BP	GO:1903047	mitotic cell cycle process	311	710	4.44e-07
GO:BP	GO:0051301	cell division	259	577	6.52e-07
GO:BP	GO:0000280	nuclear division	174	360	6.52e-07
GO:BP	GO:0048285	organelle fission	187	403	7.66e-06
GO:BP	GO:0000070	mitotic sister chromatid segregation	102	195	1.42e-05
GO:BP	GO:0051276	chromosome organization	243	553	1.64e-05
GO:BP	GO:0098813	nuclear chromosome segregation	141	292	1.88e-05
GO:BP	GO:0140014	mitotic nuclear division	131	267	1.88e-05
GO:BP	GO:0000819	sister chromatid segregation	117	236	4.56e-05
GO:BP	GO:0006261	DNA-templated DNA replication	81	151	7.01e-05
GO:BP	GO:0007051	spindle organization	96	187	7.51e-05
GO:BP	GO:1903046	meiotic cell cycle process	75	139	1.34e-04
GO:BP	GO:0006260	DNA replication	125	262	1.94e-04
GO:BP	GO:0140013	meiotic nuclear division	68	124	1.95e-04
GO:BP	GO:0045930	negative regulation of mitotic cell cycle	104	211	2.43e-04
GO:BP	GO:0051726	regulation of cell cycle	389	972	2.84e-04
GO:BP	GO:0010564	regulation of cell cycle process	264	630	3.02e-04
GO:BP	GO:0007093	mitotic cell cycle checkpoint signaling	73	138	3.91e-04
GO:BP	GO:0000075	cell cycle checkpoint signaling	91	183	6.46e-04
GO:BP	GO:0000226	microtubule cytoskeleton organization	235	560	9.82e-04
GO:BP	GO:0061982	meiosis I cell cycle process	48	83	1.02e-03
GO:BP	GO:0051716	cellular response to stimulus	1807	5143	1.31e-03
GO:BP	GO:0007017	microtubule-based process	312	775	1.67e-03
GO:BP	GO:0032465	regulation of cytokinesis	46	80	1.83e-03
GO:BP	GO:0045786	negative regulation of cell cycle	152	344	2.00e-03
GO:BP	GO:0051225	spindle assembly	62	118	2.55e-03
GO:BP	GO:1905818	regulation of chromosome separation	41	70	2.77e-03
GO:BP	GO:0006974	cellular response to DNA damage stimulus	319	800	2.77e-03
GO:BP	GO:0007127	meiosis I	45	79	2.77e-03
GO:BP	GO:0051321	meiotic cell cycle	92	192	2.78e-03
GO:BP	GO:0050896	response to stimulus	2082	5993	2.93e-03
GO:BP	GO:0051304	chromosome separation	43	75	3.21e-03
GO:BP	GO:1901988	negative regulation of cell cycle phase transition	109	236	3.25e-03
GO:BP	GO:0044770	cell cycle phase transition	211	507	3.94e-03
GO:BP	GO:1902850	microtubule cytoskeleton organization involved in mitosis	77	157	4.59e-03
GO:BP	GO:0010948	negative regulation of cell cycle process	123	274	4.60e-03
GO:BP	GO:0045132	meiotic chromosome segregation	41	72	5.64e-03
GO:BP	GO:0033046	negative regulation of sister chromatid segregation	30	48	5.77e-03
GO:BP	GO:0033048	negative regulation of mitotic sister chromatid segregation	30	48	5.77e-03
GO:BP	GO:2001251	negative regulation of chromosome organization	50	93	5.77e-03
GO:BP	GO:2000816	negative regulation of mitotic sister chromatid separation	30	48	5.77e-03
GO:BP	GO:0006996	organelle organization	1085	3030	7.98e-03
GO:BP	GO:0033047	regulation of mitotic sister chromatid segregation	32	53	8.09e-03
GO:BP	GO:0051985	negative regulation of chromosome segregation	30	49	9.36e-03
GO:BP	GO:1905819	negative regulation of chromosome separation	30	49	9.36e-03
GO:BP	GO:0045841	negative regulation of mitotic metaphase/anaphase transition	29	47	9.64e-03
GO:BP	GO:0070925	organelle assembly	320	817	9.64e-03
GO:BP	GO:0007098	centrosome cycle	63	126	9.64e-03
GO:BP	GO:0071173	spindle assembly checkpoint signaling	28	45	9.91e-03
GO:BP	GO:0071174	mitotic spindle checkpoint signaling	28	45	9.91e-03
GO:BP	GO:0007094	mitotic spindle assembly checkpoint signaling	28	45	9.91e-03
KEGG	KEGG:03030	DNA replication	25	35	1.09e-03

motif Early Response Top2 inhibitors

query	significant	p_value	term_size	query_size	intersection_size	precision	recall	term_id	source	term_name	effective_domain_size	source_order	parents
query_1	TRUE	0.0000000	2053	464	2.04e+02	0.4396552	0.0993668	GO:0006366	GO:BP	transcription by RNA polymerase II	14220	2202	GO:0006351
query_1	TRUE	0.0000000	1976	464	2.00e+02	0.4310345	0.1012146	GO:0006357	GO:BP	regulation of transcription by RNA polymerase II	14220	2195	GO:0006355, GO:0006366
query_1	TRUE	0.0000000	2761	464	2.37e+02	0.5107759	0.0858385	GO:0097659	GO:BP	nucleic acid-templated transcription	14220	19903	GO:0010467, GO:0032774
query_1	TRUE	0.0000000	2760	464	2.37e+02	0.5107759	0.0858696	GO:0006351	GO:BP	DNA-templated transcription	14220	2189	GO:0097659
query_1	TRUE	0.0000000	2792	464	2.37e+02	0.5107759	0.0848854	GO:0032774	GO:BP	RNA biosynthetic process	14220	8281	GO:0009059, GO:0016070, GO:0034654
query_1	TRUE	0.0000000	3189	464	2.54e+02	0.5474138	0.0796488	GO:0019219	GO:BP	regulation of nucleobase-containing compound metabolic process	14220	5932	GO:0006139, GO:0031323, GO:0051171, GO:0080090
query_1	TRUE	0.0000000	2654	464	2.30e+02	0.4956897	0.0866616	GO:0006355	GO:BP	regulation of DNA-templated transcription	14220	2193	GO:0006351, GO:0010468, GO:1903506
query_1	TRUE	0.0000000	2656	464	2.30e+02	0.4956897	0.0865964	GO:1903506	GO:BP	regulation of nucleic acid-templated transcription	14220	24286	GO:0097659, GO:2001141
query_1	TRUE	0.0000000	2674	464	2.30e+02	0.4956897	0.0860135	GO:2001141	GO:BP	regulation of RNA biosynthetic process	14220	27809	GO:0010556, GO:0031326, GO:0032774, GO:0051252
query_1	TRUE	0.0000000	2927	464	2.40e+02	0.5172414	0.0819952	GO:0051252	GO:BP	regulation of RNA metabolic process	14220	14451	GO:0016070, GO:0019219, GO:0060255
query_1	TRUE	0.0000000	3100	464	2.41e+02	0.5193966	0.0777419	GO:0010556	GO:BP	regulation of macromolecule biosynthetic process	14220	4326	GO:0009059, GO:0009889, GO:0060255
query_1	TRUE	0.0000000	4149	464	2.82e+02	0.6077586	0.0679682	GO:0090304	GO:BP	nucleic acid metabolic process	14220	19342	GO:0006139, GO:0043170
query_1	TRUE	0.0000000	3683	464	2.63e+02	0.5668103	0.0714092	GO:0016070	GO:BP	RNA metabolic process	14220	5254	GO:0090304
query_1	TRUE	0.0000000	3170	464	2.41e+02	0.5193966	0.0760252	GO:0034654	GO:BP	nucleobase-containing compound biosynthetic process	14220	9218	GO:0006139, GO:0018130, GO:0019438, GO:0044271, GO:1901362
query_1	TRUE	0.0000000	3212	464	2.42e+02	0.5215517	0.0753425	GO:0031326	GO:BP	regulation of cellular biosynthetic process	14220	7552	GO:0009889, GO:0031323, GO:0044249
query_1	TRUE	0.0000000	3235	464	2.42e+02	0.5215517	0.0748068	GO:0018130	GO:BP	heterocycle biosynthetic process	14220	5537	GO:0044249, GO:0046483
query_1	TRUE	0.0000000	3237	464	2.42e+02	0.5215517	0.0747606	GO:0019438	GO:BP	aromatic compound biosynthetic process	14220	6132	GO:0006725, GO:0044249
query_1	TRUE	0.0000000	3267	464	2.43e+02	0.5237069	0.0743802	GO:0009889	GO:BP	regulation of biosynthetic process	14220	3843	GO:0009058, GO:0019222
query_1	TRUE	0.0000000	4432	464	2.88e+02	0.6206897	0.0649819	GO:0031323	GO:BP	regulation of cellular metabolic process	14220	7549	GO:0019222, GO:0044237, GO:0050794
query_1	TRUE	0.0000000	3344	464	2.43e+02	0.5237069	0.0726675	GO:1901362	GO:BP	organic cyclic compound biosynthetic process	14220	22499	GO:1901360, GO:1901576
query_1	TRUE	0.0000000	3824	464	2.59e+02	0.5581897	0.0677301	GO:0009059	GO:BP	macromolecule biosynthetic process	14220	3327	GO:0043170, GO:1901576
query_1	TRUE	0.0000000	3691	464	2.53e+02	0.5452586	0.0685451	GO:0010468	GO:BP	regulation of gene expression	14220	4271	GO:0010467, GO:0060255
query_1	TRUE	0.0000000	4576	464	2.86e+02	0.6163793	0.0625000	GO:0080090	GO:BP	regulation of primary metabolic process	14220	18924	GO:0019222, GO:0044238
query_1	TRUE	0.0000000	4615	464	2.87e+02	0.6185345	0.0621885	GO:0006139	GO:BP	nucleobase-containing compound metabolic process	14220	2036	GO:0006725, GO:0034641, GO:0044238, GO:0046483, GO:1901360
query_1	TRUE	0.0000000	4456	464	2.81e+02	0.6056034	0.0630610	GO:0051171	GO:BP	regulation of nitrogen compound metabolic process	14220	14399	GO:0006807, GO:0019222
query_1	TRUE	0.0000000	4732	464	2.88e+02	0.6206897	0.0608622	GO:0046483	GO:BP	heterocycle metabolic process	14220	12974	GO:0044237
query_1	TRUE	0.0000000	4770	464	2.88e+02	0.6206897	0.0603774	GO:0006725	GO:BP	cellular aromatic compound metabolic process	14220	2497	GO:0044237
query_1	TRUE	0.0000000	3851	464	2.53e+02	0.5452586	0.0656972	GO:0044271	GO:BP	cellular nitrogen compound biosynthetic process	14220	11656	GO:0034641, GO:0044249
query_1	TRUE	0.0000000	4781	464	2.87e+02	0.6185345	0.0600293	GO:0060255	GO:BP	regulation of macromolecule metabolic process	14220	15399	GO:0019222, GO:0043170
query_1	TRUE	0.0000000	4921	464	2.90e+02	0.6250000	0.0589311	GO:1901360	GO:BP	organic cyclic compound metabolic process	14220	22497	GO:0071704
query_1	TRUE	0.0000000	5198	464	2.97e+02	0.6400862	0.0571374	GO:0019222	GO:BP	regulation of metabolic process	14220	5935	GO:0008152, GO:0050789
query_1	TRUE	0.0000000	4696	464	2.79e+02	0.6012931	0.0594123	GO:0010467	GO:BP	gene expression	14220	4270	GO:0043170
query_1	TRUE	0.0000000	5111	464	2.92e+02	0.6293103	0.0571317	GO:0034641	GO:BP	cellular nitrogen compound metabolic process	14220	9210	GO:0006807, GO:0044237
query_1	TRUE	0.0000000	4584	464	2.73e+02	0.5883621	0.0595550	GO:0044249	GO:BP	cellular biosynthetic process	14220	11645	GO:0009058, GO:0044237
query_1	TRUE	0.0000000	4658	464	2.73e+02	0.5883621	0.0586088	GO:1901576	GO:BP	organic substance biosynthetic process	14220	22687	GO:0009058, GO:0071704
query_1	TRUE	0.0000000	4721	464	2.73e+02	0.5883621	0.0578267	GO:0009058	GO:BP	biosynthetic process	14220	3326	GO:0008152
query_1	TRUE	0.0000000	7265	464	3.45e+02	0.7435345	0.0474880	GO:0043170	GO:BP	macromolecule metabolic process	14220	11211	GO:0071704
query_1	TRUE	0.0000000	1038	464	9.90e+01	0.2133621	0.0953757	GO:0045892	GO:BP	negative regulation of DNA-templated transcription	14220	12466	GO:0006351, GO:0006355, GO:1903507
query_1	TRUE	0.0000000	1040	464	9.90e+01	0.2133621	0.0951923	GO:1903507	GO:BP	negative regulation of nucleic acid-templated transcription	14220	24287	GO:0097659, GO:1902679, GO:1903506
query_1	TRUE	0.0000000	7878	464	3.57e+02	0.7693966	0.0453161	GO:0050794	GO:BP	regulation of cellular process	14220	14091	GO:0009987, GO:0050789
query_1	TRUE	0.0000000	1050	464	9.90e+01	0.2133621	0.0942857	GO:1902679	GO:BP	negative regulation of RNA biosynthetic process	14220	23602	GO:0010558, GO:0031327, GO:0032774, GO:0051253, GO:2001141
query_1	TRUE	0.0000000	1341	464	1.14e+02	0.2456897	0.0850112	GO:0045893	GO:BP	positive regulation of DNA-templated transcription	14220	12467	GO:0006351, GO:0006355, GO:1903508
query_1	TRUE	0.0000000	1341	464	1.14e+02	0.2456897	0.0850112	GO:1903508	GO:BP	positive regulation of nucleic acid-templated transcription	14220	24288	GO:0097659, GO:1902680, GO:1903506
query_1	TRUE	0.0000000	1247	464	1.09e+02	0.2349138	0.0874098	GO:0045934	GO:BP	negative regulation of nucleobase-containing compound metabolic process	14220	12504	GO:0006139, GO:0019219, GO:0031324, GO:0051172
query_1	TRUE	0.0000000	1348	464	1.14e+02	0.2456897	0.0845697	GO:1902680	GO:BP	positive regulation of RNA biosynthetic process	14220	23603	GO:0010557, GO:0031328, GO:0032774, GO:0051254, GO:2001141
query_1	TRUE	0.0000000	1469	464	1.20e+02	0.2586207	0.0816882	GO:0051254	GO:BP	positive regulation of RNA metabolic process	14220	14453	GO:0010604, GO:0016070, GO:0045935, GO:0051252
query_1	TRUE	0.0000000	1145	464	1.03e+02	0.2219828	0.0899563	GO:0051253	GO:BP	negative regulation of RNA metabolic process	14220	14452	GO:0010605, GO:0016070, GO:0045934, GO:0051252
query_1	TRUE	0.0000000	7716	464	3.49e+02	0.7521552	0.0452307	GO:0044237	GO:BP	cellular metabolic process	14220	11638	GO:0008152, GO:0009987
query_1	TRUE	0.0000000	1643	464	1.26e+02	0.2715517	0.0766890	GO:0045935	GO:BP	positive regulation of nucleobase-containing compound metabolic process	14220	12505	GO:0006139, GO:0019219, GO:0031325, GO:0051173
query_1	TRUE	0.0000000	8305	464	3.65e+02	0.7866379	0.0439494	GO:0050789	GO:BP	regulation of biological process	14220	14087	GO:0008150, GO:0065007
query_1	TRUE	0.0000000	8676	464	3.75e+02	0.8081897	0.0432227	GO:0065007	GO:BP	biological regulation	14220	16927	GO:0008150
query_1	TRUE	0.0000000	7699	464	3.46e+02	0.7456897	0.0449409	GO:0006807	GO:BP	nitrogen compound metabolic process	14220	2557	GO:0008152
query_1	TRUE	0.0000000	1542	464	1.19e+02	0.2564655	0.0771725	GO:0010557	GO:BP	positive regulation of macromolecule biosynthetic process	14220	4327	GO:0009059, GO:0009891, GO:0010556, GO:0010604
query_1	TRUE	0.0000000	8038	464	3.55e+02	0.7650862	0.0441652	GO:0044238	GO:BP	primary metabolic process	14220	11639	GO:0008152
query_1	TRUE	0.0000000	1241	464	1.04e+02	0.2241379	0.0838034	GO:0010558	GO:BP	negative regulation of macromolecule biosynthetic process	14220	4328	GO:0009059, GO:0009890, GO:0010556, GO:0010605
query_1	TRUE	0.0000000	951	464	8.80e+01	0.1896552	0.0925342	GO:0045944	GO:BP	positive regulation of transcription by RNA polymerase II	14220	12513	GO:0006357, GO:0006366, GO:0045893
query_1	TRUE	0.0000000	1825	464	1.31e+02	0.2823276	0.0717808	GO:0031324	GO:BP	negative regulation of cellular metabolic process	14220	7550	GO:0009892, GO:0031323, GO:0044237, GO:0048523
query_1	TRUE	0.0000000	1284	464	1.04e+02	0.2241379	0.0809969	GO:0031327	GO:BP	negative regulation of cellular biosynthetic process	14220	7553	GO:0009890, GO:0031324, GO:0031326, GO:0044249
query_1	TRUE	0.0000000	1617	464	1.20e+02	0.2586207	0.0742115	GO:0031328	GO:BP	positive regulation of cellular biosynthetic process	14220	7554	GO:0009891, GO:0031325, GO:0031326, GO:0044249
query_1	TRUE	0.0000000	1646	464	1.21e+02	0.2607759	0.0735115	GO:0009891	GO:BP	positive regulation of biosynthetic process	14220	3845	GO:0009058, GO:0009889, GO:0009893
query_1	TRUE	0.0000000	1310	464	1.04e+02	0.2241379	0.0793893	GO:0009890	GO:BP	negative regulation of biosynthetic process	14220	3844	GO:0009058, GO:0009889, GO:0009892
query_1	TRUE	0.0000000	759	464	7.40e+01	0.1594828	0.0974967	GO:0000122	GO:BP	negative regulation of transcription by RNA polymerase II	14220	51	GO:0006357, GO:0006366, GO:0045892
query_1	TRUE	0.0000000	8408	464	3.60e+02	0.7758621	0.0428164	GO:0071704	GO:BP	organic substance metabolic process	14220	17953	GO:0008152
query_1	TRUE	0.0000000	1912	464	1.27e+02	0.2737069	0.0664226	GO:0051172	GO:BP	negative regulation of nitrogen compound metabolic process	14220	14400	GO:0006807, GO:0009892, GO:0051171
query_1	TRUE	0.0000000	2371	464	1.46e+02	0.3146552	0.0615774	GO:0009892	GO:BP	negative regulation of metabolic process	14220	3846	GO:0008152, GO:0019222, GO:0048519
query_1	TRUE	0.0000000	2201	464	1.38e+02	0.2974138	0.0626988	GO:0010605	GO:BP	negative regulation of macromolecule metabolic process	14220	4370	GO:0009892, GO:0043170, GO:0060255
query_1	TRUE	0.0000000	2443	464	1.48e+02	0.3189655	0.0605813	GO:0031325	GO:BP	positive regulation of cellular metabolic process	14220	7551	GO:0009893, GO:0031323, GO:0044237, GO:0048522
query_1	TRUE	0.0000000	2494	464	1.49e+02	0.3211207	0.0597434	GO:0051173	GO:BP	positive regulation of nitrogen compound metabolic process	14220	14401	GO:0006807, GO:0009893, GO:0051171
query_1	TRUE	0.0000000	8768	464	3.62e+02	0.7801724	0.0412865	GO:0008152	GO:BP	metabolic process	14220	3213	GO:0008150
query_1	TRUE	0.0000000	2729	464	1.56e+02	0.3362069	0.0571638	GO:0010604	GO:BP	positive regulation of macromolecule metabolic process	14220	4369	GO:0009893, GO:0043170, GO:0060255
query_1	TRUE	0.0000000	2974	464	1.61e+02	0.3469828	0.0541358	GO:0009893	GO:BP	positive regulation of metabolic process	14220	3847	GO:0008152, GO:0019222, GO:0048518
query_1	TRUE	0.0000000	3749	464	1.90e+02	0.4094828	0.0506802	GO:0048523	GO:BP	negative regulation of cellular process	14220	13627	GO:0009987, GO:0048519, GO:0050794
query_1	TRUE	0.0000000	4169	464	2.01e+02	0.4331897	0.0482130	GO:0048519	GO:BP	negative regulation of biological process	14220	13623	GO:0008150, GO:0050789
query_1	TRUE	0.0000134	545	464	4.20e+01	0.0905172	0.0770642	GO:0006325	GO:BP	chromatin organization	14220	2182	GO:0016043
query_1	TRUE	0.0000222	4291	464	1.90e+02	0.4094828	0.0442787	GO:0048522	GO:BP	positive regulation of cellular process	14220	13626	GO:0009987, GO:0048518, GO:0050794
query_1	TRUE	0.0000807	4739	464	2.03e+02	0.4375000	0.0428360	GO:0048518	GO:BP	positive regulation of biological process	14220	13622	GO:0008150, GO:0050789
query_1	TRUE	0.0000936	427	464	3.40e+01	0.0732759	0.0796253	GO:0016570	GO:BP	histone modification	14220	5415	GO:0036211
query_1	TRUE	0.0000958	315	464	2.80e+01	0.0603448	0.0888889	GO:0006338	GO:BP	chromatin remodeling	14220	2186	GO:0006325
query_1	TRUE	0.0020020	1905	464	9.30e+01	0.2004310	0.0488189	GO:0050793	GO:BP	regulation of developmental process	14220	14090	GO:0032502, GO:0050789
query_1	TRUE	0.0044691	232	464	2.00e+01	0.0431034	0.0862069	GO:0030522	GO:BP	intracellular receptor signaling pathway	14220	7237	GO:0007165
query_1	TRUE	0.0070436	915	464	5.10e+01	0.1099138	0.0557377	GO:0072359	GO:BP	circulatory system development	14220	18474	GO:0048731
query_1	TRUE	0.0077838	4	464	3.00e+00	0.0064655	0.7500000	GO:0097676	GO:BP	histone H3-K36 dimethylation	14220	19904	GO:0010452, GO:0018027
query_1	TRUE	0.0085005	225	464	1.90e+01	0.0409483	0.0844444	GO:0006354	GO:BP	DNA-templated transcription elongation	14220	2192	GO:0006351, GO:0032774
query_1	TRUE	0.0095047	514	464	3.30e+01	0.0711207	0.0642023	GO:0007507	GO:BP	heart development	14220	3080	GO:0048513, GO:0072359
query_1	TRUE	0.0095496	122	464	1.30e+01	0.0280172	0.1065574	GO:0018022	GO:BP	peptidyl-lysine methylation	14220	5494	GO:0006479, GO:0018205
query_1	TRUE	0.0095496	122	464	1.30e+01	0.0280172	0.1065574	GO:2000779	GO:BP	regulation of double-strand break repair	14220	27478	GO:0006282, GO:0006302
query_1	TRUE	0.0117533	371	464	2.60e+01	0.0560345	0.0700809	GO:0018205	GO:BP	peptidyl-lysine modification	14220	5601	GO:0018193
query_1	TRUE	0.0121117	109	464	1.20e+01	0.0258621	0.1100917	GO:0034968	GO:BP	histone lysine methylation	14220	9262	GO:0016571, GO:0018022
query_1	TRUE	0.0129221	143	464	1.40e+01	0.0301724	0.0979021	GO:0016571	GO:BP	histone methylation	14220	5416	GO:0006479, GO:0016570
query_1	TRUE	0.0142012	198	464	1.70e+01	0.0366379	0.0858586	GO:0006282	GO:BP	regulation of DNA repair	14220	2154	GO:0006281, GO:0051052, GO:2001020
query_1	TRUE	0.0147077	551	464	3.40e+01	0.0732759	0.0617060	GO:0043009	GO:BP	chordate embryonic development	14220	11117	GO:0009792
query_1	TRUE	0.0182395	166	464	1.50e+01	0.0323276	0.0903614	GO:0007623	GO:BP	circadian rhythm	14220	3168	GO:0048511
query_1	TRUE	0.0182797	241	464	1.90e+01	0.0409483	0.0788382	GO:0048511	GO:BP	rhythmic process	14220	13617	GO:0008150
query_1	TRUE	0.0214512	151	464	1.40e+01	0.0301724	0.0927152	GO:0019827	GO:BP	stem cell population maintenance	14220	6416	GO:0032501, GO:0098727
query_1	TRUE	0.0218463	43	464	7.00e+00	0.0150862	0.1627907	GO:0042789	GO:BP	mRNA transcription by RNA polymerase II	14220	11002	GO:0006366, GO:0009299
query_1	TRUE	0.0221863	12	464	4.00e+00	0.0086207	0.3333333	GO:0010452	GO:BP	histone H3-K36 methylation	14220	4257	GO:0034968
query_1	TRUE	0.0232117	800	464	4.40e+01	0.0948276	0.0550000	GO:0006974	GO:BP	cellular response to DNA damage stimulus	14220	2675	GO:0033554
query_1	TRUE	0.0234391	568	464	3.40e+01	0.0732759	0.0598592	GO:0009792	GO:BP	embryo development ending in birth or egg hatching	14220	3773	GO:0009790
query_1	TRUE	0.0234391	153	464	1.40e+01	0.0301724	0.0915033	GO:0098727	GO:BP	maintenance of cell number	14220	20042	GO:0032502
query_1	TRUE	0.0261328	664	464	3.80e+01	0.0818966	0.0572289	GO:0016071	GO:BP	mRNA metabolic process	14220	5255	GO:0016070
query_1	TRUE	0.0265670	879	464	4.70e+01	0.1012931	0.0534699	GO:0060429	GO:BP	epithelium development	14220	15559	GO:0009888
query_1	TRUE	0.0271087	11931	464	4.14e+02	0.8922414	0.0346995	GO:0009987	GO:BP	cellular process	14220	3905	GO:0008150
query_1	TRUE	0.0276717	22	464	5.00e+00	0.0107759	0.2272727	GO:0010667	GO:BP	negative regulation of cardiac muscle cell apoptotic process	14220	4430	GO:0010659, GO:0010664, GO:0010665
query_1	TRUE	0.0289370	6	464	3.00e+00	0.0064655	0.5000000	GO:0086023	GO:BP	adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process	14220	19024	GO:0071880, GO:0086103
query_1	TRUE	0.0289370	6	464	3.00e+00	0.0064655	0.5000000	GO:0003278	GO:BP	apoptotic process involved in heart morphogenesis	14220	1737	GO:0003007, GO:0060561
query_1	TRUE	0.0306201	123	464	1.20e+01	0.0258621	0.0975610	GO:0035264	GO:BP	multicellular organism growth	14220	9459	GO:0032501, GO:0048589
query_1	TRUE	0.0309740	295	464	2.10e+01	0.0452586	0.0711864	GO:2001020	GO:BP	regulation of response to DNA damage stimulus	14220	27714	GO:0006974, GO:0080135
query_1	TRUE	0.0310587	75	464	9.00e+00	0.0193966	0.1200000	GO:2000736	GO:BP	regulation of stem cell differentiation	14220	27440	GO:0045595, GO:0048863
query_1	TRUE	0.0310587	75	464	9.00e+00	0.0193966	0.1200000	GO:0043242	GO:BP	negative regulation of protein-containing complex disassembly	14220	11225	GO:0032984, GO:0043244, GO:0051129
query_1	TRUE	0.0310587	141	464	1.30e+01	0.0280172	0.0921986	GO:0009755	GO:BP	hormone-mediated signaling pathway	14220	3746	GO:0007165, GO:0032870
query_1	TRUE	0.0313093	468	464	2.90e+01	0.0625000	0.0619658	GO:0051052	GO:BP	regulation of DNA metabolic process	14220	14305	GO:0006259, GO:0019219, GO:0060255
query_1	TRUE	0.0348113	180	464	1.50e+01	0.0323276	0.0833333	GO:0008213	GO:BP	protein alkylation	14220	3228	GO:0036211
query_1	TRUE	0.0348113	180	464	1.50e+01	0.0323276	0.0833333	GO:0006479	GO:BP	protein methylation	14220	2280	GO:0008213, GO:0043414
query_1	TRUE	0.0361542	48	464	7.00e+00	0.0150862	0.1458333	GO:0009299	GO:BP	mRNA transcription	14220	3538	GO:0006351, GO:0016071
query_1	TRUE	0.0381168	4662	464	1.84e+02	0.3965517	0.0394680	GO:0032502	GO:BP	developmental process	14220	8073	GO:0008150
query_1	TRUE	0.0398231	202	464	1.60e+01	0.0344828	0.0792079	GO:0048863	GO:BP	stem cell differentiation	14220	13929	GO:0030154
query_1	TRUE	0.0425350	2	464	2.00e+00	0.0043103	1.0000000	GO:1901898	GO:BP	negative regulation of relaxation of cardiac muscle	14220	22972	GO:0055119, GO:1901078, GO:1901897
query_1	TRUE	0.0425350	64	464	8.00e+00	0.0172414	0.1250000	GO:0010569	GO:BP	regulation of double-strand break repair via homologous recombination	14220	4339	GO:0000018, GO:0000724, GO:2000779
query_1	TRUE	0.0425350	2	464	2.00e+00	0.0043103	1.0000000	GO:0032242	GO:BP	regulation of nucleoside transport	14220	7889	GO:0015858, GO:0032239
query_1	TRUE	0.0425350	112	464	1.10e+01	0.0237069	0.0982143	GO:0043401	GO:BP	steroid hormone mediated signaling pathway	14220	11317	GO:0009755, GO:0071383
query_1	TRUE	0.0428125	25	464	5.00e+00	0.0107759	0.2000000	GO:0010664	GO:BP	negative regulation of striated muscle cell apoptotic process	14220	4427	GO:0010656, GO:0010658, GO:0010662
query_1	TRUE	0.0428125	148	464	1.30e+01	0.0280172	0.0878378	GO:0021915	GO:BP	neural tube development	14220	6867	GO:0007399, GO:0035295, GO:0043009, GO:0060429
query_1	TRUE	0.0428125	50	464	7.00e+00	0.0150862	0.1400000	GO:0035019	GO:BP	somatic stem cell population maintenance	14220	9284	GO:0019827
query_1	TRUE	0.0428125	7	464	3.00e+00	0.0064655	0.4285714	GO:1900246	GO:BP	positive regulation of RIG-I signaling pathway	14220	21551	GO:0039529, GO:0039535, GO:0062208
query_1	TRUE	0.0431198	15	464	4.00e+00	0.0086207	0.2666667	GO:0032239	GO:BP	regulation of nucleobase-containing compound transport	14220	7886	GO:0015931, GO:0051049
query_1	TRUE	0.0431198	15	464	4.00e+00	0.0086207	0.2666667	GO:0055012	GO:BP	ventricular cardiac muscle cell differentiation	14220	15117	GO:0055007
query_1	TRUE	0.0000000	424	464	5.40e+01	0.1163793	0.1273585	KEGG:05168	KEGG	Herpes simplex virus 1 infection	14220	442	KEGG:00000

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0006366	transcription by RNA polymerase II	204	2053	5.85e-52
GO:BP	GO:0006357	regulation of transcription by RNA polymerase II	200	1976	5.85e-52
GO:BP	GO:0097659	nucleic acid-templated transcription	237	2761	1.58e-51
GO:BP	GO:0006351	DNA-templated transcription	237	2760	1.58e-51
GO:BP	GO:0032774	RNA biosynthetic process	237	2792	1.08e-50
GO:BP	GO:0019219	regulation of nucleobase-containing compound metabolic process	254	3189	1.70e-50
GO:BP	GO:0006355	regulation of DNA-templated transcription	230	2654	2.28e-50
GO:BP	GO:1903506	regulation of nucleic acid-templated transcription	230	2656	2.30e-50
GO:BP	GO:2001141	regulation of RNA biosynthetic process	230	2674	7.20e-50
GO:BP	GO:0051252	regulation of RNA metabolic process	240	2927	5.15e-49
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	241	3100	6.11e-45
GO:BP	GO:0090304	nucleic acid metabolic process	282	4149	3.11e-44
GO:BP	GO:0016070	RNA metabolic process	263	3683	9.66e-44
GO:BP	GO:0034654	nucleobase-containing compound biosynthetic process	241	3170	3.16e-43
GO:BP	GO:0031326	regulation of cellular biosynthetic process	242	3212	8.61e-43
GO:BP	GO:0018130	heterocycle biosynthetic process	242	3235	3.05e-42
GO:BP	GO:0019438	aromatic compound biosynthetic process	242	3237	3.22e-42
GO:BP	GO:0009889	regulation of biosynthetic process	243	3267	4.31e-42
GO:BP	GO:0031323	regulation of cellular metabolic process	288	4432	9.67e-42
GO:BP	GO:1901362	organic cyclic compound biosynthetic process	243	3344	2.90e-40
GO:BP	GO:0009059	macromolecule biosynthetic process	259	3824	2.06e-38
GO:BP	GO:0010468	regulation of gene expression	253	3691	5.22e-38
GO:BP	GO:0080090	regulation of primary metabolic process	286	4576	1.02e-37
GO:BP	GO:0006139	nucleobase-containing compound metabolic process	287	4615	1.65e-37
GO:BP	GO:0051171	regulation of nitrogen compound metabolic process	281	4456	2.06e-37
GO:BP	GO:0046483	heterocycle metabolic process	288	4732	8.41e-36
GO:BP	GO:0006725	cellular aromatic compound metabolic process	288	4770	4.30e-35
GO:BP	GO:0044271	cellular nitrogen compound biosynthetic process	253	3851	1.08e-34
GO:BP	GO:0060255	regulation of macromolecule metabolic process	287	4781	2.17e-34
GO:BP	GO:1901360	organic cyclic compound metabolic process	290	4921	2.21e-33
GO:BP	GO:0019222	regulation of metabolic process	297	5198	4.87e-32
GO:BP	GO:0010467	gene expression	279	4696	7.05e-32
GO:BP	GO:0034641	cellular nitrogen compound metabolic process	292	5111	4.62e-31
GO:BP	GO:0044249	cellular biosynthetic process	273	4584	6.34e-31
GO:BP	GO:1901576	organic substance biosynthetic process	273	4658	1.28e-29
GO:BP	GO:0009058	biosynthetic process	273	4721	1.53e-28
GO:BP	GO:0043170	macromolecule metabolic process	345	7265	2.14e-23
GO:BP	GO:0045892	negative regulation of DNA-templated transcription	99	1038	6.40e-21
GO:BP	GO:1903507	negative regulation of nucleic acid-templated transcription	99	1040	7.21e-21
GO:BP	GO:0050794	regulation of cellular process	357	7878	1.02e-20
GO:BP	GO:1902679	negative regulation of RNA biosynthetic process	99	1050	1.41e-20
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	114	1341	2.05e-20
GO:BP	GO:1903508	positive regulation of nucleic acid-templated transcription	114	1341	2.05e-20
GO:BP	GO:0045934	negative regulation of nucleobase-containing compound metabolic process	109	1247	2.45e-20
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	114	1348	3.02e-20
GO:BP	GO:0051254	positive regulation of RNA metabolic process	120	1469	3.22e-20
GO:BP	GO:0051253	negative regulation of RNA metabolic process	103	1145	5.12e-20
GO:BP	GO:0044237	cellular metabolic process	349	7716	2.22e-19
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	126	1643	5.00e-19
GO:BP	GO:0050789	regulation of biological process	365	8305	5.74e-19
GO:BP	GO:0065007	biological regulation	375	8676	8.13e-19
GO:BP	GO:0006807	nitrogen compound metabolic process	346	7699	2.23e-18
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	119	1542	5.05e-18
GO:BP	GO:0044238	primary metabolic process	355	8038	5.22e-18
GO:BP	GO:0010558	negative regulation of macromolecule biosynthetic process	104	1241	5.56e-18
GO:BP	GO:0045944	positive regulation of transcription by RNA polymerase II	88	951	1.34e-17
GO:BP	GO:0031324	negative regulation of cellular metabolic process	131	1825	1.85e-17
GO:BP	GO:0031327	negative regulation of cellular biosynthetic process	104	1284	6.43e-17
GO:BP	GO:0031328	positive regulation of cellular biosynthetic process	120	1617	7.28e-17
GO:BP	GO:0009891	positive regulation of biosynthetic process	121	1646	1.05e-16
GO:BP	GO:0009890	negative regulation of biosynthetic process	104	1310	2.61e-16
GO:BP	GO:0000122	negative regulation of transcription by RNA polymerase II	74	759	8.51e-16
GO:BP	GO:0071704	organic substance metabolic process	360	8408	8.57e-16
GO:BP	GO:0051172	negative regulation of nitrogen compound metabolic process	127	1912	4.08e-14
GO:BP	GO:0009892	negative regulation of metabolic process	146	2371	7.78e-14
GO:BP	GO:0010605	negative regulation of macromolecule metabolic process	138	2201	1.58e-13
GO:BP	GO:0031325	positive regulation of cellular metabolic process	148	2443	1.80e-13
GO:BP	GO:0051173	positive regulation of nitrogen compound metabolic process	149	2494	4.56e-13
GO:BP	GO:0008152	metabolic process	362	8768	1.01e-12
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	156	2729	3.62e-12
GO:BP	GO:0009893	positive regulation of metabolic process	161	2974	1.31e-10
GO:BP	GO:0048523	negative regulation of cellular process	190	3749	1.82e-10
GO:BP	GO:0048519	negative regulation of biological process	201	4169	3.37e-09
GO:BP	GO:0006325	chromatin organization	42	545	1.34e-05
GO:BP	GO:0048522	positive regulation of cellular process	190	4291	2.22e-05
GO:BP	GO:0048518	positive regulation of biological process	203	4739	8.07e-05
GO:BP	GO:0016570	histone modification	34	427	9.36e-05
GO:BP	GO:0006338	chromatin remodeling	28	315	9.58e-05
GO:BP	GO:0050793	regulation of developmental process	93	1905	2.00e-03
GO:BP	GO:0030522	intracellular receptor signaling pathway	20	232	4.47e-03
GO:BP	GO:0072359	circulatory system development	51	915	7.04e-03
GO:BP	GO:0097676	histone H3-K36 dimethylation	3	4	7.78e-03
GO:BP	GO:0006354	DNA-templated transcription elongation	19	225	8.50e-03
GO:BP	GO:0007507	heart development	33	514	9.50e-03
GO:BP	GO:0018022	peptidyl-lysine methylation	13	122	9.55e-03
GO:BP	GO:2000779	regulation of double-strand break repair	13	122	9.55e-03
GO:BP	GO:0018205	peptidyl-lysine modification	26	371	1.18e-02
GO:BP	GO:0034968	histone lysine methylation	12	109	1.21e-02
GO:BP	GO:0016571	histone methylation	14	143	1.29e-02
GO:BP	GO:0006282	regulation of DNA repair	17	198	1.42e-02
GO:BP	GO:0043009	chordate embryonic development	34	551	1.47e-02
GO:BP	GO:0007623	circadian rhythm	15	166	1.82e-02
GO:BP	GO:0048511	rhythmic process	19	241	1.83e-02
GO:BP	GO:0019827	stem cell population maintenance	14	151	2.15e-02
GO:BP	GO:0042789	mRNA transcription by RNA polymerase II	7	43	2.18e-02
GO:BP	GO:0010452	histone H3-K36 methylation	4	12	2.22e-02
GO:BP	GO:0006974	cellular response to DNA damage stimulus	44	800	2.32e-02
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	34	568	2.34e-02
GO:BP	GO:0098727	maintenance of cell number	14	153	2.34e-02
GO:BP	GO:0016071	mRNA metabolic process	38	664	2.61e-02
GO:BP	GO:0060429	epithelium development	47	879	2.66e-02
GO:BP	GO:0009987	cellular process	414	11931	2.71e-02
GO:BP	GO:0010667	negative regulation of cardiac muscle cell apoptotic process	5	22	2.77e-02
GO:BP	GO:0086023	adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process	3	6	2.89e-02
GO:BP	GO:0003278	apoptotic process involved in heart morphogenesis	3	6	2.89e-02
GO:BP	GO:0035264	multicellular organism growth	12	123	3.06e-02
GO:BP	GO:2001020	regulation of response to DNA damage stimulus	21	295	3.10e-02
GO:BP	GO:2000736	regulation of stem cell differentiation	9	75	3.11e-02
GO:BP	GO:0043242	negative regulation of protein-containing complex disassembly	9	75	3.11e-02
GO:BP	GO:0009755	hormone-mediated signaling pathway	13	141	3.11e-02
GO:BP	GO:0051052	regulation of DNA metabolic process	29	468	3.13e-02
GO:BP	GO:0008213	protein alkylation	15	180	3.48e-02
GO:BP	GO:0006479	protein methylation	15	180	3.48e-02
GO:BP	GO:0009299	mRNA transcription	7	48	3.62e-02
GO:BP	GO:0032502	developmental process	184	4662	3.81e-02
GO:BP	GO:0048863	stem cell differentiation	16	202	3.98e-02
GO:BP	GO:1901898	negative regulation of relaxation of cardiac muscle	2	2	4.25e-02
GO:BP	GO:0010569	regulation of double-strand break repair via homologous recombination	8	64	4.25e-02
GO:BP	GO:0032242	regulation of nucleoside transport	2	2	4.25e-02
GO:BP	GO:0043401	steroid hormone mediated signaling pathway	11	112	4.25e-02
GO:BP	GO:0010664	negative regulation of striated muscle cell apoptotic process	5	25	4.28e-02
GO:BP	GO:0021915	neural tube development	13	148	4.28e-02
GO:BP	GO:0035019	somatic stem cell population maintenance	7	50	4.28e-02
GO:BP	GO:1900246	positive regulation of RIG-I signaling pathway	3	7	4.28e-02
GO:BP	GO:0032239	regulation of nucleobase-containing compound transport	4	15	4.31e-02
GO:BP	GO:0055012	ventricular cardiac muscle cell differentiation	4	15	4.31e-02
KEGG	KEGG:05168	Herpes simplex virus 1 infection	54	424	9.82e-16

##motif time independent response genes

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0051252	regulation of RNA metabolic process	156	2927	2.90e-12
GO:BP	GO:0006351	DNA-templated transcription	147	2760	9.65e-12
GO:BP	GO:0019219	regulation of nucleobase-containing compound metabolic process	163	3189	9.65e-12
GO:BP	GO:0097659	nucleic acid-templated transcription	147	2761	9.65e-12
GO:BP	GO:0032774	RNA biosynthetic process	147	2792	1.50e-11
GO:BP	GO:0006355	regulation of DNA-templated transcription	142	2654	1.50e-11
GO:BP	GO:1903506	regulation of nucleic acid-templated transcription	142	2656	1.50e-11
GO:BP	GO:0010468	regulation of gene expression	178	3691	1.83e-11
GO:BP	GO:2001141	regulation of RNA biosynthetic process	142	2674	2.04e-11
GO:BP	GO:0060255	regulation of macromolecule metabolic process	212	4781	5.32e-11
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	155	3100	1.06e-10
GO:BP	GO:0090304	nucleic acid metabolic process	190	4149	1.50e-10
GO:BP	GO:0031326	regulation of cellular biosynthetic process	157	3212	3.97e-10
GO:BP	GO:0051171	regulation of nitrogen compound metabolic process	198	4456	5.45e-10
GO:BP	GO:0009889	regulation of biosynthetic process	158	3267	6.72e-10
GO:BP	GO:0006366	transcription by RNA polymerase II	114	2053	6.72e-10
GO:BP	GO:0080090	regulation of primary metabolic process	201	4576	8.22e-10
GO:BP	GO:0006357	regulation of transcription by RNA polymerase II	110	1976	1.46e-09
GO:BP	GO:1901362	organic cyclic compound biosynthetic process	159	3344	1.85e-09
GO:BP	GO:0031323	regulation of cellular metabolic process	195	4432	1.85e-09
GO:BP	GO:0019222	regulation of metabolic process	219	5198	1.92e-09
GO:BP	GO:0018130	heterocycle biosynthetic process	155	3235	1.92e-09
GO:BP	GO:0034654	nucleobase-containing compound biosynthetic process	152	3170	3.20e-09
GO:BP	GO:0019438	aromatic compound biosynthetic process	154	3237	3.85e-09
GO:BP	GO:0016070	RNA metabolic process	169	3683	4.06e-09
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	133	2729	3.81e-08
GO:BP	GO:0009059	macromolecule biosynthetic process	169	3824	9.05e-08
GO:BP	GO:0010467	gene expression	196	4696	1.76e-07
GO:BP	GO:0009893	positive regulation of metabolic process	139	2974	2.04e-07
GO:BP	GO:0044271	cellular nitrogen compound biosynthetic process	168	3851	2.75e-07
GO:BP	GO:0006139	nucleobase-containing compound metabolic process	192	4615	3.87e-07
GO:BP	GO:0051173	positive regulation of nitrogen compound metabolic process	121	2494	4.13e-07
GO:BP	GO:1901576	organic substance biosynthetic process	193	4658	4.52e-07
GO:BP	GO:1901360	organic cyclic compound metabolic process	201	4921	5.10e-07
GO:BP	GO:0046483	heterocycle metabolic process	195	4732	5.21e-07
GO:BP	GO:0009058	biosynthetic process	194	4721	7.48e-07
GO:BP	GO:0051253	negative regulation of RNA metabolic process	68	1145	1.63e-06
GO:BP	GO:0006725	cellular aromatic compound metabolic process	194	4770	1.75e-06
GO:BP	GO:0044249	cellular biosynthetic process	188	4584	1.86e-06
GO:BP	GO:0043170	macromolecule metabolic process	268	7265	2.14e-06
GO:BP	GO:0034641	cellular nitrogen compound metabolic process	203	5111	4.04e-06
GO:BP	GO:0031325	positive regulation of cellular metabolic process	114	2443	1.00e-05
GO:BP	GO:0045934	negative regulation of nucleobase-containing compound metabolic process	69	1247	1.74e-05
GO:BP	GO:0051254	positive regulation of RNA metabolic process	76	1469	5.40e-05
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	82	1643	7.50e-05
GO:BP	GO:0048518	positive regulation of biological process	185	4739	1.11e-04
GO:BP	GO:0048255	mRNA stabilization	10	49	1.26e-04
GO:BP	GO:0050789	regulation of biological process	289	8305	1.50e-04
GO:BP	GO:0050794	regulation of cellular process	277	7878	1.55e-04
GO:BP	GO:0009890	negative regulation of biosynthetic process	68	1310	1.91e-04
GO:BP	GO:0071704	organic substance metabolic process	291	8408	2.17e-04
GO:BP	GO:0044238	primary metabolic process	280	8038	3.04e-04
GO:BP	GO:1902369	negative regulation of RNA catabolic process	11	68	3.62e-04
GO:BP	GO:0031327	negative regulation of cellular biosynthetic process	66	1284	3.62e-04
GO:BP	GO:0045944	positive regulation of transcription by RNA polymerase II	53	951	3.68e-04
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	68	1341	3.68e-04
GO:BP	GO:1902373	negative regulation of mRNA catabolic process	10	56	3.68e-04
GO:BP	GO:1903508	positive regulation of nucleic acid-templated transcription	68	1341	3.68e-04
GO:BP	GO:0048522	positive regulation of cellular process	168	4291	3.68e-04
GO:BP	GO:0044237	cellular metabolic process	270	7716	4.08e-04
GO:BP	GO:0010558	negative regulation of macromolecule biosynthetic process	64	1241	4.08e-04
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	68	1348	4.12e-04
GO:BP	GO:0045892	negative regulation of DNA-templated transcription	56	1038	4.48e-04
GO:BP	GO:1903507	negative regulation of nucleic acid-templated transcription	56	1040	4.60e-04
GO:BP	GO:0043489	RNA stabilization	10	58	4.60e-04
GO:BP	GO:0007049	cell cycle	75	1550	5.30e-04
GO:BP	GO:0051726	regulation of cell cycle	53	972	5.70e-04
GO:BP	GO:1902679	negative regulation of RNA biosynthetic process	56	1050	5.83e-04
GO:BP	GO:0006807	nitrogen compound metabolic process	268	7699	7.26e-04
GO:BP	GO:0000122	negative regulation of transcription by RNA polymerase II	44	759	7.78e-04
GO:BP	GO:0010628	positive regulation of gene expression	46	810	8.12e-04
GO:BP	GO:0008152	metabolic process	297	8768	1.03e-03
GO:BP	GO:0065007	biological regulation	294	8676	1.26e-03
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	73	1542	1.36e-03
GO:BP	GO:1903312	negative regulation of mRNA metabolic process	11	81	1.46e-03
GO:BP	GO:0031328	positive regulation of cellular biosynthetic process	75	1617	2.01e-03
GO:BP	GO:0031324	negative regulation of cellular metabolic process	82	1825	2.46e-03
GO:BP	GO:0009891	positive regulation of biosynthetic process	75	1646	3.55e-03
GO:BP	GO:0009892	negative regulation of metabolic process	99	2371	6.00e-03
KEGG	KEGG:04115	p53 signaling pathway	11	68	8.65e-04

###long go frame

NR1f <- tableNR %>% dplyr::filter(source=="GO:BP") %>% 
    dplyr::select(p_value,term_name,intersection_size) %>%
    slice_min(., n=10 ,order_by=p_value) %>%
    mutate(log_val = -log10(p_value)) %>%mutate(order_val=rev(as.numeric(rownames(.))))

LR3f <- tabletop2Bi_LR %>% dplyr::filter(source=="GO:BP") %>% 
    dplyr::select(p_value,term_name,intersection_size) %>%
    slice_min(., n=9 ,order_by=p_value) %>%
    mutate(log_val = -log10(p_value))  %>%  mutate(order_val=rev(as.numeric(rownames(.))))


TI3f <- tabletop2Bi_TI %>% 
    dplyr::filter(source =="GO:BP") %>% 
    dplyr::select(p_value,term_name,intersection_size) %>%
    slice_min(., n=10 ,order_by=p_value) %>%
    mutate(log_val = -log10(p_value))  %>% mutate(order_val=rev(as.numeric(rownames(.))))

ER3f <- tabletop2Bi_ER %>% 
    dplyr::filter(source =="GO:BP") %>% 
    dplyr::select(p_value,term_name,intersection_size) %>%
    slice_min(., n=10 ,order_by=p_value) %>%
    mutate(log_val = -log10(p_value))  %>% mutate(order_val=rev(as.numeric(rownames(.))))

GOmotiflong <-list("Early Response"=ER3f,"Late Response"=LR3f,"Time-Independent\nResponse"=TI3f, "No Response"=NR1f)
GOBPlong <- data.table::rbindlist(GOmotiflong, idcol = "motif")
p <- GOBPlong %>% mutate(motif=fct_inorder(motif)) %>% 
  
ggplot(., aes(x = log_val, y=reorder(term_name, order_val, desc=FALSE),col=motif)) +
    geom_point(aes(size = intersection_size, col=motif)) +
  scale_y_discrete(labels = wrap_format(40))+
  facet_grid(motif~., scales = "free_y")+
  
    guides(col=guide_legend(title="Motif group"), size=guide_legend(title = "# of intersected \n terms"))+
    ggtitle('Top 10 enriched GO:BP terms for each motif') +
     xlab(expression("-log"[10]~"(p-value)"))+
    #scale_x_continuous(expand = expansion(mult = .2))+
    ylab("GO:BP term")+
      theme_bw()+
 theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 8, color = "black", angle = 0),
        strip.text.x = element_text(size = 15, color = "black", face = "bold"))


#https://stackoverflow.com/questions/41631806/change-facet-label-text-and-background-colour/60046113#60046113
g <- ggplot_gtable(ggplot_build(p))
stripr <- which(grepl('strip-r', g$layout$name))
fills <- c("#F8766D", "#7CAE00", "#00BFC4", "#C77CFF")
k <- 1
for (i in stripr) {
  j <- which(grepl('rect', g$grobs[[i]]$grobs[[1]]$childrenOrder))
  g$grobs[[i]]$grobs[[1]]$children[[j]]$gp$fill <- fills[k]
  k <- k+1
}
#print(grid::grid.draw(g))
grid.draw(g)

#hex <- hue_pal()(4)

#hex
#> hex (red/green/blue/purple default in ggplot)
#[1] "#F8766D" "#7CAE00" "#00BFC4" "#C77CFF"
#p

###long go kegg break

LR3fk <- tabletop2Bi_LR %>% dplyr::filter(source=="KEGG") %>% 
    dplyr::select(p_value,term_name,intersection_size) %>%
    slice_min(., n=10 ,order_by=p_value) %>%
    mutate(log_val = -log10(p_value))


TI3fk <- tabletop2Bi_TI %>% 
    dplyr::filter(source =="KEGG") %>% 
    dplyr::select(p_value,term_name,intersection_size) %>%
    slice_min(., n=10 ,order_by=p_value) %>%
    mutate(log_val = -log10(p_value)) 

ER3fk <- tabletop2Bi_ER %>% 
    dplyr::filter(source =="KEGG") %>% 
    dplyr::select(p_value,term_name,intersection_size) %>%
    slice_min(., n=10 ,order_by=p_value) %>%
    mutate(log_val = -log10(p_value)) 

KEGGmotiflong <-list("ER"=ER3fk,"LR"=LR3fk,"TI"=TI3fk)
KEGGlong <- data.table::rbindlist(KEGGmotiflong, idcol = "motif")
KEGGlong %>% group_by(motif) %>% 
ggplot(., aes(x = log_val, y =reorder(term_name,p_value,desc=FALSE),col=motif)) +
    geom_point(aes(size = intersection_size, col=motif)) +
  scale_y_discrete(limits=rev,labels = wrap_format(30))+
    guides(col=guide_legend(title="Motif group"), size=guide_legend(title = "# of intersected \n terms"))+
    ggtitle('Top enriched KEGG terms for each motif') +
    xlab(expression("-log"[10]~"(p-value)"))+
    #scale_x_continuous(expand = expansion(mult = .2))+
    ylab("KEGG term")+
      theme_bw()+
 theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 9, color = "black", angle = 0),
        strip.text.x = element_text(size = 15, color = "black", face = "bold"))

sessionInfo()

R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] ggVennDiagram_1.2.2 scales_1.2.1        kableExtra_1.3.4   
 [4] VennDiagram_1.7.3   futile.logger_1.4.3 gridExtra_2.3      
 [7] BiocGenerics_0.42.0 gprofiler2_0.2.1    lubridate_1.9.2    
[10] forcats_1.0.0       stringr_1.5.0       dplyr_1.1.0        
[13] purrr_1.0.1         readr_2.1.4         tidyr_1.3.0        
[16] tibble_3.1.8        ggplot2_3.4.1       tidyverse_2.0.0    
[19] workflowr_1.7.0    

loaded via a namespace (and not attached):
 [1] httr_1.4.5           sass_0.4.5           jsonlite_1.8.4      
 [4] viridisLite_0.4.1    bslib_0.4.2          shiny_1.7.4         
 [7] getPass_0.2-2        highr_0.10           yaml_2.3.7          
[10] pillar_1.8.1         glue_1.6.2           digest_0.6.31       
[13] promises_1.2.0.1     rvest_1.0.3          RVenn_1.1.0         
[16] colorspace_2.1-0     htmltools_0.5.4      httpuv_1.6.9        
[19] pkgconfig_2.0.3      xtable_1.8-4         webshot_0.5.4       
[22] processx_3.8.0       svglite_2.1.1        whisker_0.4.1       
[25] later_1.3.0          tzdb_0.3.0           timechange_0.2.0    
[28] git2r_0.31.0         farver_2.1.1         generics_0.1.3      
[31] ellipsis_0.3.2       cachem_1.0.7         withr_2.5.0         
[34] lazyeval_0.2.2       cli_3.6.0            mime_0.12           
[37] magrittr_2.0.3       evaluate_0.20        ps_1.7.2            
[40] fs_1.6.1             fansi_1.0.4          xml2_1.3.3          
[43] tools_4.2.2          data.table_1.14.8    hms_1.1.2           
[46] formatR_1.14         lifecycle_1.0.3      plotly_4.10.1       
[49] munsell_0.5.0        lambda.r_1.2.4       callr_3.7.3         
[52] compiler_4.2.2       jquerylib_0.1.4      systemfonts_1.0.4   
[55] rlang_1.0.6          rstudioapi_0.14      htmlwidgets_1.6.1   
[58] crosstalk_1.2.0      labeling_0.4.2       rmarkdown_2.20      
[61] gtable_0.3.1         R6_2.5.1             knitr_1.42          
[64] fastmap_1.1.1        utf8_1.2.3           rprojroot_2.0.3     
[67] futile.options_1.0.1 stringi_1.7.12       Rcpp_1.0.10         
[70] vctrs_0.5.2          tidyselect_1.2.0     xfun_0.37

Cormotifcluster_analysis

ERM

2023-04-16

motif Late response Top2inhibitors

motif Early Response Top2 inhibitors