Last updated: 2023-02-10

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Rmd	ea3f948	reneeisnowhere	2023-02-10	updates for the week
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Rmd	8c41736	reneeisnowhere	2023-02-07	update with corrMotif
html	f147cf9	reneeisnowhere	2023-02-01	Build site.
Rmd	1657edd	reneeisnowhere	2023-02-01	updating Go tables
html	eed4dc5	reneeisnowhere	2023-01-31	Build site.
Rmd	848eb1a	reneeisnowhere	2023-01-31	updating GO plots
Rmd	82b31a0	reneeisnowhere	2023-01-31	updating GEA
Rmd	34a525c	reneeisnowhere	2023-01-26	link update
html	41b5f9c	reneeisnowhere	2023-01-23	Build site.
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html	6c21cf8	reneeisnowhere	2023-01-20	Build site.
Rmd	443a9f3	reneeisnowhere	2023-01-20	adding in GO analysis

GO Analysis

I have created several files from the RNA analysis that contain the significant genes(determined by adj.P.val < 0.1) from each Time and Condition. The names of the files are in the following format: ‘sigV’+Drug(2 letters)+time.

example: ‘sigVDA3.txt’ means this file contains the significant DE genes from the Daunorubicin 3 hour compared to Vehicle Control 3 hour analysis

library(gprofiler2)
library(tidyverse)
library(ggplot2)
library(readr)
library(BiocGenerics)
library(gridExtra)
library(VennDiagram)
library(kableExtra)
library(scales)
library(ggVennDiagram)

The analysis is based on all genes that passed the rowMeans>0 from the previous page link

Below is the analysis of differentially expressed genes for each treatment at 3 hours and 24 hours.

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0006366	transcription by RNA polymerase II	212	2055	1.51e-31
GO:BP	GO:0006357	regulation of transcription by RNA polymerase II	206	1978	3.06e-31
GO:BP	GO:0097659	nucleic acid-templated transcription	243	2767	3.81e-27
GO:BP	GO:0006351	DNA-templated transcription	243	2766	3.81e-27
GO:BP	GO:0032774	RNA biosynthetic process	243	2782	7.23e-27
GO:BP	GO:0051252	regulation of RNA metabolic process	247	2921	1.06e-25
GO:BP	GO:1903506	regulation of nucleic acid-templated transcription	234	2663	1.13e-25
GO:BP	GO:0006355	regulation of DNA-templated transcription	234	2662	1.13e-25
GO:BP	GO:2001141	regulation of RNA biosynthetic process	234	2670	1.50e-25
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	248	3088	3.55e-23
GO:BP	GO:0019219	regulation of nucleobase-containing compound metabolic process	214	3181	7.80e-23
GO:BP	GO:0034654	nucleobase-containing compound biosynthetic process	202	3149	3.21e-21
GO:BP	GO:0031326	regulation of cellular biosynthetic process	211	3204	3.83e-21
GO:BP	GO:0018130	heterocycle biosynthetic process	249	3210	7.32e-21
GO:BP	GO:0019438	aromatic compound biosynthetic process	186	3212	1.37e-20
GO:BP	GO:0009889	regulation of biosynthetic process	211	3255	2.37e-20
GO:BP	GO:1901362	organic cyclic compound biosynthetic process	188	3319	1.13e-19
GO:BP	GO:0009059	macromolecule biosynthetic process	220	3801	3.12e-19
GO:BP	GO:0044271	cellular nitrogen compound biosynthetic process	222	3820	3.95e-16
GO:BP	GO:0031323	regulation of cellular metabolic process	234	4432	1.89e-15
GO:BP	GO:0080090	regulation of primary metabolic process	234	4567	3.53e-13
GO:BP	GO:0051171	regulation of nitrogen compound metabolic process	239	4443	4.83e-13
GO:BP	GO:0044249	cellular biosynthetic process	208	4569	2.48e-12
GO:BP	GO:0000122	negative regulation of transcription by RNA polymerase II	83	761	2.91e-12
GO:BP	GO:1901576	organic substance biosynthetic process	208	4628	1.02e-11
GO:BP	GO:0045892	negative regulation of DNA-templated transcription	100	1041	1.05e-11
GO:BP	GO:1903507	negative regulation of nucleic acid-templated transcription	100	1043	1.12e-11
GO:BP	GO:1902679	negative regulation of RNA biosynthetic process	100	1044	1.19e-11
GO:BP	GO:0051253	negative regulation of RNA metabolic process	105	1137	1.71e-11
GO:BP	GO:0009058	biosynthetic process	209	4691	2.15e-11
GO:BP	GO:0010558	negative regulation of macromolecule biosynthetic process	106	1237	1.20e-09
GO:BP	GO:0045934	negative regulation of nucleobase-containing compound metabolic process	106	1239	1.41e-09
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	108	1342	3.35e-09
GO:BP	GO:1903508	positive regulation of nucleic acid-templated transcription	108	1342	3.35e-09
GO:BP	GO:0010468	regulation of gene expression	212	3687	3.35e-09
GO:BP	GO:0051254	positive regulation of RNA metabolic process	114	1469	3.59e-09
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	108	1348	3.93e-09
GO:BP	GO:0031327	negative regulation of cellular biosynthetic process	106	1279	9.70e-09
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	116	1537	1.15e-08
GO:BP	GO:0009890	negative regulation of biosynthetic process	106	1304	2.77e-08
GO:BP	GO:0031328	positive regulation of cellular biosynthetic process	119	1614	3.64e-08
GO:BP	GO:0045944	positive regulation of transcription by RNA polymerase II	83	952	8.69e-08
GO:BP	GO:0009891	positive regulation of biosynthetic process	119	1640	1.04e-07
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	117	1641	2.23e-07
GO:BP	GO:0031324	negative regulation of cellular metabolic process	127	1830	8.08e-07
GO:BP	GO:0060255	regulation of macromolecule metabolic process	111	4772	2.49e-06
GO:BP	GO:0019222	regulation of metabolic process	115	5189	1.10e-05
GO:BP	GO:0031325	positive regulation of cellular metabolic process	123	2446	1.78e-05
GO:BP	GO:0051173	positive regulation of nitrogen compound metabolic process	123	2497	5.00e-05
GO:BP	GO:0051172	negative regulation of nitrogen compound metabolic process	126	1905	5.02e-05
GO:CC	GO:0090575	RNA polymerase II transcription regulator complex	14	219	3.93e-05
GO:CC	GO:0005667	transcription regulator complex	42	413	3.93e-05
GO:MF	GO:0003677	DNA binding	197	1908	9.77e-29
GO:MF	GO:0140110	transcription regulator activity	168	1431	1.30e-28
GO:MF	GO:0000976	transcription cis-regulatory region binding	143	1082	4.97e-28
GO:MF	GO:0001067	transcription regulatory region nucleic acid binding	143	1084	4.97e-28
GO:MF	GO:0003700	DNA-binding transcription factor activity	138	975	4.97e-28
GO:MF	GO:0000977	RNA polymerase II transcription regulatory region sequence-specific DNA binding	136	998	3.16e-27
GO:MF	GO:1990837	sequence-specific double-stranded DNA binding	144	1128	4.86e-27
GO:MF	GO:0043565	sequence-specific DNA binding	148	1220	3.07e-26
GO:MF	GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	130	935	1.74e-25
GO:MF	GO:0003690	double-stranded DNA binding	145	1209	7.19e-25
GO:MF	GO:0000987	cis-regulatory region sequence-specific DNA binding	92	860	1.13e-22
GO:MF	GO:0000978	RNA polymerase II cis-regulatory region sequence-specific DNA binding	91	843	1.33e-22
GO:MF	GO:0001217	DNA-binding transcription repressor activity	35	246	2.35e-07
GO:MF	GO:0001228	DNA-binding transcription activator activity, RNA polymerase II-specific	39	304	3.92e-07
GO:MF	GO:0001216	DNA-binding transcription activator activity	39	308	4.64e-07
GO:MF	GO:0001227	DNA-binding transcription repressor activity, RNA polymerase II-specific	33	242	1.69e-06
GO:MF	GO:0046872	metal ion binding	204	3328	4.40e-06
GO:MF	GO:0043169	cation binding	204	3392	2.37e-05

I first looked at the data with all genes from the sigDA3 dataset. I used the list of all genes based on my rowMeans>0 filtering as background.

Analysis of Up versus Down

I then separated the VDA3 file by log2 Fold Change to see how the gene sets are enriched. Nothing showed up in the GO-BP/CC/MG-down regulated gene-set at a significant level, p<0.05.

Note this is at three hour for Daunorubicin

I next wanted to see what happened at 24 hours with daunorubicin. I used the sigVDA24 file to do this.

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0000070	mitotic sister chromatid segregation	74	192	8.62e-05
GO:BP	GO:0000819	sister chromatid segregation	81	215	8.62e-05
GO:BP	GO:0045930	negative regulation of mitotic cell cycle	83	212	8.62e-05
GO:CC	GO:0098687	chromosomal region	126	353	2.75e-08
GO:CC	GO:0000775	chromosome, centromeric region	89	229	2.23e-06
GO:CC	GO:0000940	outer kinetochore	11	12	2.39e-05
GO:CC	GO:0000779	condensed chromosome, centromeric region	64	167	4.66e-05

Here I was able to visualize the 24 hour GO analysis of daunorubicin.

##Venn Diagrams

[1] 8887

[1] 554

[1] 7732

[1] 6808

[1] 6858

[1] 1251

[1] 8925

Tell me more! what are those genes at 24 hours?? give me some GO! # Graphing GO

# list24totvenn <- get.venn.partitions(total24)
# all24hour <- listvenn$values[1]

##From Cormotif
response_cluster24h <-  read_csv("data/response_cluster24h.csv", 
    col_types = cols(...1 = col_skip()))
length(response_cluster24h$x)

[1] 1489

gostrescorm24 <- gost(query = response_cluster24h$x,  organism = "hsapiens",
  ordered_query = FALSE,
  domain_scope = "custom",
  measure_underrepresentation = FALSE,
  evcodes = FALSE,
  user_threshold = 0.0001,
  correction_method = c("fdr"),
  custom_bg = backGL$ENTREZID,
  sources=c("GO:BP","GO:MF", "GO:CC"))
pDA24 <- gostplot(gostrescorm24, capped = FALSE, interactive = TRUE)
pDA24

# (gostres$result$p_value)
table3 <- gostrescorm24$result %>%
  dplyr::select(c(source, term_id, term_name,intersection_size, term_size, p_value)) %>% 
  mutate_at(.cols = 6, .funs= scientific_format()) %>% 
  kable(.,) %>% 
  kable_paper("striped", full_width = FALSE) %>%  
  kable_styling(full_width = FALSE, position = "left",bootstrap_options = c("striped","hover"))
  table3

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0007049	cell cycle	308	1529	5.34e-32
GO:BP	GO:0000278	mitotic cell cycle	200	841	4.69e-29
GO:BP	GO:1903047	mitotic cell cycle process	177	704	1.30e-28
GO:BP	GO:0022402	cell cycle process	227	1051	3.54e-27
GO:BP	GO:0051726	regulation of cell cycle	205	959	1.30e-23
GO:BP	GO:0051301	cell division	145	577	3.65e-23
GO:BP	GO:0000280	nuclear division	113	389	3.65e-23
GO:BP	GO:0010564	regulation of cell cycle process	152	622	4.32e-23
GO:BP	GO:0007059	chromosome segregation	100	327	3.02e-22
GO:BP	GO:0051276	chromosome organization	133	523	1.05e-21
GO:BP	GO:0140014	mitotic nuclear division	92	297	7.73e-21
GO:BP	GO:0048285	organelle fission	114	432	8.20e-20
GO:BP	GO:0098813	nuclear chromosome segregation	85	269	8.20e-20
GO:BP	GO:0000819	sister chromatid segregation	73	215	7.06e-19
GO:BP	GO:0000070	mitotic sister chromatid segregation	68	192	1.14e-18
GO:BP	GO:0000075	cell cycle checkpoint signaling	65	182	4.96e-18
GO:BP	GO:0007093	mitotic cell cycle checkpoint signaling	55	139	1.84e-17
GO:BP	GO:0007346	regulation of mitotic cell cycle	108	447	1.09e-15
GO:BP	GO:0045786	negative regulation of cell cycle	91	344	1.10e-15
GO:BP	GO:0044770	cell cycle phase transition	115	504	7.51e-15
GO:BP	GO:0045930	negative regulation of mitotic cell cycle	66	212	7.51e-15
GO:BP	GO:0006260	DNA replication	75	262	8.66e-15
GO:BP	GO:1901988	negative regulation of cell cycle phase transition	70	235	9.68e-15
GO:BP	GO:1901987	regulation of cell cycle phase transition	96	392	2.61e-14
GO:BP	GO:0010948	negative regulation of cell cycle process	76	273	2.61e-14
GO:BP	GO:0051783	regulation of nuclear division	46	118	2.89e-14
GO:BP	GO:0044772	mitotic cell cycle phase transition	100	419	3.41e-14
GO:BP	GO:0007088	regulation of mitotic nuclear division	42	103	8.64e-14
GO:BP	GO:0090068	positive regulation of cell cycle process	63	207	9.72e-14
GO:BP	GO:0006261	DNA-templated DNA replication	52	152	1.66e-13
GO:BP	GO:0051983	regulation of chromosome segregation	45	119	2.03e-13
GO:BP	GO:1901990	regulation of mitotic cell cycle phase transition	80	310	3.58e-13
GO:BP	GO:1901991	negative regulation of mitotic cell cycle phase transition	54	167	6.55e-13
GO:BP	GO:0033048	negative regulation of mitotic sister chromatid segregation	27	48	7.12e-13
GO:BP	GO:0033046	negative regulation of sister chromatid segregation	27	48	7.12e-13
GO:BP	GO:2000816	negative regulation of mitotic sister chromatid separation	27	48	7.12e-13
GO:BP	GO:1905819	negative regulation of chromosome separation	27	49	1.36e-12
GO:BP	GO:0051985	negative regulation of chromosome segregation	27	49	1.36e-12
GO:BP	GO:0033047	regulation of mitotic sister chromatid segregation	28	53	1.72e-12
GO:BP	GO:0007051	spindle organization	57	187	1.72e-12
GO:BP	GO:1903046	meiotic cell cycle process	48	141	2.01e-12
GO:BP	GO:0000226	microtubule cytoskeleton organization	116	554	2.08e-12
GO:BP	GO:1905818	regulation of chromosome separation	40	103	2.08e-12
GO:BP	GO:0045841	negative regulation of mitotic metaphase/anaphase transition	26	47	3.29e-12
GO:BP	GO:1902100	negative regulation of metaphase/anaphase transition of cell cycle	26	48	6.35e-12
GO:BP	GO:0051304	chromosome separation	43	121	7.89e-12
GO:BP	GO:0071173	spindle assembly checkpoint signaling	25	45	8.30e-12
GO:BP	GO:0007094	mitotic spindle assembly checkpoint signaling	25	45	8.30e-12
GO:BP	GO:0071174	mitotic spindle checkpoint signaling	25	45	8.30e-12
GO:BP	GO:0045787	positive regulation of cell cycle	72	282	1.12e-11
GO:BP	GO:0031577	spindle checkpoint signaling	25	46	1.58e-11
GO:BP	GO:1902850	microtubule cytoskeleton organization involved in mitosis	49	154	1.64e-11
GO:BP	GO:0051321	meiotic cell cycle	56	193	2.27e-11
GO:BP	GO:0006259	DNA metabolic process	162	908	2.45e-11
GO:BP	GO:0051784	negative regulation of nuclear division	28	58	2.45e-11
GO:BP	GO:0045839	negative regulation of mitotic nuclear division	27	55	3.87e-11
GO:BP	GO:0033045	regulation of sister chromatid segregation	37	99	6.33e-11
GO:BP	GO:0010965	regulation of mitotic sister chromatid separation	35	92	1.45e-10
GO:BP	GO:0140013	meiotic nuclear division	42	126	1.46e-10
GO:BP	GO:0006974	cellular response to DNA damage stimulus	145	801	1.54e-10
GO:BP	GO:0031570	DNA integrity checkpoint signaling	42	127	1.91e-10
GO:BP	GO:0007052	mitotic spindle organization	42	129	3.39e-10
GO:BP	GO:0051306	mitotic sister chromatid separation	35	95	3.99e-10
GO:BP	GO:0007091	metaphase/anaphase transition of mitotic cell cycle	34	91	5.06e-10
GO:BP	GO:0044784	metaphase/anaphase transition of cell cycle	34	92	7.14e-10
GO:BP	GO:0007017	microtubule-based process	138	769	1.00e-09
GO:BP	GO:0065004	protein-DNA complex assembly	50	177	1.10e-09
GO:BP	GO:0030071	regulation of mitotic metaphase/anaphase transition	33	89	1.26e-09
GO:BP	GO:1902099	regulation of metaphase/anaphase transition of cell cycle	33	90	1.77e-09
GO:BP	GO:2001251	negative regulation of chromosome organization	33	93	4.89e-09
GO:BP	GO:0016043	cellular component organization	634	5135	5.47e-09
GO:BP	GO:0006996	organelle organization	403	3007	5.93e-09
GO:BP	GO:0051225	spindle assembly	38	119	6.09e-09
GO:BP	GO:0008608	attachment of spindle microtubules to kinetochore	21	42	8.57e-09
GO:BP	GO:0033554	cellular response to stress	250	1699	1.48e-08
GO:BP	GO:0044839	cell cycle G2/M phase transition	43	150	1.65e-08
GO:BP	GO:0051716	cellular response to stimulus	631	5146	2.34e-08
GO:BP	GO:0000086	G2/M transition of mitotic cell cycle	40	135	2.34e-08
GO:BP	GO:0044774	mitotic DNA integrity checkpoint signaling	30	84	2.76e-08
GO:BP	GO:0051310	metaphase plate congression	27	70	2.85e-08
GO:BP	GO:0032465	regulation of cytokinesis	29	80	3.52e-08
GO:BP	GO:0050896	response to stimulus	716	5975	3.52e-08
GO:BP	GO:0000910	cytokinesis	44	164	9.35e-08
GO:BP	GO:0050000	chromosome localization	29	83	9.35e-08
GO:BP	GO:0006270	DNA replication initiation	18	35	9.35e-08
GO:BP	GO:0071459	protein localization to chromosome, centromeric region	18	35	9.35e-08
GO:BP	GO:0006281	DNA repair	100	539	1.10e-07
GO:BP	GO:0051302	regulation of cell division	41	148	1.18e-07
GO:BP	GO:0071840	cellular component organization or biogenesis	644	5328	1.72e-07
GO:BP	GO:0035556	intracellular signal transduction	293	2117	2.09e-07
GO:BP	GO:0051303	establishment of chromosome localization	27	76	2.14e-07
GO:BP	GO:0090329	regulation of DNA-templated DNA replication	22	53	2.17e-07
GO:BP	GO:0033044	regulation of chromosome organization	55	238	2.99e-07
GO:BP	GO:0000077	DNA damage checkpoint signaling	35	119	3.21e-07
GO:BP	GO:0051383	kinetochore organization	14	23	3.37e-07
GO:BP	GO:0061982	meiosis I cell cycle process	28	83	3.95e-07
GO:BP	GO:0071824	protein-DNA complex subunit organization	50	209	4.35e-07
GO:BP	GO:0034508	centromere complex assembly	16	31	6.65e-07
GO:BP	GO:0042770	signal transduction in response to DNA damage	44	175	7.05e-07
GO:BP	GO:0044773	mitotic DNA damage checkpoint signaling	27	80	7.05e-07
GO:BP	GO:0034502	protein localization to chromosome	31	103	1.27e-06
GO:BP	GO:0010389	regulation of G2/M transition of mitotic cell cycle	29	93	1.50e-06
GO:BP	GO:0006275	regulation of DNA replication	34	122	2.19e-06
GO:BP	GO:0000076	DNA replication checkpoint signaling	11	16	2.42e-06
GO:BP	GO:0006950	response to stress	367	2838	3.55e-06
GO:BP	GO:0007080	mitotic metaphase plate congression	21	56	3.70e-06
GO:BP	GO:0001932	regulation of protein phosphorylation	134	842	3.90e-06
GO:BP	GO:0009314	response to radiation	70	359	3.92e-06
GO:BP	GO:0000281	mitotic cytokinesis	26	81	3.93e-06
GO:BP	GO:0007098	centrosome cycle	34	125	3.97e-06
GO:BP	GO:1902749	regulation of cell cycle G2/M phase transition	30	104	5.70e-06
GO:BP	GO:0051256	mitotic spindle midzone assembly	8	9	6.67e-06
GO:BP	GO:0010212	response to ionizing radiation	35	134	7.46e-06
GO:BP	GO:0044786	cell cycle DNA replication	17	40	7.64e-06
GO:BP	GO:0007127	meiosis I	25	79	9.13e-06
GO:BP	GO:0006468	protein phosphorylation	180	1231	9.13e-06
GO:BP	GO:0065009	regulation of molecular function	316	2407	9.17e-06
GO:BP	GO:0071478	cellular response to radiation	39	161	1.21e-05
GO:BP	GO:0051984	positive regulation of chromosome segregation	13	25	1.26e-05
GO:BP	GO:0051988	regulation of attachment of spindle microtubules to kinetochore	11	18	1.26e-05
GO:BP	GO:0051255	spindle midzone assembly	9	12	1.26e-05
GO:BP	GO:0048523	negative regulation of cellular process	461	3736	1.26e-05
GO:BP	GO:0033043	regulation of organelle organization	156	1040	1.33e-05
GO:BP	GO:0007010	cytoskeleton organization	180	1239	1.34e-05
GO:BP	GO:0032467	positive regulation of cytokinesis	15	33	1.34e-05
GO:BP	GO:0016310	phosphorylation	210	1493	1.39e-05
GO:BP	GO:0048518	positive regulation of biological process	564	4711	1.60e-05
GO:BP	GO:0042325	regulation of phosphorylation	146	962	1.61e-05
GO:BP	GO:0009411	response to UV	35	139	1.73e-05
GO:BP	GO:0010639	negative regulation of organelle organization	63	326	2.10e-05
GO:BP	GO:0032508	DNA duplex unwinding	26	88	2.10e-05
GO:BP	GO:0007154	cell communication	529	4390	2.12e-05
GO:BP	GO:0045132	meiotic chromosome segregation	22	67	2.18e-05
GO:BP	GO:0042771	intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	17	43	2.28e-05
GO:BP	GO:0032392	DNA geometric change	27	94	2.28e-05
GO:BP	GO:0140694	non-membrane-bounded organelle assembly	67	356	2.38e-05
GO:BP	GO:0031023	microtubule organizing center organization	34	135	2.38e-05
GO:BP	GO:0000022	mitotic spindle elongation	8	10	2.47e-05
GO:BP	GO:0051338	regulation of transferase activity	117	740	3.16e-05
GO:BP	GO:0008283	cell population proliferation	201	1438	3.76e-05
GO:BP	GO:0023052	signaling	521	4341	4.58e-05
GO:BP	GO:0033260	nuclear DNA replication	15	36	4.73e-05
GO:BP	GO:0061640	cytoskeleton-dependent cytokinesis	28	104	5.65e-05
GO:BP	GO:0048522	positive regulation of cellular process	514	4283	5.74e-05
GO:BP	GO:0050790	regulation of catalytic activity	248	1856	6.13e-05
GO:BP	GO:0072332	intrinsic apoptotic signaling pathway by p53 class mediator	23	77	7.19e-05
GO:BP	GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity	26	94	7.62e-05
GO:BP	GO:0051231	spindle elongation	8	11	7.68e-05
GO:BP	GO:1902969	mitotic DNA replication	9	14	7.69e-05
GO:BP	GO:0045859	regulation of protein kinase activity	89	534	7.85e-05
GO:BP	GO:0007143	female meiotic nuclear division	12	25	9.15e-05
GO:CC	GO:0000775	chromosome, centromeric region	74	229	1.81e-17
GO:CC	GO:0098687	chromosomal region	95	353	6.41e-17
GO:CC	GO:0000793	condensed chromosome	74	239	9.76e-17
GO:CC	GO:0005694	chromosome	242	1392	3.48e-16
GO:CC	GO:0005819	spindle	96	388	7.85e-15
GO:CC	GO:0000779	condensed chromosome, centromeric region	54	167	4.56e-13
GO:CC	GO:0000776	kinetochore	52	158	5.65e-13
GO:CC	GO:0015630	microtubule cytoskeleton	200	1179	3.92e-12
GO:CC	GO:0043232	intracellular non-membrane-bounded organelle	548	4181	7.20e-12
GO:CC	GO:0043228	non-membrane-bounded organelle	548	4181	7.20e-12
GO:CC	GO:0072686	mitotic spindle	51	166	1.45e-11
GO:CC	GO:0005856	cytoskeleton	284	1894	4.43e-11
GO:CC	GO:0000922	spindle pole	47	161	8.46e-10
GO:CC	GO:0044815	DNA packaging complex	37	111	1.74e-09
GO:CC	GO:0000228	nuclear chromosome	52	207	2.75e-08
GO:CC	GO:0099513	polymeric cytoskeletal fiber	101	539	3.52e-08
GO:CC	GO:0099080	supramolecular complex	171	1075	3.67e-08
GO:CC	GO:0005815	microtubule organizing center	126	743	1.66e-07
GO:CC	GO:0005874	microtubule	77	387	2.38e-07
GO:CC	GO:0099512	supramolecular fiber	126	749	2.48e-07
GO:CC	GO:0030496	midbody	47	192	3.35e-07
GO:CC	GO:0099081	supramolecular polymer	126	757	4.34e-07
GO:CC	GO:0005813	centrosome	102	577	5.18e-07
GO:CC	GO:0051233	spindle midzone	16	34	1.87e-06
GO:CC	GO:0071162	CMG complex	9	11	2.12e-06
GO:CC	GO:0032993	protein-DNA complex	40	164	3.96e-06
GO:CC	GO:0005876	spindle microtubule	25	79	4.95e-06
GO:CC	GO:0005657	replication fork	23	69	5.21e-06
GO:CC	GO:0031261	DNA replication preinitiation complex	9	12	6.64e-06
GO:CC	GO:0000794	condensed nuclear chromosome	19	53	1.64e-05
GO:CC	GO:0005875	microtubule associated complex	33	136	4.87e-05
GO:CC	GO:0000786	nucleosome	22	73	5.95e-05
GO:CC	GO:0005871	kinesin complex	16	43	6.76e-05
GO:MF	GO:0017116	single-stranded DNA helicase activity	15	23	2.26e-07
GO:MF	GO:0030527	structural constituent of chromatin	22	47	2.26e-07
GO:MF	GO:0003774	cytoskeletal motor activity	30	90	7.91e-07
GO:MF	GO:0003777	microtubule motor activity	23	56	7.91e-07
GO:MF	GO:0140657	ATP-dependent activity	83	451	1.59e-05
GO:MF	GO:0046982	protein heterodimerization activity	52	247	5.93e-05
GO:MF	GO:0005515	protein binding	1204	11164	5.93e-05

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 forcats_1.0.0       stringr_1.5.0      
[10] dplyr_1.1.0         purrr_1.0.1         readr_2.1.3        
[13] tidyr_1.3.0         tibble_3.1.8        ggplot2_3.4.0      
[16] tidyverse_1.3.2     gprofiler2_0.2.1    workflowr_1.7.0    

loaded via a namespace (and not attached):
  [1] googledrive_2.0.0    colorspace_2.1-0     class_7.3-21        
  [4] ellipsis_0.3.2       rprojroot_2.0.3      fs_1.6.1            
  [7] proxy_0.4-27         rstudioapi_0.14      farver_2.1.1        
 [10] bit64_4.0.5          fansi_1.0.4          lubridate_1.9.1     
 [13] xml2_1.3.3           cachem_1.0.6         knitr_1.42          
 [16] jsonlite_1.8.4       broom_1.0.3          dbplyr_2.3.0        
 [19] shiny_1.7.4          compiler_4.2.2       httr_1.4.4          
 [22] backports_1.4.1      assertthat_0.2.1     fastmap_1.1.0       
 [25] lazyeval_0.2.2       gargle_1.3.0         cli_3.6.0           
 [28] later_1.3.0          formatR_1.14         htmltools_0.5.4     
 [31] tools_4.2.2          gtable_0.3.1         glue_1.6.2          
 [34] Rcpp_1.0.10          cellranger_1.1.0     jquerylib_0.1.4     
 [37] vctrs_0.5.2          svglite_2.1.1        crosstalk_1.2.0     
 [40] xfun_0.37            ps_1.7.2             rvest_1.0.3         
 [43] timechange_0.2.0     mime_0.12            lifecycle_1.0.3     
 [46] googlesheets4_1.0.1  getPass_0.2-2        vroom_1.6.1         
 [49] hms_1.1.2            promises_1.2.0.1     parallel_4.2.2      
 [52] lambda.r_1.2.4       yaml_2.3.7           sass_0.4.5          
 [55] stringi_1.7.12       highr_0.10           e1071_1.7-13        
 [58] rlang_1.0.6          pkgconfig_2.0.3      systemfonts_1.0.4   
 [61] bitops_1.0-7         evaluate_0.20        sf_1.0-9            
 [64] htmlwidgets_1.6.1    labeling_0.4.2       bit_4.0.5           
 [67] processx_3.8.0       tidyselect_1.2.0     magrittr_2.0.3      
 [70] R6_2.5.1             generics_0.1.3       DBI_1.1.3           
 [73] pillar_1.8.1         haven_2.5.1          whisker_0.4.1       
 [76] withr_2.5.0          units_0.8-1          RCurl_1.98-1.10     
 [79] modelr_0.1.10        crayon_1.5.2         futile.options_1.0.1
 [82] KernSmooth_2.23-20   utf8_1.2.3           plotly_4.10.1       
 [85] RVenn_1.1.0          tzdb_0.3.0           rmarkdown_2.20      
 [88] readxl_1.4.1         data.table_1.14.6    callr_3.7.3         
 [91] git2r_0.31.0         reprex_2.0.2         digest_0.6.31       
 [94] classInt_0.4-8       webshot_0.5.4        xtable_1.8-4        
 [97] httpuv_1.6.8         munsell_0.5.0        viridisLite_0.4.1   
[100] bslib_0.4.2

GO analysis

ERM

2023-02-10

GO Analysis

Analysis of Up versus Down

I next wanted to see what happened at 24 hours with daunorubicin. I used the sigVDA24 file to do this.