Histone Acetyl RNA-seq Enrichment analysis

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

Introduction

In this study we are looking at the effect of knock-down of two genes which are required for the supply of acetyl units. It is hypothesised that knock-down of these genes could lead to problems with the response to exercise. We have both ctrl and kd under either sedentary or exercise conditions.

The focus of this report is to perform mitch enrichment analysis of the DE tables I have already generated.

Here are the DE analyses I’ve already performed.

Contrast number	DE file	Contrast
1	dge1pkd.tsv	Effect of ATP-CL KD in Sed animals
2	dge2pkd.tsv	Effect of ATP-CL KD in Ex animals
3	dge3pkd.tsv	Effect of ACSS2 KD in Sed animals
4	dge4pkd.tsv	Effect of ACSS2 KD in Ex animals
5	dge5.tsv	Effect of Sed vs Ex (ATP-CL gene ctrl)
6	dge6kd.tsv	Effect of Sed vs Ex (ATP-CL gene KO)
7	dge7.tsv	Effect of Sed vs Ex (ACSS2 gene ctrl)
8	dge8kd.tsv	Effect of Sed vs Ex (ACSS2 gene kd)

First I will run mitch with each contrast separately, then joint enrichment in the following ways:

• #1 and #2 effect of ATP-CL KD in Sed and Ex animals

• #3 and #4 effect of ACSS2 KD in Sed and Ex animals

• #5 and #6 Effect of Sed vs Ex in ctrl and ATP-CL gene KD

• #7 and #8 Effect of Sed vs Ex in ctrl and ACSS2 gene KD

Finally all contrasts altogether.

suppressPackageStartupMessages({
    library("plyr")
    library("zoo")
    library("tidyverse")
    library("reshape2")
    library("DESeq2")
    library("gplots")
    library("fgsea")
    library("MASS")
    library("mitch")
    library("eulerr")
    library("limma")
    library("topconfects")
    library("kableExtra")
    library("vioplot")
    library("beeswarm")
})

Import DE data

de1 <- read.csv("dge1pkd.tsv",header=TRUE,row.names=1,sep="\t")
de2 <- read.csv("dge2pkd.tsv",header=TRUE,row.names=1,sep="\t")
de3 <- read.csv("dge3pkd.tsv",header=TRUE,row.names=1,sep="\t")
de4 <- read.csv("dge4pkd.tsv",header=TRUE,row.names=1,sep="\t")
de5 <- read.csv("dge5.tsv",header=TRUE,row.names=1,sep="\t")
de6 <- read.csv("dge6kd.tsv",header=TRUE,row.names=1,sep="\t")
de7 <- read.csv("dge7.tsv",header=TRUE,row.names=1,sep="\t")
de8 <- read.csv("dge8kd.tsv",header=TRUE,row.names=1,sep="\t")

Unidimensional mitch

First format the data into a friendly format.

genesets <- gmt_import("https://ziemann-lab.net/public/msigdb_mouse/reactome.v5.2.symbols_mouse.gmt")

de1$gene <- sapply(strsplit(rownames(de1)," "),"[[",2)
de1 <- aggregate(stat ~ gene,de1,mean)
de1rn <- de1
rownames(de1) <- de1$gene
de1$gene=NULL

de2$gene <- sapply(strsplit(rownames(de2)," "),"[[",2)
de2 <- aggregate(stat ~ gene,de2,mean)
de2rn <- de2
rownames(de2) <- de2$gene
de2$gene=NULL

de3$gene <- sapply(strsplit(rownames(de3)," "),"[[",2)
de3 <- aggregate(stat ~ gene,de3,mean)
de3rn <- de3
rownames(de3) <- de3$gene
de3$gene=NULL

de4$gene <- sapply(strsplit(rownames(de4)," "),"[[",2)
de4 <- aggregate(stat ~ gene,de4,mean)
de4rn <- de4
rownames(de4) <- de4$gene
de4$gene=NULL

de5$gene <- sapply(strsplit(rownames(de5)," "),"[[",2)
de5 <- aggregate(stat ~ gene,de5,mean)
de5rn <- de5
rownames(de5) <- de5$gene
de5$gene=NULL

de6$gene <- sapply(strsplit(rownames(de6)," "),"[[",2)
de6 <- aggregate(stat ~ gene,de6,mean)
de6rn <- de6
rownames(de6) <- de6$gene
de6$gene=NULL

de7$gene <- sapply(strsplit(rownames(de7)," "),"[[",2)
de7 <- aggregate(stat ~ gene,de7,mean)
de7rn <- de7
rownames(de7) <- de7$gene
de7$gene=NULL

de8$gene <- sapply(strsplit(rownames(de8)," "),"[[",2)
de8 <- aggregate(stat ~ gene,de8,mean)
de8rn <- de8
rownames(de8) <- de8$gene
de8$gene=NULL

Enrich it.

res1 <- mitch_calc(de1, genesets, priority="effect")

## Note: Enrichments with large effect sizes may not be
##             statistically significant.

head(res1$enrichment_result,20) %>% kbl(caption="DE1: Reactome") %>% kable_styling()

DE1: Reactome

	set	setSize	pANOVA	s.dist	p.adjustANOVA
414	REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING	12	0.0000008	0.8226249	0.0000314
408	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_	73	0.0000000	0.6487780	0.0000000
334	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT	59	0.0000000	0.6429788	0.0000000
293	REACTOME_PYRUVATE_METABOLISM	16	0.0000235	0.6106047	0.0006931
24	REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT	107	0.0000000	0.5992902	0.0000000
137	REACTOME_REGULATION_OF_PYRUVATE_DEHYDROGENASE_PDH_COMPLEX	11	0.0007065	0.5898468	0.0118837
224	REACTOME_CITRIC_ACID_CYCLE_TCA_CYCLE	19	0.0000179	0.5685241	0.0005622
433	REACTOME_COMPLEMENT_CASCADE	10	0.0019901	-0.5646901	0.0275686
72	REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS	22	0.0000141	-0.5348194	0.0004760
170	REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION	13	0.0009052	0.5316493	0.0137534
345	REACTOME_N_GLYCAN_TRIMMING_IN_THE_ER_AND_CALNEXIN_CALRETICULIN_CYCLE	13	0.0014561	-0.5100085	0.0207826
5	REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE	38	0.0000001	0.5090744	0.0000024
168	REACTOME_PEPTIDE_CHAIN_ELONGATION	67	0.0000000	-0.5059419	0.0000000
341	REACTOME_CALNEXIN_CALRETICULIN_CYCLE	11	0.0042709	-0.4976554	0.0468306
189	REACTOME_G_PROTEIN_ACTIVATION	10	0.0143542	-0.4472102	0.1057812
136	REACTOME_TCR_SIGNALING	30	0.0000280	-0.4420948	0.0007380
173	REACTOME_METABOLISM_OF_POLYAMINES	13	0.0061455	0.4390026	0.0590724
445	REACTOME_ANTIGEN_PRESENTATION_FOLDING_ASSEMBLY_AND_PEPTIDE_LOADING_OF_CLASS_I_MHC	15	0.0043626	-0.4252481	0.0468306
320	REACTOME_EFFECTS_OF_PIP2_HYDROLYSIS	15	0.0057955	-0.4115975	0.0580779
57	REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE	89	0.0000000	-0.4099893	0.0000000

#mitch_report(res=res1,outfile="mitch_de1.html",overwrite=TRUE)

res2 <- mitch_calc(de2, genesets, priority="effect")

## Note: Enrichments with large effect sizes may not be
##             statistically significant.

head(res2$enrichment_result,20) %>% kbl(caption="DE2: Reactome") %>% kable_styling()

DE2: Reactome

	set	setSize	pANOVA	s.dist	p.adjustANOVA
164	REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION	13	0.0000514	-0.6486328	0.0086276
1	REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS	11	0.0021459	0.5345378	0.0320500
226	REACTOME_TRAFFICKING_OF_AMPA_RECEPTORS	16	0.0005999	0.4956504	0.0185156
174	REACTOME_MITOCHONDRIAL_TRNA_AMINOACYLATION	20	0.0001257	0.4954555	0.0102074
218	REACTOME_CITRIC_ACID_CYCLE_TCA_CYCLE	19	0.0041981	-0.3795465	0.0474079
227	REACTOME_NCAM1_INTERACTIONS	18	0.0056145	0.3772112	0.0560395
358	REACTOME_INTERFERON_GAMMA_SIGNALING	24	0.0013908	0.3771435	0.0279975
447	REACTOME_APC_CDC20_MEDIATED_DEGRADATION_OF_NEK2A	17	0.0130386	0.3479511	0.0948804
425	REACTOME_COMPLEMENT_CASCADE	11	0.0459373	0.3476648	0.2192679
185	REACTOME_TRNA_AMINOACYLATION	39	0.0001896	0.3457053	0.0110201
382	REACTOME_HORMONE_SENSITIVE_LIPASE_HSL_MEDIATED_TRIACYLGLYCEROL_HYDROLYSIS	11	0.0522975	-0.3380357	0.2266670
253	REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA	12	0.0428140	-0.3378088	0.2108815
415	REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_CYCLIN_B	16	0.0197938	0.3366208	0.1255417
131	REACTOME_REGULATION_OF_PYRUVATE_DEHYDROGENASE_PDH_COMPLEX	11	0.0545748	-0.3348261	0.2275022
243	REACTOME_ADP_SIGNALLING_THROUGH_P2RY1	12	0.0480875	-0.3296508	0.2265547
372	REACTOME_MEIOTIC_RECOMBINATION	11	0.0616156	0.3255622	0.2465504
277	REACTOME_SMOOTH_MUSCLE_CONTRACTION	19	0.0162433	-0.3186516	0.1122487
262	REACTOME_G_PROTEIN_BETA_GAMMA_SIGNALLING	13	0.0492115	-0.3151585	0.2266670
5	REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE	38	0.0009466	-0.3102044	0.0246514
269	REACTOME_BRANCHED_CHAIN_AMINO_ACID_CATABOLISM	16	0.0372862	-0.3008593	0.1918166

#mitch_report(res=res2,outfile="mitch_de2.html",overwrite=TRUE)

res3 <- mitch_calc(de3, genesets, priority="effect")

## Note: Enrichments with large effect sizes may not be
##             statistically significant.

head(res3$enrichment_result,20) %>% kbl(caption="DE3: Reactome") %>% kable_styling()

DE3: Reactome

	set	setSize	pANOVA	s.dist	p.adjustANOVA
1	REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS	11	0.0004191	0.6143424	0.0974310
408	REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING	12	0.0008287	0.5574333	0.1245268
427	REACTOME_COMPLEMENT_CASCADE	11	0.0040091	-0.5011450	0.1387213
384	REACTOME_HORMONE_SENSITIVE_LIPASE_HSL_MEDIATED_TRIACYLGLYCEROL_HYDROLYSIS	11	0.0044749	-0.4950767	0.1387213
191	REACTOME_INTEGRIN_ALPHAIIB_BETA3_SIGNALING	17	0.0026495	-0.4212165	0.1368906
376	REACTOME_PLATELET_AGGREGATION_PLUG_FORMATION	18	0.0022923	-0.4153275	0.1332426
386	REACTOME_SIGNAL_ATTENUATION	10	0.0240391	-0.4121944	0.3924953
23	REACTOME_SPRY_REGULATION_OF_FGF_SIGNALING	12	0.0155220	-0.4035723	0.3137852
221	REACTOME_CITRIC_ACID_CYCLE_TCA_CYCLE	19	0.0029488	0.3941398	0.1371198
204	REACTOME_GPVI_MEDIATED_ACTIVATION_CASCADE	16	0.0076820	-0.3850677	0.1880066
328	REACTOME_DCC_MEDIATED_ATTRACTIVE_SIGNALING	10	0.0365582	-0.3819079	0.4612707
175	REACTOME_GLUCONEOGENESIS	21	0.0032488	0.3711764	0.1373361
163	REACTOME_AMINO_ACID_TRANSPORT_ACROSS_THE_PLASMA_MEMBRANE	13	0.0269037	0.3545923	0.4035549
170	REACTOME_METABOLISM_OF_POLYAMINES	11	0.0463678	0.3469773	0.4762814
219	REACTOME_PURINE_RIBONUCLEOSIDE_MONOPHOSPHATE_BIOSYNTHESIS	11	0.0481016	0.3442676	0.4762814
391	REACTOME_LIPID_DIGESTION_MOBILIZATION_AND_TRANSPORT	22	0.0068432	-0.3332505	0.1806195
178	REACTOME_MITOCHONDRIAL_TRNA_AMINOACYLATION	20	0.0103770	0.3312165	0.2412655
426	REACTOME_GLUTATHIONE_CONJUGATION	12	0.0474432	0.3306042	0.4762814
267	REACTOME_CTLA4_INHIBITORY_SIGNALING	15	0.0317322	-0.3204256	0.4471357
277	REACTOME_DOUBLE_STRAND_BREAK_REPAIR	12	0.0674721	0.3049578	0.5273033

#mitch_report(res=res3,outfile="mitch_de3.html",overwrite=TRUE)

res4 <- mitch_calc(de4, genesets, priority="effect")

## Note: Enrichments with large effect sizes may not be
##             statistically significant.

head(res4$enrichment_result,20) %>% kbl(caption="DE4: Reactome") %>% kable_styling()

DE4: Reactome

	set	setSize	pANOVA	s.dist	p.adjustANOVA
408	REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING	12	0.0000000	-0.9599323	0.0000005
219	REACTOME_CITRIC_ACID_CYCLE_TCA_CYCLE	19	0.0000000	-0.9036350	0.0000000
330	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT	59	0.0000000	-0.8867475	0.0000000
402	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_	73	0.0000000	-0.8645092	0.0000000
24	REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT	107	0.0000000	-0.8290590	0.0000000
5	REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE	38	0.0000000	-0.7617993	0.0000000
165	REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION	13	0.0000031	-0.7473201	0.0001191
228	REACTOME_NCAM1_INTERACTIONS	16	0.0000019	0.6884585	0.0000865
133	REACTOME_REGULATION_OF_PYRUVATE_DEHYDROGENASE_PDH_COMPLEX	11	0.0001120	-0.6726888	0.0030627
62	REACTOME_MITOCHONDRIAL_PROTEIN_IMPORT	42	0.0000000	-0.6526067	0.0000000
289	REACTOME_PYRUVATE_METABOLISM	16	0.0000231	-0.6112639	0.0008255
74	REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION	36	0.0000000	0.6054937	0.0000000
92	REACTOME_COLLAGEN_FORMATION	31	0.0000000	0.5785675	0.0000013
427	REACTOME_COMPLEMENT_CASCADE	11	0.0026577	0.5233135	0.0386201
237	REACTOME_GLUCAGON_TYPE_LIGAND_RECEPTORS	10	0.0045825	-0.5178311	0.0575904
244	REACTOME_ADP_SIGNALLING_THROUGH_P2RY1	12	0.0023249	-0.5078056	0.0360359
269	REACTOME_BRANCHED_CHAIN_AMINO_ACID_CATABOLISM	16	0.0007886	-0.4848361	0.0166685
1	REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS	11	0.0076743	0.4643475	0.0915015
231	REACTOME_INHIBITION_OF_INSULIN_SECRETION_BY_ADRENALINE_NORADRENALINE	11	0.0081428	-0.4608687	0.0927141
285	REACTOME_THROMBOXANE_SIGNALLING_THROUGH_TP_RECEPTOR	11	0.0084179	-0.4589083	0.0931983

#mitch_report(res=res4,outfile="mitch_de4.html",overwrite=TRUE)

res5 <- mitch_calc(de5, genesets, priority="effect")

## Note: Enrichments with large effect sizes may not be
##             statistically significant.

head(res5$enrichment_result,20) %>% kbl(caption="DE5: Reactome") %>% kable_styling()

DE5: Reactome

	set	setSize	pANOVA	s.dist	p.adjustANOVA
170	REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION	13	0.0000002	0.8275900	0.0000093
416	REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING	12	0.0000008	0.8211374	0.0000305
224	REACTOME_CITRIC_ACID_CYCLE_TCA_CYCLE	19	0.0000000	0.8032594	0.0000001
343	REACTOME_AMINO_ACID_SYNTHESIS_AND_INTERCONVERSION_TRANSAMINATION	10	0.0000350	0.7556702	0.0009201
410	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_	73	0.0000000	0.7083478	0.0000000
137	REACTOME_REGULATION_OF_PYRUVATE_DEHYDROGENASE_PDH_COMPLEX	11	0.0000512	0.7052444	0.0012170
336	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT	59	0.0000000	0.7030013	0.0000000
24	REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT	107	0.0000000	0.6924928	0.0000000
5	REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE	38	0.0000000	0.6713672	0.0000000
295	REACTOME_PYRUVATE_METABOLISM	16	0.0000532	0.5835829	0.0012170
275	REACTOME_BRANCHED_CHAIN_AMINO_ACID_CATABOLISM	16	0.0007548	0.4865772	0.0123103
64	REACTOME_MITOCHONDRIAL_PROTEIN_IMPORT	42	0.0000001	0.4857991	0.0000025
168	REACTOME_PEPTIDE_CHAIN_ELONGATION	67	0.0000000	-0.4821899	0.0000000
435	REACTOME_COMPLEMENT_CASCADE	11	0.0057074	-0.4814148	0.0729616
65	REACTOME_SIGNALING_BY_HIPPO	15	0.0018195	-0.4651387	0.0277624
254	REACTOME_SEMA3A_PAK_DEPENDENT_AXON_REPULSION	10	0.0117628	-0.4601589	0.1203877
348	REACTOME_N_GLYCAN_TRIMMING_IN_THE_ER_AND_CALNEXIN_CALRETICULIN_CYCLE	13	0.0055367	-0.4444674	0.0727455
56	REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE	89	0.0000000	-0.4095501	0.0000000
276	REACTOME_RECEPTOR_LIGAND_BINDING_INITIATES_THE_SECOND_PROTEOLYTIC_CLEAVAGE_OF_NOTCH_RECEPTOR	11	0.0236673	-0.3940707	0.1811249
402	REACTOME_INFLUENZA_VIRAL_RNA_TRANSCRIPTION_AND_REPLICATION	83	0.0000000	-0.3887478	0.0000001

#mitch_report(res=res5,outfile="mitch_de5.html",overwrite=TRUE)

res6 <- mitch_calc(de6, genesets, priority="effect")

## Note: Enrichments with large effect sizes may not be
##             statistically significant.

head(res6$enrichment_result,20) %>% kbl(caption="DE6: Reactome") %>% kable_styling()

DE6: Reactome

	set	setSize	pANOVA	s.dist	p.adjustANOVA
1	REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS	11	0.0004162	0.6146648	0.0041441
20	REACTOME_CROSS_PRESENTATION_OF_SOLUBLE_EXOGENOUS_ANTIGENS_ENDOSOMES	40	0.0000002	0.4752447	0.0000176
421	REACTOME_SCF_BETA_TRCP_MEDIATED_DEGRADATION_OF_EMI1	42	0.0000002	0.4684085	0.0000176
124	REACTOME_CDK_MEDIATED_PHOSPHORYLATION_AND_REMOVAL_OF_CDC6	40	0.0000004	0.4653759	0.0000176
99	REACTOME_P53_INDEPENDENT_G1_S_DNA_DAMAGE_CHECKPOINT	42	0.0000003	0.4546684	0.0000176
280	REACTOME_AUTODEGRADATION_OF_THE_E3_UBIQUITIN_LIGASE_COP1	42	0.0000004	0.4533671	0.0000176
271	REACTOME_CDT1_ASSOCIATION_WITH_THE_CDC6_ORC_ORIGIN_COMPLEX	45	0.0000003	0.4426604	0.0000176
153	REACTOME_REGULATION_OF_ORNITHINE_DECARBOXYLASE_ODC	43	0.0000008	0.4347441	0.0000285
442	REACTOME_ANTIGEN_PRESENTATION_FOLDING_ASSEMBLY_AND_PEPTIDE_LOADING_OF_CLASS_I_MHC	14	0.0049096	0.4343329	0.0314751
30	REACTOME_ER_PHAGOSOME_PATHWAY	48	0.0000002	0.4333934	0.0000176
460	REACTOME_VIF_MEDIATED_DEGRADATION_OF_APOBEC3G	42	0.0000013	0.4324189	0.0000348
462	REACTOME_SYNTHESIS_OF_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI	13	0.0069714	-0.4323334	0.0397882
437	REACTOME_VOLTAGE_GATED_POTASSIUM_CHANNELS	10	0.0234067	-0.4140667	0.0995228
335	REACTOME_ASSEMBLY_OF_THE_PRE_REPLICATIVE_COMPLEX	48	0.0000009	0.4097903	0.0000288
66	REACTOME_SIGNALING_BY_NOTCH4	11	0.0188932	-0.4089057	0.0834150
46	REACTOME_ORC1_REMOVAL_FROM_CHROMATIN	49	0.0000010	0.4044499	0.0000290
80	REACTOME_SIGNALING_BY_NOTCH3	11	0.0208317	-0.4025306	0.0902708
456	REACTOME_SCFSKP2_MEDIATED_DEGRADATION_OF_P27_P21	43	0.0000053	0.4014143	0.0001252
26	REACTOME_ANTIGEN_PROCESSING_CROSS_PRESENTATION	56	0.0000003	0.3983522	0.0000176
178	REACTOME_CYTOSOLIC_TRNA_AMINOACYLATION	22	0.0013545	0.3948177	0.0115252

#mitch_report(res=res6,outfile="mitch_de6.html",overwrite=TRUE)

res7 <- mitch_calc(de7, genesets, priority="effect")

## Note: Enrichments with large effect sizes may not be
##             statistically significant.

head(res7$enrichment_result,20) %>% kbl(caption="DE7: Reactome") %>% kable_styling()

DE7: Reactome

	set	setSize	pANOVA	s.dist	p.adjustANOVA
225	REACTOME_CITRIC_ACID_CYCLE_TCA_CYCLE	19	0.0000000	-0.7853233	0.0000001
168	REACTOME_PEPTIDE_CHAIN_ELONGATION	67	0.0000000	0.7065104	0.0000000
337	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT	59	0.0000000	-0.6913717	0.0000000
416	REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING	12	0.0000400	-0.6848377	0.0008591
170	REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION	13	0.0000258	-0.6739610	0.0005818
9	REACTOME_FORMATION_OF_THE_TERNARY_COMPLEX_AND_SUBSEQUENTLY_THE_43S_COMPLEX	42	0.0000000	0.6728207	0.0000000
221	REACTOME_3_UTR_MEDIATED_TRANSLATIONAL_REGULATION	86	0.0000000	0.6540954	0.0000000
144	REACTOME_ACTIVATION_OF_THE_MRNA_UPON_BINDING_OF_THE_CAP_BINDING_COMPLEX_AND_EIFS_AND_SUBSEQUENT_BINDING_TO_43S	49	0.0000000	0.6496979	0.0000000
410	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_	73	0.0000000	-0.6471521	0.0000000
57	REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE	89	0.0000000	0.5946497	0.0000000
25	REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT	107	0.0000000	-0.5882675	0.0000000
2	REACTOME_TRANSLATION	124	0.0000000	0.5695214	0.0000000
402	REACTOME_INFLUENZA_VIRAL_RNA_TRANSCRIPTION_AND_REPLICATION	83	0.0000000	0.5659880	0.0000000
138	REACTOME_REGULATION_OF_PYRUVATE_DEHYDROGENASE_PDH_COMPLEX	11	0.0020183	-0.5377138	0.0353577
449	REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX	85	0.0000000	0.5272457	0.0000000
1	REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS	11	0.0030134	0.5166232	0.0491495
5	REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE	38	0.0000001	-0.4962705	0.0000030
401	REACTOME_INFLUENZA_LIFE_CYCLE	115	0.0000000	0.4340295	0.0000000
296	REACTOME_PYRUVATE_METABOLISM	16	0.0133511	-0.3574166	0.1477763
173	REACTOME_METABOLISM_OF_POLYAMINES	12	0.0328482	0.3558821	0.2589532

#mitch_report(res=res7,outfile="mitch_de7.html",overwrite=TRUE)

res8 <- mitch_calc(de8, genesets, priority="effect")

## Note: Enrichments with large effect sizes may not be
##             statistically significant.

head(res8$enrichment_result,20) %>% kbl(caption="DE8: Reactome") %>% kable_styling()

DE8: Reactome

	set	setSize	pANOVA	s.dist	p.adjustANOVA
64	REACTOME_SIGNALING_BY_HIPPO	15	0.0000169	-0.6416532	0.0078218
233	REACTOME_ACTIVATION_OF_CHAPERONES_BY_ATF6_ALPHA	11	0.0054765	0.4837666	0.4793826
277	REACTOME_METAL_ION_SLC_TRANSPORTERS	12	0.0259737	0.3713412	0.4995849
93	REACTOME_COLLAGEN_FORMATION	26	0.0015372	0.3591101	0.3558723
255	REACTOME_TRANSPORT_OF_GLUCOSE_AND_OTHER_SUGARS_BILE_SALTS_AND_ORGANIC_ACIDS_METAL_IONS_AND_AMINE_COMPOUNDS	24	0.0038391	0.3411284	0.4793826
423	REACTOME_PHOSPHORYLATION_OF_THE_APC_C	14	0.0273428	-0.3407423	0.4995849
218	REACTOME_PURINE_RIBONUCLEOSIDE_MONOPHOSPHATE_BIOSYNTHESIS	11	0.0515818	0.3390730	0.5775364
4	REACTOME_INHIBITION_OF_THE_PROTEOLYTIC_ACTIVITY_OF_APC_C_REQUIRED_FOR_THE_ONSET_OF_ANAPHASE_BY_MITOTIC_SPINDLE_CHECKPOINT_COMPONENTS	15	0.0238262	-0.3371605	0.4995849
123	REACTOME_A_TETRASACCHARIDE_LINKER_SEQUENCE_IS_REQUIRED_FOR_GAG_SYNTHESIS	14	0.0290266	0.3371200	0.4995849
228	REACTOME_TRAFFICKING_OF_AMPA_RECEPTORS	16	0.0259303	-0.3217543	0.4995849
350	REACTOME_TRAF6_MEDIATED_NFKB_ACTIVATION	13	0.0469457	0.3183731	0.5775364
98	REACTOME_SIGNALLING_TO_P38_VIA_RIT_AND_RIN	11	0.0702240	-0.3153627	0.6708612
208	REACTOME_STRIATED_MUSCLE_CONTRACTION	22	0.0108856	0.3137934	0.4793826
173	REACTOME_GLUCONEOGENESIS	19	0.0188733	-0.3113178	0.4793826
139	REACTOME_SHC1_EVENTS_IN_EGFR_SIGNALING	14	0.0523899	-0.2995715	0.5775364
258	REACTOME_CELL_CELL_JUNCTION_ORGANIZATION	15	0.0493541	-0.2932484	0.5775364
18	REACTOME_INSULIN_RECEPTOR_RECYCLING	15	0.0506621	0.2915794	0.5775364
39	REACTOME_BOTULINUM_NEUROTOXICITY	10	0.1171524	0.2862381	0.7187855
42	REACTOME_PROTEOLYTIC_CLEAVAGE_OF_SNARE_COMPLEX_PROTEINS	10	0.1171524	0.2862381	0.7187855
114	REACTOME_CHONDROITIN_SULFATE_DERMATAN_SULFATE_METABOLISM	22	0.0205036	0.2855390	0.4793826

#mitch_report(res=res8,outfile="mitch_de8.html",overwrite=TRUE)

Bidimensional

B1 (DE1 and DE2): effect of ATP-CL KD in Sed and Ex animals

b1 <- merge(de1,de2,by=0)
rownames(b1) <- b1$Row.names
b1$Row.names=NULL
colnames(b1) <- c("Sed","Ex")
resb1 <- mitch_calc(b1, genesets, priority="effect")

## Note: Enrichments with large effect sizes may not be 
##             statistically significant.

head(resb1$enrichment_result,20) %>% kbl(caption="effect of ATP-CL KD in Sed and Ex animals") %>% kable_styling()

effect of ATP-CL KD in Sed and Ex animals

	set	setSize	pMANOVA	s.Sed	s.Ex	p.Sed	p.Ex	s.dist	SD	p.adjustMANOVA
163	REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION	13	0.0000019	0.5209219	-0.6501227	0.0011485	0.0000494	0.8330781	0.8280536	0.0000679
400	REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING	12	0.0000059	0.8178852	-0.0399813	0.0000009	0.8105628	0.8188618	0.6066032	0.0001795
217	REACTOME_CITRIC_ACID_CYCLE_TCA_CYCLE	19	0.0000031	0.5583710	-0.3820019	0.0000252	0.0039598	0.6765380	0.6649441	0.0001006
130	REACTOME_REGULATION_OF_PYRUVATE_DEHYDROGENASE_PDH_COMPLEX	11	0.0007021	0.5814269	-0.3366497	0.0008420	0.0532744	0.6718558	0.6491782	0.0072921
419	REACTOME_COMPLEMENT_CASCADE	10	0.0016485	-0.5817474	0.3151817	0.0014471	0.0844745	0.6616415	0.6342246	0.0136979
283	REACTOME_PYRUVATE_METABOLISM	16	0.0000469	0.6021830	-0.2478630	0.0000305	0.0862233	0.6511992	0.6010733	0.0011271
394	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_	73	0.0000000	0.6411063	-0.0373644	0.0000000	0.5818475	0.6421942	0.4797512	0.0000000
324	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT	59	0.0000000	0.6346839	-0.0454010	0.0000000	0.5471620	0.6363057	0.4808927	0.0000000
23	REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT	107	0.0000000	0.5905743	-0.1269286	0.0000000	0.0237630	0.6040604	0.5073512	0.0000000
335	REACTOME_N_GLYCAN_TRIMMING_IN_THE_ER_AND_CALNEXIN_CALRETICULIN_CYCLE	13	0.0012034	-0.5297416	0.2691600	0.0009449	0.0930304	0.5941998	0.5649088	0.0107835
161	REACTOME_PEPTIDE_CHAIN_ELONGATION	66	0.0000000	-0.5283662	0.2603400	0.0000000	0.0002612	0.5890228	0.5576995	0.0000000
5	REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE	38	0.0000000	0.4982932	-0.3123245	0.0000001	0.0008734	0.5880839	0.5731932	0.0000002
182	REACTOME_G_PROTEIN_ACTIVATION	10	0.0090150	-0.4700043	-0.2916955	0.0100809	0.1103296	0.5531639	0.1260834	0.0457764
1	REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS	11	0.0061646	0.1363489	0.5344534	0.4337995	0.0021496	0.5515718	0.2815024	0.0352153
250	REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA	11	0.0066609	-0.3387929	-0.4250125	0.0517754	0.0146823	0.5435221	0.0609665	0.0375806
331	REACTOME_CALNEXIN_CALRETICULIN_CYCLE	11	0.0088612	-0.5165410	0.1559916	0.0030185	0.3705361	0.5395813	0.4755524	0.0455006
166	REACTOME_METABOLISM_OF_POLYAMINES	12	0.0046489	0.4604333	0.2809864	0.0057624	0.0920413	0.5393999	0.1268882	0.0291034
376	REACTOME_HORMONE_SENSITIVE_LIPASE_HSL_MEDIATED_TRIACYLGLYCEROL_HYDROLYSIS	11	0.0074193	-0.4171279	-0.3391665	0.0166276	0.0515177	0.5376147	0.0551270	0.0401151
241	REACTOME_ADP_SIGNALLING_THROUGH_P2RY1	11	0.0074861	-0.3392058	-0.4164594	0.0514907	0.0168025	0.5371211	0.0546265	0.0401151
226	REACTOME_NCAM1_INTERACTIONS	15	0.0020274	-0.1969418	0.4925024	0.1868553	0.0009612	0.5304194	0.4875107	0.0159746

#mitch_report(res=resb1,outfile="mitch_b1.html",overwrite=TRUE)

B2 (DE3 and DE4): effect of ACSS2 KD in Sed and Ex animals

b2 <- merge(de3,de4,by=0)
rownames(b2) <- b2$Row.names
b2$Row.names=NULL
colnames(b2) <- c("Sed","Ex")
resb2 <- mitch_calc(b2, genesets, priority="effect")

## Note: Enrichments with large effect sizes may not be 
##             statistically significant.

head(resb2$enrichment_result,20) %>% kbl(caption="effect of ACSS2 KD in Sed and Ex animals") %>% kable_styling()

effect of ACSS2 KD in Sed and Ex animals

	set	setSize	pMANOVA	s.Sed	s.Ex	p.Sed	p.Ex	s.dist	SD	p.adjustMANOVA
398	REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING	12	0.0000000	0.5550517	-0.9589161	0.0008726	0.0000000	1.1079722	1.0705369	0.0000000
215	REACTOME_CITRIC_ACID_CYCLE_TCA_CYCLE	19	0.0000000	0.3914880	-0.9017812	0.0031480	0.0000000	0.9830932	0.9144795	0.0000000
323	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT	59	0.0000000	0.1183797	-0.8850175	0.1164725	0.0000000	0.8928997	0.7095090	0.0000000
392	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_	73	0.0000000	0.1890429	-0.8628811	0.0053260	0.0000000	0.8833465	0.7438226	0.0000000
23	REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT	107	0.0000000	0.2030618	-0.8273468	0.0002973	0.0000000	0.8519019	0.7286089	0.0000000
162	REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION	13	0.0000027	0.2927549	-0.7453158	0.0677188	0.0000033	0.8007503	0.7340268	0.0001239
5	REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE	38	0.0000000	0.2495992	-0.7596399	0.0078231	0.0000000	0.7995952	0.7136398	0.0000000
1	REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS	11	0.0000758	0.6132018	0.4676559	0.0004296	0.0072524	0.7711800	0.1029165	0.0021549
417	REACTOME_COMPLEMENT_CASCADE	11	0.0001125	-0.5050604	0.5262557	0.0037331	0.0025141	0.7294046	0.7292506	0.0030106
224	REACTOME_NCAM1_INTERACTIONS	16	0.0000052	-0.1497595	0.6903968	0.2999470	0.0000017	0.7064529	0.5940802	0.0002170
130	REACTOME_REGULATION_OF_PYRUVATE_DEHYDROGENASE_PDH_COMPLEX	11	0.0004184	0.1275786	-0.6700138	0.4639523	0.0001193	0.6820519	0.5639830	0.0086537
60	REACTOME_MITOCHONDRIAL_PROTEIN_IMPORT	42	0.0000000	0.1266848	-0.6496591	0.1559994	0.0000000	0.6618958	0.5489581	0.0000000
72	REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION	32	0.0000000	-0.2449765	0.6053302	0.0165695	0.0000000	0.6530223	0.6012576	0.0000000
283	REACTOME_PYRUVATE_METABOLISM	16	0.0000686	0.1491583	-0.6089036	0.3018915	0.0000248	0.6269065	0.5360307	0.0020808
89	REACTOME_COLLAGEN_FORMATION	27	0.0000002	-0.2117520	0.5739748	0.0570553	0.0000002	0.6117891	0.5555927	0.0000094
169	REACTOME_GLUCONEOGENESIS	18	0.0000336	0.5606215	-0.2402629	0.0000384	0.0777760	0.6099367	0.5663108	0.0011765
239	REACTOME_ADP_SIGNALLING_THROUGH_P2RY1	11	0.0075441	-0.1644270	-0.5245275	0.3452268	0.0025978	0.5496956	0.2546295	0.0837210
280	REACTOME_THROMBOXANE_SIGNALLING_THROUGH_TP_RECEPTOR	10	0.0160853	-0.2453572	-0.4724274	0.1792635	0.0097013	0.5323418	0.1605628	0.1591042
248	REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA	11	0.0175081	-0.1738228	-0.4697218	0.3183631	0.0069990	0.5008522	0.2092322	0.1680227
264	REACTOME_BRANCHED_CHAIN_AMINO_ACID_CATABOLISM	16	0.0038352	-0.0411565	-0.4812117	0.7757563	0.0008636	0.4829685	0.3111660	0.0545318

#mitch_report(res=resb2,outfile="mitch_b2.html",overwrite=TRUE)

B3 (DE5 and DE6): Effect of Sed vs Ex in ctrl and ATP-CL gene KD

b3 <- merge(de5,de6,by=0)
rownames(b3) <- b3$Row.names
b3$Row.names=NULL
colnames(b3) <- c("ctrl","AcyKD")
resb3 <- mitch_calc(b3, genesets, priority="effect")

## Note: Enrichments with large effect sizes may not be 
##             statistically significant.

head(resb3$enrichment_result,20) %>% kbl(caption="effect of  Sed vs Ex in ctrl and ATP-CL gene KD") %>% kable_styling()

effect of Sed vs Ex in ctrl and ATP-CL gene KD

	set	setSize	pMANOVA	s.ctrl	s.AcyKD	p.ctrl	p.AcyKD	s.dist	SD	p.adjustMANOVA
167	REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION	13	0.0000016	0.8240523	0.1889110	0.0000003	0.2384755	0.8454286	0.4491127	0.0000307
221	REACTOME_CITRIC_ACID_CYCLE_TCA_CYCLE	19	0.0000000	0.7991404	0.2165893	0.0000000	0.1023779	0.8279712	0.4119258	0.0000004
411	REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING	12	0.0000061	0.8170846	0.1237570	0.0000009	0.4581043	0.8264037	0.4902566	0.0000749
340	REACTOME_AMINO_ACID_SYNTHESIS_AND_INTERCONVERSION_TRANSAMINATION	10	0.0001845	0.7509617	0.2101578	0.0000392	0.2500014	0.7798140	0.3824062	0.0015147
134	REACTOME_REGULATION_OF_PYRUVATE_DEHYDROGENASE_PDH_COMPLEX	11	0.0001617	0.7002446	0.3013372	0.0000578	0.0836431	0.7623297	0.2820702	0.0013510
405	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_	73	0.0000000	0.7030359	0.1053994	0.0000000	0.1203030	0.7108927	0.4225928	0.0000000
24	REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT	107	0.0000000	0.6872767	0.1548226	0.0000000	0.0058156	0.7044993	0.3765019	0.0000000
5	REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE	38	0.0000000	0.6661894	0.2285532	0.0000000	0.0148782	0.7043045	0.3094555	0.0000000
333	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT	59	0.0000000	0.6974047	0.0779624	0.0000000	0.3012275	0.7017488	0.4380118	0.0000000
292	REACTOME_PYRUVATE_METABOLISM	16	0.0002043	0.5774086	0.2306580	0.0000638	0.1103640	0.6217747	0.2451897	0.0016483
1	REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS	11	0.0019170	0.0539678	0.6147883	0.7567161	0.0004151	0.6171525	0.3965600	0.0118046
430	REACTOME_COMPLEMENT_CASCADE	11	0.0009718	-0.4946111	0.3398898	0.0045132	0.0510219	0.6001376	0.5900812	0.0064059
251	REACTOME_SEMA3A_PAK_DEPENDENT_AXON_REPULSION	10	0.0097009	-0.4722715	-0.3618327	0.0097250	0.0476236	0.5949481	0.0780920	0.0460877
165	REACTOME_PEPTIDE_CHAIN_ELONGATION	67	0.0000000	-0.4955217	0.1893447	0.0000000	0.0074762	0.5304651	0.4842737	0.0000000
178	REACTOME_CYTOSOLIC_TRNA_AMINOACYLATION	22	0.0005542	0.3239165	0.3953099	0.0085758	0.0013359	0.5110693	0.0504828	0.0039299
66	REACTOME_SIGNALING_BY_NOTCH4	11	0.0240770	-0.3020642	-0.4087225	0.0828998	0.0189471	0.5082291	0.0754188	0.0908711
462	REACTOME_SYNTHESIS_OF_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI	13	0.0129223	-0.2542844	-0.4321944	0.1125615	0.0069899	0.5014505	0.1258014	0.0590793
72	REACTOME_SIGNALING_BY_NOTCH2	11	0.0280676	-0.3397326	-0.3661613	0.0511293	0.0355397	0.4994921	0.0186880	0.1017860
63	REACTOME_MITOCHONDRIAL_PROTEIN_IMPORT	42	0.0000005	0.4784212	0.1320755	0.0000001	0.1391225	0.4963172	0.2449034	0.0000119
230	REACTOME_NCAM1_INTERACTIONS	15	0.0016087	-0.3122572	0.3821602	0.0363533	0.0104179	0.4935089	0.4910273	0.0100381

#mitch_report(res=resb3,outfile="mitch_b3.html",overwrite=TRUE)

B4 (DE7 and DE8): Effect of Sed vs Ex in ctrl and ACSS2 gene KD

b4 <- merge(de7,de8,by=0)
rownames(b4) <- b4$Row.names
b4$Row.names=NULL
colnames(b4) <- c("ctrl","Acss2KD")
resb4 <- mitch_calc(b4, genesets, priority="effect")

## Note: Enrichments with large effect sizes may not be 
##             statistically significant.

head(resb4$enrichment_result,20) %>% kbl(caption="effect of  Sed vs Ex in ctrl and Acss2 gene KD") %>% kable_styling()

effect of Sed vs Ex in ctrl and Acss2 gene KD

	set	setSize	pMANOVA	s.ctrl	s.Acss2KD	p.ctrl	p.Acss2KD	s.dist	SD	p.adjustMANOVA
219	REACTOME_CITRIC_ACID_CYCLE_TCA_CYCLE	19	0.0000000	-0.7842552	0.1551710	0.0000000	0.2419236	0.7994587	0.6642746	0.0000001
163	REACTOME_PEPTIDE_CHAIN_ELONGATION	66	0.0000000	0.7147108	-0.1963968	0.0000000	0.0058903	0.7412039	0.6442503	0.0000000
165	REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION	13	0.0000130	-0.6735533	0.2609233	0.0000261	0.1034798	0.7223261	0.6607748	0.0002868
9	REACTOME_FORMATION_OF_THE_TERNARY_COMPLEX_AND_SUBSEQUENTLY_THE_43S_COMPLEX	41	0.0000000	0.6860474	-0.2169392	0.0000000	0.0163653	0.7195301	0.6385079	0.0000000
329	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT	59	0.0000000	-0.6906437	0.0418972	0.0000000	0.5785193	0.6919134	0.5179847	0.0000000
405	REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING	12	0.0002224	-0.6835234	-0.0686583	0.0000414	0.6806122	0.6869631	0.4347753	0.0044673
139	REACTOME_ACTIVATION_OF_THE_MRNA_UPON_BINDING_OF_THE_CAP_BINDING_COMPLEX_AND_EIFS_AND_SUBSEQUENT_BINDING_TO_43S	48	0.0000000	0.6604455	-0.1721880	0.0000000	0.0393196	0.6825225	0.5887608	0.0000000
215	REACTOME_3_UTR_MEDIATED_TRANSLATIONAL_REGULATION	85	0.0000000	0.6596880	-0.1641815	0.0000000	0.0090600	0.6798116	0.5825637	0.0000000
63	REACTOME_SIGNALING_BY_HIPPO	15	0.0000857	-0.1466348	-0.6422807	0.3257316	0.0000166	0.6588067	0.3504746	0.0017998
399	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_	73	0.0000000	-0.6464333	0.0253568	0.0000000	0.7086209	0.6469305	0.4750274	0.0000000
54	REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE	88	0.0000000	0.5993649	-0.1659883	0.0000000	0.0072694	0.6219248	0.5411864	0.0000000
133	REACTOME_REGULATION_OF_PYRUVATE_DEHYDROGENASE_PDH_COMPLEX	11	0.0015127	-0.5370608	0.2522663	0.0020443	0.1475666	0.5933571	0.5581386	0.0249598
391	REACTOME_INFLUENZA_VIRAL_RNA_TRANSCRIPTION_AND_REPLICATION	82	0.0000000	0.5707010	-0.1591293	0.0000000	0.0129625	0.5924709	0.5160680	0.0000000
25	REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT	107	0.0000000	-0.5877448	0.0620187	0.0000000	0.2693437	0.5910078	0.4594522	0.0000000
2	REACTOME_TRANSLATION	123	0.0000000	0.5725199	-0.1230356	0.0000000	0.0188924	0.5855910	0.4918320	0.0000000
1	REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS	11	0.0042505	0.5156321	-0.1865977	0.0030703	0.2840929	0.5483568	0.4965514	0.0577569
438	REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX	84	0.0000000	0.5314832	-0.1284862	0.0000000	0.0423270	0.5467934	0.4666688	0.0000000
5	REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE	38	0.0000001	-0.4957827	0.1281931	0.0000001	0.1720059	0.5120878	0.4412175	0.0000024
232	REACTOME_ACTIVATION_OF_CHAPERONES_BY_ATF6_ALPHA	11	0.0192582	-0.0157012	0.4831039	0.9281834	0.0055411	0.4833590	0.3527085	0.1842350
390	REACTOME_INFLUENZA_LIFE_CYCLE	113	0.0000000	0.4395433	-0.0626847	0.0000000	0.2514080	0.4439906	0.3551288	0.0000000

#mitch_report(res=resb4,outfile="mitch_b4.html",overwrite=TRUE)

Multi-dimensional

colnames(de1rn) <- c("gene","de1")
colnames(de2rn) <- c("gene","de2")
colnames(de3rn) <- c("gene","de3")
colnames(de4rn) <- c("gene","de4")
colnames(de5rn) <- c("gene","de5")
colnames(de6rn) <- c("gene","de6")
colnames(de7rn) <- c("gene","de7")
colnames(de8rn) <- c("gene","de8")

ll <- list("de1"=de1rn,"de2"=de2rn,"de3"=de3rn,"de4"=de4rn,"de5"=de5rn,"de6"=de6rn,"de7"=de7rn,"de8"=de8rn)
jj <- join_all(ll)

## Joining by: gene
## Joining by: gene
## Joining by: gene
## Joining by: gene
## Joining by: gene
## Joining by: gene
## Joining by: gene

head(jj)

##            gene        de1        de2         de3        de4         de5
## 1 0610009B22Rik  1.6344600  1.1168615 -0.68382677 -0.5935749 -0.08990061
## 2 0610009L18Rik  1.0145872  0.2160756  0.56527326  0.2161104 -0.33354482
## 3 0610010K14Rik  0.1633529  0.6692320  0.66424429 -0.1134635 -1.90686802
## 4 0610012G03Rik  0.5937955  0.4088542 -0.18505314 -0.3269221  0.01318114
## 5 0610030E20Rik -0.7027218  0.2111877 -0.38884282 -0.0645616 -0.84194359
## 6 0610040J01Rik -0.0895336 -1.4975473  0.04555983 -1.2938364  0.62289268
##          de6        de7        de8
## 1  0.3047981 -0.5488684 -0.3845554
## 2 -0.2679990  0.7010761  0.7909020
## 3 -0.7218075 -0.2062781  0.5031172
## 4 -0.1786497 -1.0685616 -0.5693632
## 5 -0.4541127  1.0067021  1.1957467
## 6 -1.3376144 -0.6151338 -1.1105356

rownames(jj) <- jj$gene
jj$gene=NULL
dim(jj)

## [1] 9724    8

resm <- mitch_calc(jj, genesets, priority="effect")

## Note: Enrichments with large effect sizes may not be 
##             statistically significant.

head(resm$enrichment_result,20) %>% kbl(caption="Multimitch") %>% kable_styling()

Multimitch

	set	setSize	pMANOVA	s.de1	s.de2	s.de3	s.de4	s.de5	s.de6	s.de7	s.de8	p.de1	p.de2	p.de3	p.de4	p.de5	p.de6	p.de7	p.de8	s.dist	SD	p.adjustMANOVA
414	REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING	12	0.0000000	0.8226249	-0.0380652	0.5301830	-0.9134113	0.8064967	0.1207172	-0.6644794	-0.0660742	0.0000012	0.8010703	0.0009498	0.0000000	0.0000013	0.4729125	0.0000390	0.6519432	1.7042545	0.6391718	0.0000000
224	REACTOME_CITRIC_ACID_CYCLE_TCA_CYCLE	19	0.0000000	0.5685241	-0.3636954	0.3745084	-0.8595655	0.7890440	0.2094241	-0.7617879	0.1456713	0.0000330	0.0037201	0.0034492	0.0000000	0.0000000	0.1082477	0.0000000	0.2600267	1.6132554	0.6096005	0.0000000
170	REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION	13	0.0000000	0.5316493	-0.6189671	0.2805325	-0.7102337	0.8126295	0.1829372	-0.6540764	0.2456248	0.0013684	0.0000456	0.0712164	0.0000036	0.0000004	0.2480171	0.0000251	0.1110286	1.5591285	0.5892207	0.0000000
334	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT	59	0.0000000	0.6429788	-0.0432253	0.1145213	-0.8434162	0.6915688	0.0772004	-0.6709942	0.0386399	0.0000000	0.5290469	0.1276910	0.0000000	0.0000000	0.3268435	0.0000000	0.6349252	1.4407324	0.5445448	0.0000000
408	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_	73	0.0000000	0.6487780	-0.0355738	0.1817873	-0.8222784	0.6966603	0.1032874	-0.6281428	0.0229931	0.0000000	0.5612041	0.0062555	0.0000000	0.0000000	0.1351791	0.0000000	0.7771681	1.4221331	0.5370495	0.0000000
24	REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT	107	0.0000000	0.5992902	-0.1208458	0.1951994	-0.7884863	0.6811166	0.1504467	-0.5711051	0.0576573	0.0000000	0.0214046	0.0003776	0.0000000	0.0000000	0.0071734	0.0000000	0.3189384	1.3600020	0.5133142	0.0000000
137	REACTOME_REGULATION_OF_PYRUVATE_DEHYDROGENASE_PDH_COMPLEX	11	0.0000001	0.5898468	-0.3205166	0.1235805	-0.6388054	0.6932387	0.2899464	-0.5221029	0.2377477	0.0010226	0.0515176	0.4751926	0.0001277	0.0000728	0.0875292	0.0019662	0.1561729	1.3295709	0.4988723	0.0000011
5	REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE	38	0.0000000	0.5090744	-0.2973570	0.2396040	-0.7241774	0.6601098	0.2207848	-0.4817981	0.1202226	0.0000002	0.0007932	0.0087174	0.0000000	0.0000000	0.0165534	0.0000001	0.1923742	1.2886018	0.4859309	0.0000000
1	REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS	11	0.0000076	0.1540672	0.5088410	0.5853485	0.4445467	0.0684384	0.5878020	0.4995269	-0.1771127	0.4566851	0.0021967	0.0004705	0.0068736	0.7744501	0.0004531	0.0031946	0.2678669	1.2058198	0.2833260	0.0000627
433	REACTOME_COMPLEMENT_CASCADE	10	0.0001287	-0.5646901	0.3000773	-0.5422132	0.5260309	-0.5173466	0.2660420	0.1198722	-0.0241316	0.0010227	0.0859453	0.0016642	0.0023194	0.0025614	0.1358126	0.5030795	0.8663499	1.1545573	0.4324682	0.0009051
293	REACTOME_PYRUVATE_METABOLISM	16	0.0000000	0.6106047	-0.2359848	0.1440549	-0.5804585	0.5743908	0.2226696	-0.3473480	0.1991075	0.0000402	0.0832486	0.3126503	0.0000273	0.0000819	0.1162995	0.0129408	0.1538405	1.1515259	0.4281080	0.0000003
168	REACTOME_PEPTIDE_CHAIN_ELONGATION	67	0.0000000	-0.5059419	0.2478638	-0.1256702	-0.2491166	-0.4694293	0.1831149	0.6835364	-0.1865753	0.0000000	0.0002841	0.0820185	0.0005295	0.0000000	0.0087330	0.0000000	0.0044011	1.0729366	0.4015878	0.0000000
233	REACTOME_NCAM1_INTERACTIONS	15	0.0000005	-0.1745803	0.4689004	-0.1159766	0.6893109	-0.2904063	0.3661420	-0.1548812	0.3162299	0.1717237	0.0009889	0.3946320	0.0000011	0.0329750	0.0113455	0.2813714	0.0268508	1.0398708	0.3642557	0.0000056
65	REACTOME_MITOCHONDRIAL_PROTEIN_IMPORT	42	0.0000000	0.3391173	-0.1669244	0.1224814	-0.6196990	0.4789327	0.1286660	-0.3150371	0.0001919	0.0003762	0.0466952	0.1675889	0.0000000	0.0000001	0.1515472	0.0002628	0.9556477	0.9418454	0.3559580	0.0000000
9	REACTOME_FORMATION_OF_THE_TERNARY_COMPLEX_AND_SUBSEQUENTLY_THE_43S_COMPLEX	42	0.0000000	-0.4074965	0.1878295	0.0464286	-0.1734376	-0.3314050	0.2703585	0.6507831	-0.2058779	0.0000010	0.0304066	0.4454578	0.0780649	0.0000368	0.0017993	0.0000000	0.0133658	0.9393598	0.3550099	0.0000000
57	REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE	89	0.0000000	-0.4099893	0.2364230	-0.0969018	-0.2052520	-0.3982051	0.1792394	0.5751212	-0.1578175	0.0000000	0.0000656	0.1175607	0.0010173	0.0000000	0.0031705	0.0000000	0.0052471	0.9065706	0.3406407	0.0000000
400	REACTOME_INFLUENZA_VIRAL_RNA_TRANSCRIPTION_AND_REPLICATION	83	0.0000000	-0.4074241	0.1771024	-0.0708412	-0.2846171	-0.3776863	0.1724075	0.5473307	-0.1513529	0.0000000	0.0039915	0.2858293	0.0000074	0.0000000	0.0061980	0.0000000	0.0096465	0.8821762	0.3292250	0.0000000
220	REACTOME_3_UTR_MEDIATED_TRANSLATIONAL_REGULATION	86	0.0000000	-0.3610068	0.1744426	-0.0361430	-0.2256968	-0.2951896	0.2157669	0.6327667	-0.1561313	0.0000000	0.0039009	0.6120158	0.0003562	0.0000002	0.0004328	0.0000000	0.0066195	0.8783304	0.3319072	0.0000000
274	REACTOME_BRANCHED_CHAIN_AMINO_ACID_CATABOLISM	16	0.0021428	0.3268696	-0.2879823	-0.0370986	-0.4594014	0.4797106	-0.0355406	-0.2599670	-0.1938536	0.0347238	0.0347837	0.7594738	0.0009198	0.0010908	0.7578121	0.0625990	0.1445943	0.8595062	0.3188056	0.0110907
143	REACTOME_ACTIVATION_OF_THE_MRNA_UPON_BINDING_OF_THE_CAP_BINDING_COMPLEX_AND_EIFS_AND_SUBSEQUENT_BINDING_TO_43S	49	0.0000000	-0.3022370	0.1603938	0.0532640	-0.1584119	-0.2413958	0.2790070	0.6284358	-0.1635790	0.0000694	0.0459466	0.3851424	0.0808024	0.0009226	0.0005039	0.0000000	0.0324625	0.8383384	0.3150176	0.0000000

#mitch_report(res=resm,outfile="mitch_m.html",overwrite=TRUE)

Session information

sessionInfo()

## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.1 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] beeswarm_0.4.0              vioplot_0.3.7              
##  [3] sm_2.2-5.7                  kableExtra_1.3.4           
##  [5] topconfects_1.12.0          limma_3.52.1               
##  [7] eulerr_6.1.1                mitch_1.8.0                
##  [9] MASS_7.3-58                 fgsea_1.22.0               
## [11] gplots_3.1.3                DESeq2_1.36.0              
## [13] SummarizedExperiment_1.26.1 Biobase_2.56.0             
## [15] MatrixGenerics_1.8.0        matrixStats_0.62.0         
## [17] GenomicRanges_1.48.0        GenomeInfoDb_1.32.2        
## [19] IRanges_2.30.0              S4Vectors_0.34.0           
## [21] BiocGenerics_0.42.0         reshape2_1.4.4             
## [23] forcats_0.5.1               stringr_1.4.0              
## [25] dplyr_1.0.9                 purrr_0.3.4                
## [27] readr_2.1.2                 tidyr_1.2.0                
## [29] tibble_3.1.7                ggplot2_3.3.6              
## [31] tidyverse_1.3.1             zoo_1.8-10                 
## [33] plyr_1.8.7                 
## 
## loaded via a namespace (and not attached):
##   [1] colorspace_2.0-3       ellipsis_0.3.2         XVector_0.36.0        
##   [4] fs_1.5.2               rstudioapi_0.13        bit64_4.0.5           
##   [7] AnnotationDbi_1.58.0   fansi_1.0.3            lubridate_1.8.0       
##  [10] xml2_1.3.3             codetools_0.2-18       splines_4.2.1         
##  [13] cachem_1.0.6           geneplotter_1.74.0     knitr_1.39            
##  [16] jsonlite_1.8.0         broom_0.8.0            annotate_1.74.0       
##  [19] dbplyr_2.2.1           png_0.1-7              shiny_1.7.1           
##  [22] compiler_4.2.1         httr_1.4.3             backports_1.4.1       
##  [25] assertthat_0.2.1       Matrix_1.4-1           fastmap_1.1.0         
##  [28] cli_3.3.0              later_1.3.0            htmltools_0.5.2       
##  [31] tools_4.2.1            gtable_0.3.0           glue_1.6.2            
##  [34] GenomeInfoDbData_1.2.8 fastmatch_1.1-3        Rcpp_1.0.8.3          
##  [37] cellranger_1.1.0       jquerylib_0.1.4        vctrs_0.4.1           
##  [40] Biostrings_2.64.0      svglite_2.1.0          xfun_0.31             
##  [43] rvest_1.0.2            mime_0.12              lifecycle_1.0.1       
##  [46] gtools_3.9.2.2         XML_3.99-0.10          zlibbioc_1.42.0       
##  [49] scales_1.2.0           promises_1.2.0.1       hms_1.1.1             
##  [52] parallel_4.2.1         RColorBrewer_1.1-3     yaml_2.3.5            
##  [55] gridExtra_2.3          memoise_2.0.1          sass_0.4.1            
##  [58] reshape_0.8.9          stringi_1.7.6          RSQLite_2.2.14        
##  [61] highr_0.9              genefilter_1.78.0      caTools_1.18.2        
##  [64] BiocParallel_1.30.3    echarts4r_0.4.4        systemfonts_1.0.4     
##  [67] rlang_1.0.3            pkgconfig_2.0.3        bitops_1.0-7          
##  [70] evaluate_0.15          lattice_0.20-45        htmlwidgets_1.5.4     
##  [73] bit_4.0.4              tidyselect_1.1.2       GGally_2.1.2          
##  [76] magrittr_2.0.3         R6_2.5.1               generics_0.1.2        
##  [79] DelayedArray_0.22.0    DBI_1.1.3              pillar_1.7.0          
##  [82] haven_2.5.0            withr_2.5.0            survival_3.4-0        
##  [85] KEGGREST_1.36.2        RCurl_1.98-1.7         modelr_0.1.8          
##  [88] crayon_1.5.1           KernSmooth_2.23-20     utf8_1.2.2            
##  [91] tzdb_0.3.0             rmarkdown_2.14         locfit_1.5-9.5        
##  [94] grid_4.2.1             readxl_1.4.0           data.table_1.14.2     
##  [97] blob_1.2.3             webshot_0.5.3          reprex_2.0.1          
## [100] digest_0.6.29          xtable_1.8-4           httpuv_1.6.5          
## [103] munsell_0.5.0          viridisLite_0.4.0      bslib_0.3.1