diff–over–undiff

TwoGroupsAnalysis_Result

Settings

	Setting
Analysis:	NGS two group analysis
Reference:	Homo_sapiens/GENCODE/GRCh38.p13/Annotation/Release_42-2023-01-30
Feature level:	gene
Data Column Used:	matchCounts
Method:	glm
Comparison:	diff–over–undiff
Normalization:	TMM
Differential expression test:	QL
Log2 signal threshold:	3.322
Linear signal threshold:	10

Result summary

	Number
reference:	Homo_sapiens/GENCODE/GRCh38.p13/Annotation/Release_42-2023-01-30
Number of features:	21057
Number of features with counts above threshold:	1826

Number of significants by p-value and fold-change

	#significants	FDR	fc >= 1	fc >= 1.5	fc >= 2	fc >= 3	fc >= 4	fc >= 8	fc >= 10
p < 0.1	761	0.2383000	761	635	288	121	67	22	16
p < 0.05	616	0.1460000	616	584	288	121	67	22	16
p < 0.01	395	0.0450100	395	395	277	121	67	22	16
p < 0.001	271	0.0066650	271	271	237	121	67	22	16
p < 1e-04	198	0.0007600	198	198	193	117	67	22	16
p < 1e-05	160	0.0001094	160	160	158	105	66	22	16

Full result table in xlsx format for opening with a spreadsheet program (e.g. Excel).

result–diff–over–undiff.xlsx

Live Report and Visualizations

Inspection of significant genes

Between-group comparison

	Number
P-value threshold:	p <= 0.01
Log ratio threshold:	log ratio >= 0.5
Number of significant genes:	395

Subsequent plots highlight significant genes in blue.

Interactive table of significant genes

Interactive comparison plot (64-bit Chrome or Safari is recommended for best performance!)

Inspection of significant genes (Advanced plots)

Intra-group Comparison: undiff

Intra-group Comparison: diff

Clustering of significant features

	Number
Significance threshold:	0.01
log2 Ratio threshold:	0.5
Number of significant features:	395

Cluster plot

GO categories of feature clusters
	BP	CC	Enrichr
Cluster 1	Cluster-BP-1.html		Enrichr
Cluster 2	Cluster-BP-2.html	Cluster-CC-2.html	Enrichr
Cluster 3	Cluster-BP-3.html	Cluster-CC-3.html	Enrichr
Cluster 4		Cluster-CC-4.html	Enrichr
Cluster 5		Cluster-CC-5.html	Enrichr
Cluster 6	Cluster-BP-6.html	Cluster-CC-6.html	Enrichr
Note:
Cluster font color corresponds to the row colors in the heatmap plot.

GO cluster tables

Enrichr

Description

Enrichr is a web server which collects in one website many different databases that can be interrogated using gene lists. It takes as input a subset of genes passing certain p-value/fold-change thresholds (i.e., differentially expressed genes). It is recommended to search in one go various databases such as cell type, transcription factors, mutations, diseases. Further details: Visit the enrichr bioconductor page

	Number of Genes	External	Precomputed	CutOffs
upGenes	241	Analyse at Enrichr website	Not run	p <= 0.01 , log2 ratio > 0
downGenes	154	Analyse at Enrichr website	Not run	p <= 0.01 , log2 ratio < 0
bothGenes	395	Analyse at Enrichr website	Not run	p <= 0.01

Overrepresentation Analysis (ORA)

Overview

Description

The Over Representation Analysis (ORA), also known as the hypergeometric test, gives an estimate of whether a set of selected genes is enriched for genes in specific Gene Ontology categories. It takes as input a subset of genes passing certain p-value/fold-change thresholds (i.e., differentially expressed genes). It is recommended when the difference between groups is large (e.g., 500+ genes above p-value/fold-change thresholds). There are many implementations of this test and in SUSHI we use the R package clusterProfiler. Further details: Visit the clusterProfiler bioconductor page

Cut Offs:

Gene Selection: p <= 0.01, Up: log2 ratio >0/Down: log2 ratio < 0
Candidate Terms: fdr <= 0.05

Hypergeometric Over-representation Test
	Number of Significant Terms
BP: upGenes	18
BP: downGenes	1
BP: bothGenes	20
MF: upGenes	8
MF: downGenes	0
MF: bothGenes	5
CC: upGenes	9
CC: downGenes	1
CC: bothGenes	8

BP

upGenes

ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	geneName
GO:0006955	immune response	29/230	45/1769	3.899324e-16	1.395958e-13	PXDN/IL1R1/ITGB6/CCL20/ACKR3/TNFSF10/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/CD74/HLA-A/HLA-C/HLA-B/TAPBP/ITGB8/TRIM22/FTH1/CTSC/B2M/SMAD3/IL32/CX3CL1/TNFSF12-TNFSF13/TNFSF13/C3/SLPI/XBP1
GO:0006935	chemotaxis	12/230	21/1769	1.781788e-06	3.189401e-04	S100A9/CCL20/ACKR3/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/PLAU/CX3CL1/CXCL16/CXCL17
GO:0006954	inflammatory response	20/230	53/1769	3.289123e-06	3.230789e-04	HSPG2/ZC3H12A/S100A9/ELF3/CYP26B1/IL1R1/ITGB6/CCL20/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/IDO1/NINJ1/SERPINA3/CX3CL1/ALOX15/C3/PLD3
GO:0006952	defense response	10/230	16/1769	4.512275e-06	3.230789e-04	CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/CD74/HLA-B/DUOX2/IL32/CX3CL1
GO:0030593	neutrophil chemotaxis	10/230	16/1769	4.512275e-06	3.230789e-04	S100A9/TGFB2/CCL20/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/SAA1/CX3CL1
GO:0006508	proteolysis	20/230	61/1769	3.812646e-05	2.274879e-03	ECE1/TINAGL1/CAPN13/UBD/ENSG00000244255/CFB/PLAU/ENSG00000250644/CTSD/CTSC/TMPRSS4/ST14/CTSH/PRSS22/PRSS8/MMP2/CPD/WFDC2/CTSA/TMPRSS2
GO:0010951	negative regulation of endopeptidase activity	13/230	31/1769	5.182293e-05	2.650373e-03	RARRES1/SERPINB1/SERPINA3/SPINT1/SERPINF1/TIMP2/SERPINB3/SERPINB7/C3/PI3/SLPI/WFDC2/CSTB
GO:0001525	angiogenesis	19/230	58/1769	6.105905e-05	2.732392e-03	HSPG2/ZC3H12A/GLUL/PXDN/CYP1B1/EPAS1/FN1/ACKR3/CXCL8/CCN2/NINJ1/TNFAIP2/MFGE8/MMP2/CXCL17/EMC10/ID1/XBP1/SAT1
GO:0045087	innate immune response	18/230	57/1769	1.648113e-04	6.349369e-03	S100A9/ATP1B1/SLC15A2/HLA-A/HLA-C/HLA-B/ENSG00000244255/CFB/LCN2/TRIM22/C3/BPIFA1/BPIFB1/SERINC3/PI3/SLPI/WFDC2/APOL1
GO:0010466	negative regulation of peptidase activity	10/230	22/1769	1.773567e-04	6.349369e-03	SERPINB1/SERPINA3/SPINT1/TIMP2/SERPINB3/SERPINB7/PI3/SLPI/WFDC2/CSTB
GO:0061844	antimicrobial humoral immune response mediated by antimicrobial peptide	7/230	12/1769	2.557547e-04	7.929051e-03	S100A9/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/BPIFA1
GO:0002376	immune system process	20/230	69/1769	2.657782e-04	7.929051e-03	ZC3H12A/S100A9/ATP1B1/SLC15A2/CD74/HLA-A/HLA-C/HLA-B/ENSG00000244255/CFB/IDO1/LCN2/B2M/TNFSF13/C3/PLD3/BPIFA1/BPIFB1/SERINC3/SLPI
GO:0007186	G protein-coupled receptor signaling pathway	12/230	32/1769	3.616421e-04	9.959067e-03	ECE1/CCL20/ACKR3/CXCL8/CXCL1/GABBR1/AKR1C2/GPRC5A/GPRC5B/CX3CL1/C3/INSR
GO:0007165	signal transduction	38/230	176/1769	5.668690e-04	1.443810e-02	CRABP2/EPAS1/IL1R1/IGFBP2/CCL20/ACKR3/TNFSF10/CXCL8/CXCL6/CXCL1/CXCL5/NEDD9/GABBR1/CCN2/IFNGR1/GPNMB/FAM83A/PTGES/PLAU/MDK/SCGB1A1/ARHGAP32/GPRC5A/IRAK3/TXNRD1/PRKAB1/IL32/GPRC5B/ABR/CXCL16/TNFSF12-TNFSF13/TNFSF13/GRN/LGALS3BP/C3/GDF15/CEACAM6/PLXNB2
GO:0060395	SMAD protein signal transduction	6/230	10/1769	6.049483e-04	1.443810e-02	TGFB2/ITGB6/TF/SMAD3/HEXA/GDF15
GO:0045766	positive regulation of angiogenesis	11/230	30/1769	8.009403e-04	1.792104e-02	ZC3H12A/CYP1B1/CXCL8/ITGB8/HSPB1/NINJ1/CTSH/GRN/C3/EMC10/XBP1
GO:0006629	lipid metabolic process	27/230	119/1769	1.780930e-03	3.750429e-02	DHRS3/HSPG2/EPHX1/CYP1B1/CYP26B1/DHRS9/SGPP2/IP6K2/ASAH1/RDH10/PTGES/AKR1C2/PSAP/PNPLA2/PRKAB1/LRP10/HEXA/ALDH1A3/ALOX15/ACADVL/FUT3/C3/FUT2/GPCPD1/B4GALT5/XBP1/APOL1
GO:0007267	cell-cell signaling	9/230	24/1769	2.025296e-03	4.028089e-02	S100A9/CCL20/TNFSF10/CXCL6/CXCL5/PCDH1/GPNMB/CX3CL1/GDF15

downGenes

ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	geneName
GO:0008544	epidermis development	9/148	21/1769	1.943445e-05	0.00658828	YBX1/LAMC2/TP63/DSP/EGFR/KRT5/BNC1/KRT14/LAMA3

bothGenes

ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	geneName
GO:0006955	immune response	31/378	45/1769	5.021857e-12	2.089093e-09	PXDN/IL1R1/ITGB6/CCL20/ACKR3/TNFSF10/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/CD74/HLA-A/HLA-C/HLA-B/TAPBP/ITGB8/TRIM22/FTH1/CTSC/B2M/SMAD3/IL32/CX3CL1/TNFSF12-TNFSF13/TNFSF13/C3/SLPI/XBP1/ETS1/PNP
GO:0006935	chemotaxis	14/378	21/1769	8.831175e-06	1.836884e-03	S100A9/CCL20/ACKR3/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/PLAU/CX3CL1/CXCL16/CXCL17/FOSL1/PLP2
GO:0008544	epidermis development	13/378	21/1769	6.043077e-05	6.853277e-03	CRABP2/CCN2/SPINT1/INSR/YBX1/LAMC2/TP63/DSP/EGFR/KRT5/BNC1/KRT14/LAMA3
GO:0006954	inflammatory response	24/378	53/1769	6.589689e-05	6.853277e-03	HSPG2/ZC3H12A/S100A9/ELF3/CYP26B1/IL1R1/ITGB6/CCL20/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/IDO1/NINJ1/SERPINA3/CX3CL1/ALOX15/C3/PLD3/PTGS2/CD44/ACER3/FASN
GO:0032526	response to retinoic acid	8/378	10/1769	1.220379e-04	1.015355e-02	CYP26B1/IGFBP2/CTSH/MMP2/TRIM16/TFRC/DKK1/GJB2
GO:0010951	negative regulation of endopeptidase activity	16/378	31/1769	1.740042e-04	1.206429e-02	RARRES1/SERPINB1/SERPINA3/SPINT1/SERPINF1/TIMP2/SERPINB3/SERPINB7/C3/PI3/SLPI/WFDC2/CSTB/SERPINE2/SERPINB5/SERPINB2
GO:0008285	negative regulation of cell population proliferation	28/378	71/1769	3.155097e-04	1.666131e-02	TGFB2/CYP1B1/ACKR3/RARRES1/CXCL8/CXCL1/GABBR1/CDKN1A/SOD2/GPNMB/IGFBP3/PTGES/FTH1/SMAD3/NUPR1/PTGS2/PTPN14/SERPINE2/FGFBP1/NPM1/HMGA1/CAV1/NDRG1/FOSL1/ETS1/RB1/CDH13/ADAMTS1
GO:0006952	defense response	10/378	16/1769	4.099619e-04	1.666131e-02	CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/CD74/HLA-B/DUOX2/IL32/CX3CL1
GO:0030593	neutrophil chemotaxis	10/378	16/1769	4.099619e-04	1.666131e-02	S100A9/TGFB2/CCL20/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/SAA1/CX3CL1
GO:0045766	positive regulation of angiogenesis	15/378	30/1769	4.380709e-04	1.666131e-02	ZC3H12A/CYP1B1/CXCL8/ITGB8/HSPB1/NINJ1/CTSH/GRN/C3/EMC10/XBP1/F3/AGO2/ETS1/HMGA2
GO:0006629	lipid metabolic process	41/378	119/1769	4.405634e-04	1.666131e-02	DHRS3/HSPG2/EPHX1/CYP1B1/CYP26B1/DHRS9/SGPP2/IP6K2/ASAH1/RDH10/PTGES/AKR1C2/PSAP/PNPLA2/PRKAB1/LRP10/HEXA/ALDH1A3/ALOX15/ACADVL/FUT3/C3/FUT2/GPCPD1/B4GALT5/XBP1/APOL1/SLC16A1/FDPS/PTGS2/LPIN1/INPP4B/MSMO1/HMGCS1/ACAT2/SQLE/SCD/ACER3/PTGES3/ACLY/FASN
GO:0010466	negative regulation of peptidase activity	12/378	22/1769	6.092666e-04	2.112124e-02	SERPINB1/SERPINA3/SPINT1/TIMP2/SERPINB3/SERPINB7/PI3/SLPI/WFDC2/CSTB/SERPINE2/SERPINB2
GO:0007165	signal transduction	55/378	176/1769	7.976044e-04	2.552334e-02	CRABP2/EPAS1/IL1R1/IGFBP2/CCL20/ACKR3/TNFSF10/CXCL8/CXCL6/CXCL1/CXCL5/NEDD9/GABBR1/CCN2/IFNGR1/GPNMB/FAM83A/PTGES/PLAU/MDK/SCGB1A1/ARHGAP32/GPRC5A/IRAK3/TXNRD1/PRKAB1/IL32/GPRC5B/ABR/CXCL16/TNFSF12-TNFSF13/TNFSF13/GRN/LGALS3BP/C3/GDF15/CEACAM6/PLXNB2/SFN/BCAR3/ARHGAP29/S100A6/PKP1/FLNB/TFRC/FGFBP1/INPP4B/TENM2/NPM1/FAM83B/EGFR/NRG1/NDRG1/PTGES3/GPI
GO:0061844	antimicrobial humoral immune response mediated by antimicrobial peptide	8/378	12/1769	8.903262e-04	2.645541e-02	S100A9/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/BPIFA1/KRT6A
GO:0048146	positive regulation of fibroblast proliferation	9/378	15/1769	1.237485e-03	3.303805e-02	FOSL2/FN1/CD74/CDKN1A/FBLN1/S100A6/CCNB1/EGFR/MYC
GO:0060395	SMAD protein signal transduction	7/378	10/1769	1.270694e-03	3.303805e-02	TGFB2/ITGB6/TF/SMAD3/HEXA/GDF15/SUB1
GO:0120162	positive regulation of cold-induced thermogenesis	10/378	18/1769	1.476466e-03	3.613000e-02	EPAS1/LCN2/UCP2/PRKAB1/MFN2/G0S2/LPIN1/CAV1/SCD/DYNC1H1
GO:0010628	positive regulation of gene expression	27/378	74/1769	1.668309e-03	3.855647e-02	ZC3H12A/CYP26B1/FN1/CXCL8/CD74/CCN2/IFNGR1/AGR2/ITGB8/GSN/PRKAB1/SMAD3/CTSH/ID1/FBLN1/RPL11/F3/PKP1/TFRC/CAV1/NRG1/MYC/AGO2/DKK1/ETS1/HMGA2/MSN
GO:0045087	innate immune response	22/378	57/1769	1.956118e-03	4.282869e-02	S100A9/ATP1B1/SLC15A2/HLA-A/HLA-C/HLA-B/ENSG00000244255/CFB/LCN2/TRIM22/C3/BPIFA1/BPIFB1/SERINC3/PI3/SLPI/WFDC2/APOL1/TMEM43/SKP2/PRKDC/DDX21
GO:0042060	wound healing	16/378	37/1769	2.065761e-03	4.296783e-02	TGFB2/ITGB6/FN1/CDKN1A/TPM1/SMAD3/CX3CL1/ALOX15/COL1A1/MACF1/DSP/DST/NRG1/PLEC/KRT6A/SERPINB2

MF

upGenes

ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	geneName
GO:0005125	cytokine activity	15/236	28/1785	3.296268e-07	4.416999e-05	TGFB2/CCL20/TNFSF10/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/IL32/CX3CL1/CXCL16/TNFSF12-TNFSF13/TNFSF13/GRN/GDF15
GO:0004252	serine-type endopeptidase activity	12/236	23/1785	7.718027e-06	5.171078e-04	ENSG00000244255/CFB/RHBDD2/PLAU/CTSC/TMPRSS4/ST14/CTSH/PRSS22/PRSS8/MMP2/TMPRSS2
GO:0030414	peptidase inhibitor activity	10/236	21/1785	1.263434e-04	5.643341e-03	SERPINB1/SERPINA3/SPINT1/TIMP2/SERPINB3/SERPINB7/PI3/SLPI/WFDC2/CSTB
GO:0008233	peptidase activity	17/236	53/1785	2.518359e-04	8.436504e-03	ECE1/CAPN13/ENSG00000244255/CFB/PLAU/ENSG00000250644/CTSD/CTSC/TMPRSS4/ST14/CTSH/PRSS22/PRSS8/MMP2/CPD/CTSA/TMPRSS2
GO:0008236	serine-type peptidase activity	8/236	16/1785	4.127049e-04	1.106049e-02	ENSG00000244255/CFB/PLAU/TMPRSS4/ST14/PRSS22/PRSS8/TMPRSS2
GO:0016491	oxidoreductase activity	22/236	85/1785	9.699631e-04	1.853558e-02	DHRS3/PXDN/XDH/CYP1B1/CYP26B1/DHRS9/CP/SOD2/STEAP4/IDO1/RDH10/PTGES/AKR1C2/CYB561A3/FTH1/TXNRD1/DUOX2/ALDH1A3/ALOX15/ACADVL/MT-ND2/MT-CYB
GO:0020037	heme binding	7/236	14/1785	9.748545e-04	1.853558e-02	PXDN/CYP1B1/CYP26B1/STEAP4/IDO1/DUOX2/MT-CO1
GO:0004867	serine-type endopeptidase inhibitor activity	9/236	22/1785	1.106602e-03	1.853558e-02	SERPINB1/SERPINA3/SPINT1/SERPINF1/SERPINB3/SERPINB7/PI3/SLPI/WFDC2

downGenes

No significant GO terms detected.

bothGenes

ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	geneName
GO:0005125	cytokine activity	17/386	28/1785	7.192942e-06	0.001136485	TGFB2/CCL20/TNFSF10/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/IL32/CX3CL1/CXCL16/TNFSF12-TNFSF13/TNFSF13/GRN/GDF15/NRG1/GPI
GO:0004252	serine-type endopeptidase activity	13/386	23/1785	2.526555e-04	0.019959781	ENSG00000244255/CFB/RHBDD2/PLAU/CTSC/TMPRSS4/ST14/CTSH/PRSS22/PRSS8/MMP2/TMPRSS2/F3
GO:0030414	peptidase inhibitor activity	12/386	21/1785	3.856452e-04	0.020310649	SERPINB1/SERPINA3/SPINT1/TIMP2/SERPINB3/SERPINB7/PI3/SLPI/WFDC2/CSTB/SERPINE2/SERPINB2
GO:0020037	heme binding	9/386	14/1785	6.692914e-04	0.021642633	PXDN/CYP1B1/CYP26B1/STEAP4/IDO1/DUOX2/MT-CO1/PTGS2/CYCS
GO:0004867	serine-type endopeptidase inhibitor activity	12/386	22/1785	6.848934e-04	0.021642633	SERPINB1/SERPINA3/SPINT1/SERPINF1/SERPINB3/SERPINB7/PI3/SLPI/WFDC2/SERPINE2/SERPINB5/SERPINB2

CC

upGenes

ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	geneName
GO:0005615	extracellular space	82/237	219/1799	3.491531e-23	5.551534e-21	HSPG2/TINAGL1/TACSTD2/S100A9/MUC1/PIGR/TGFB2/PXDN/XDH/FN1/IGFBP2/CCL20/LRRN1/TF/CP/RARRES1/TNFSF10/MUC4/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/VCAN/SERPINB1/GABBR1/CFB/CCN2/AGR2/IGFBP3/HSPB1/MTUS1/ASAH1/GOLM1/GSN/STOM/LCN2/PSAP/PLAU/MUC5B/CTSD/SCGB1A1/CTSC/TMPRSS4/ST14/SERPINA3/TNFAIP2/SPINT1/B2M/CTSH/MFGE8/PRSS22/IL32/GPRC5B/PRSS8/MMP2/CX3CL1/SERPINF1/CXCL16/VMO1/TNFSF12-TNFSF13/TNFSF13/CPD/GRN/COL1A1/TIMP2/LGALS3BP/SERPINB3/SERPINB7/C3/ICAM1/GDF15/CEACAM6/CXCL17/BPIFA1/BPIFB1/PI3/SLPI/WFDC2/CSTB/APOL1/FBLN1
GO:0005576	extracellular region	86/237	296/1799	6.451431e-16	5.128888e-14	HSPG2/TINAGL1/S100A9/MUC1/PIGR/TGFB2/PXDN/XDH/IL1R1/FN1/IGFBP2/CCL20/TF/CP/TNFSF10/MUC20/MUC4/S100P/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/VCAN/SERPINB1/GABBR1/ENSG00000244255/CFB/CCN2/AGR2/IGFBP3/ASAH1/PSCA/NINJ1/GSN/LCN2/PSAP/PLAU/MUC5B/CTSD/SAA2/SAA1/MDK/FTH1/SCGB1A1/CTSC/TMPRSS4/ST14/NTN4/SERPINA3/SPINT1/B2M/CTSH/MFGE8/PRSS22/IL32/PRSS8/MMP2/CX3CL1/SERPINF1/CXCL16/VMO1/TNFSF13/NTN1/GRN/COL1A1/TIMP2/LGALS3BP/SERPINB3/C3/NOTCH3/GDF15/CEACAM7/CEACAM5/CXCL17/EMC10/BPIFA1/BPIFB1/PI3/SLPI/WFDC2/CTSA/TMPRSS2/CSTB/APOL1/FBLN1
GO:0062023	collagen-containing extracellular matrix	26/237	67/1799	6.642134e-08	3.520331e-06	HSPG2/TINAGL1/S100A9/TGFB2/PXDN/FN1/VCAN/SERPINB1/CCN2/PSAP/CTSD/MDK/CTSC/SERPINA3/CTSH/MFGE8/MMP2/SERPINF1/COL1A1/TIMP2/LGALS3BP/ICAM1/GDF15/SLPI/CSTB/FBLN1
GO:0016324	apical plasma membrane	19/237	57/1799	5.641108e-05	2.242340e-03	MUC1/ATP1B1/PROM2/FN1/IGFBP2/SLC15A2/TF/MUC20/SLC34A2/SLC44A4/CLDN4/SLC26A4/SCNN1A/SLC11A2/DUOX2/CEACAM7/CEACAM5/CEACAM6/SLC6A14
GO:0072562	blood microparticle	10/237	22/1799	1.989964e-04	5.334434e-03	FN1/TF/CP/CFB/GSN/STOM/SERPINA3/LGALS3BP/C3/APOL1
GO:0031012	extracellular matrix	12/237	30/1799	2.012994e-04	5.334434e-03	PXDN/FN1/LRRN1/MUC4/VCAN/CCN2/MUC5B/MMP2/COL1A1/TIMP2/PI3/FBLN1
GO:1904724	tertiary granule lumen	8/237	18/1799	1.078357e-03	2.449411e-02	CXCL1/ASAH1/CTSD/FTH1/B2M/CTSH/TIMP2/CSTB
GO:0005764	lysosome	21/237	83/1799	1.661094e-03	3.301424e-02	TINAGL1/TSPAN1/VAMP8/MFSD1/CD74/SERPINB1/ASAH1/PSAP/CTSD/ACP2/CYB561A3/CTSC/SLC11A2/DRAM1/HEXA/CTSH/LITAF/GRN/INSR/PLD3/CTSA
GO:0043202	lysosomal lumen	10/237	29/1799	2.640886e-03	4.665566e-02	HSPG2/VCAN/CD74/ASAH1/PSAP/CTSD/ACP2/HEXA/PLD3/CTSA

downGenes

ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	geneName
GO:0005882	intermediate filament	9/153	19/1799	8.150014e-06	0.001246952	MACF1/PKP1/DSP/DST/PLEC/KRT6A/KRT5/KRT18/KRT14

bothGenes

ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	geneName
GO:0005615	extracellular space	104/390	219/1799	5.734768e-20	1.066667e-17	HSPG2/TINAGL1/TACSTD2/S100A9/MUC1/PIGR/TGFB2/PXDN/XDH/FN1/IGFBP2/CCL20/LRRN1/TF/CP/RARRES1/TNFSF10/MUC4/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/VCAN/SERPINB1/GABBR1/CFB/CCN2/AGR2/IGFBP3/HSPB1/MTUS1/ASAH1/GOLM1/GSN/STOM/LCN2/PSAP/PLAU/MUC5B/CTSD/SCGB1A1/CTSC/TMPRSS4/ST14/SERPINA3/TNFAIP2/SPINT1/B2M/CTSH/MFGE8/PRSS22/IL32/GPRC5B/PRSS8/MMP2/CX3CL1/SERPINF1/CXCL16/VMO1/TNFSF12-TNFSF13/TNFSF13/CPD/GRN/COL1A1/TIMP2/LGALS3BP/SERPINB3/SERPINB7/C3/ICAM1/GDF15/CEACAM6/CXCL17/BPIFA1/BPIFB1/PI3/SLPI/WFDC2/CSTB/APOL1/FBLN1/ENO1/SFN/F3/LAMC2/HSPD1/BMPR2/SERPINE2/TFRC/FGFBP1/FST/EGFR/NRG1/DKK1/SORL1/LTBP2/CDH13/SERPINB5/SERPINB2/GPI/PVR/MSN/PGK1
GO:0005576	extracellular region	112/390	296/1799	1.962546e-12	1.825168e-10	HSPG2/TINAGL1/S100A9/MUC1/PIGR/TGFB2/PXDN/XDH/IL1R1/FN1/IGFBP2/CCL20/TF/CP/TNFSF10/MUC20/MUC4/S100P/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/VCAN/SERPINB1/GABBR1/ENSG00000244255/CFB/CCN2/AGR2/IGFBP3/ASAH1/PSCA/NINJ1/GSN/LCN2/PSAP/PLAU/MUC5B/CTSD/SAA2/SAA1/MDK/FTH1/SCGB1A1/CTSC/TMPRSS4/ST14/NTN4/SERPINA3/SPINT1/B2M/CTSH/MFGE8/PRSS22/IL32/PRSS8/MMP2/CX3CL1/SERPINF1/CXCL16/VMO1/TNFSF13/NTN1/GRN/COL1A1/TIMP2/LGALS3BP/SERPINB3/C3/NOTCH3/GDF15/CEACAM7/CEACAM5/CXCL17/EMC10/BPIFA1/BPIFB1/PI3/SLPI/WFDC2/CTSA/TMPRSS2/CSTB/APOL1/FBLN1/SFN/YBX1/F3/S100A6/LAMC2/SERPINE2/CDCP1/TFRC/FGFBP1/FST/FBN2/EGFR/NRG1/DKK1/SORL1/PNP/LTBP2/DYNC1H1/CDH13/ACLY/LAMA3/SERPINB5/SERPINB2/GPI/PVR/ADAMTS1
GO:0062023	collagen-containing extracellular matrix	35/390	67/1799	2.027755e-08	1.257208e-06	HSPG2/TINAGL1/S100A9/TGFB2/PXDN/FN1/VCAN/SERPINB1/CCN2/PSAP/CTSD/MDK/CTSC/SERPINA3/CTSH/MFGE8/MMP2/SERPINF1/COL1A1/TIMP2/LGALS3BP/ICAM1/GDF15/SLPI/CSTB/FBLN1/F3/S100A6/LAMC2/SERPINE2/FBN2/LTBP2/CDH13/LAMA3/ADAMTS1
GO:0031012	extracellular matrix	16/390	30/1799	1.258415e-04	5.214363e-03	PXDN/FN1/LRRN1/MUC4/VCAN/CCN2/MUC5B/MMP2/COL1A1/TIMP2/PI3/FBLN1/LAMC2/FBN2/LTBP2/ADAMTS1
GO:0072562	blood microparticle	13/390	22/1799	1.401710e-04	5.214363e-03	FN1/TF/CP/CFB/GSN/STOM/SERPINA3/LGALS3BP/C3/APOL1/SLC2A1/TFRC/MSN
GO:0031901	early endosome membrane	16/390	32/1799	3.362645e-04	9.018055e-03	VAMP8/HLA-A/HLA-C/HLA-B/GPNMB/STEAP4/B2M/LITAF/PLD3/PMEPA1/ATP13A3/EGFR/CAV1/DKK1/SORL1/SNX5
GO:0016324	apical plasma membrane	24/390	57/1799	3.393892e-04	9.018055e-03	MUC1/ATP1B1/PROM2/FN1/IGFBP2/SLC15A2/TF/MUC20/SLC34A2/SLC44A4/CLDN4/SLC26A4/SCNN1A/SLC11A2/DUOX2/CEACAM7/CEACAM5/CEACAM6/SLC6A14/SLC2A1/SLC16A1/SEPTIN7/CD44/MSN
GO:0009986	cell surface	39/390	114/1799	9.831047e-04	2.285718e-02	PXDN/ANTXR1/PROM2/IL1R1/ITGB6/ACKR3/TF/CD74/HLA-A/HLA-C/HLA-B/ITGB8/PLAU/SLC11A2/B2M/DUOX2/GPRC5B/CX3CL1/C3/ICAM1/NOTCH3/CEACAM5/CEACAM6/NECTIN2/PLXNB2/ENO1/F3/HNRNPU/ITGA6/HSPD1/BMPR2/TFRC/FGFBP1/NT5E/EGFR/CD44/SORL1/PVR/MSN

Gene set enrichment analysis

Overview

Description

Gene Set Enrichment Analysis (GSEA) calculates an enrichment score for each annotation category (e.g., those in GO BP) by screening all the genes from a differential expression analysis and their associated fold-changes. It does not require a pre-selection based on p-value/fold-change. It is recommended when the difference between groups is small (i.e., applying thresholds would result in very few genes selected) or when combining results from different experiments. Similar to the ORA test, we use the package clusterProfiler to perform GSEA analysis in SUSHI. Further details: Visit the clusterProfiler bioconductor page

Cut Off:

Candidate Terms: fdr <= 0.05

Gene Ranking:

all present genes are sorted by log2 ratio

BP

## Picking joint bandwidth of 0.259

ID	Description	setSize	enrichmentScore	NES	pvalue	p.adjust	geneName
GO:0006412	translation	133	-0.8125626	-2.252759	1.000000e-10	2.160000e-08	RPS3/EIF3I/SARS1/EIF3K/KARS1/RPLP0/EIF3E/LARP1/HARS1/RPL36/EIF4G3/EEF2/EEF1A1/RPL27A/EIF4A1/RPS15/RPS5/EIF3L/RPL24/RPS12/RPS26/RPS27/RPL3/RPL14/RPL6/TARS1/RPL18/LARS1/RPL29/UBA52/EIF3B/RPL7/RPL15/RPS20/RPS4Y1/RPS21/RPS14/RPL7A/RPS9/RPS25/MRPL3/ENSG00000260342/RACK1/EIF3M/RPL35/RPL19/RPS7/EIF4G1/RPL26/EPRS1/EEF1B2/ETF1/RPL23/NARS1/RPL13/RPL31/GARS1/EIF3A/RPS10/PABPC4/RPS27A/RPL10/FAU/RPS15A/RPS23/RPS29/RPL23A/IARS1/RPS24/RPL38/RPL18A/RPL37/RPL9/RPL30/NACA/EEF1G/RPL36A-HNRNPH2/RPL17-C18orf32/RPS8/RPL17/RPL32/RPL35A/RPL27/RPS4X/RPL36A/EIF5B/RPL10A/EIF2S3/IARS2/EIF3G/RPL22L1/RPS17/MRPL19/RPL8/RPS2/RPS18/EIF3D/GSPT1/RPL5/RPSA/AGO2/EIF5A/RPS13/RPS3A/RPS6/RPL11/RPS16/RPL4
GO:0002181	cytoplasmic translation	79	-0.8620669	-2.220503	1.000000e-10	2.160000e-08	RPL27A/RPS15/RPS5/RPL24/RPS12/RPS26/RPS27/RPL3/RPL14/RPL6/RPL18/RPL29/UBA52/RPL7/RPL15/RPS20/RPS21/RPS14/RPL7A/RPS9/RPS25/RACK1/RPL35/RPL19/RPS7/RPL26/RPL23/RPL13/RPL31/RPS10/RPS27A/RPL10/FAU/RPS15A/RPS23/RPS29/RPL23A/RPS24/RPL38/RPL18A/RPL37/RPL9/RPL30/RPS8/RPL17/RPL32/RPL35A/RPL27/RPS4X/RPL36A/RPL10A/RPL22L1/RPS17/RPL8/RPS2/RPS18/RPL5/RPSA/RPS13/RPS3A/RPS6/RPL11/RPS16/RPL4
GO:0006397	mRNA processing	55	-0.8245587	-2.007952	2.072465e-07	2.984350e-05	SF3B3/HNRNPC/SRRM2/SF3B2/CPSF2/PAPOLA/RNPS1/SF3B4/ESRP1/STRAP/DDX39B/SRPK1/SFPQ/RBM25/CELF1/SRRM1/SF1/SRSF3/SYNCRIP/GRSF1/PRPF8/HNRNPR/RBMX/SON/HNRNPA3/SRSF2/THRAP3/LSM4/PTBP3/DHX9/KHSRP/TRA2B/HNRNPL/HNRNPA1/SRSF1/SNRPD2/HSPA8/HNRNPU/YBX1
GO:0008380	RNA splicing	52	-0.8098964	-1.942629	8.630581e-07	8.258976e-05	SF3B3/HNRNPC/SRRM2/SF3B2/RNPS1/SF3B4/ESRP1/STRAP/DDX39B/SRPK1/SFPQ/RBM25/CELF1/SRRM1/SF1/SRSF3/SYNCRIP/PRPF8/FUS/HNRNPR/RBMX/SON/HNRNPA3/SRSF2/THRAP3/LSM4/PTBP3/DHX9/KHSRP/TRA2B/HNRNPA1/SRSF1/SNRPD2/HSPA8/HNRNPU/YBX1
GO:0006955	immune response	45	0.8814159	1.940959	9.559000e-07	8.258976e-05	C3/CXCL6/SLPI/CXCL5/HLA-B/XBP1/CXCL1/ACKR3/CX3CL1/ITGB6/TNFSF10/ITGB8/IL1R1/CXCL3/CXCL8/TAPBP/HLA-C/CD74/FTH1/TNFSF13/B2M/TNFSF12-TNFSF13/HLA-A/TRIM22/IL1B/CTSC/IL32/SMAD3/PXDN/CCL20/CSF3/LTBR/IL1RN
GO:0006508	proteolysis	61	0.8284324	1.899531	3.881395e-06	2.794604e-04	WFDC2/CFB/ENSG00000244255/CTSD/ENSG00000250644/CTSH/PRSS22/UBD/CTSA/TMPRSS4/CAPN13/MMP2/TMPRSS2/CPD/TINAGL1/PLAU/MMP14/CTSC/PRSS8/ST14/NCSTN/ECE1/PRSS23/TPP1/BMP1/FAP/ADAM9/CTSB/CFH
GO:0000398	mRNA splicing, via spliceosome	32	-0.8494663	-1.863566	1.518027e-05	9.368395e-04	PABPC1/SF3B3/HNRNPC/SRRM2/SF3B2/RNPS1/SF3B4/DDX39B/SRRM1/SF1/SRSF3/SYNCRIP/PRPF8/SNRPC/HNRNPR/RBMX/HNRNPA3/SRSF2/LSM4/TRA2B/HNRNPA1/SRSF1/SNRPD2/HSPA8/HNRNPU
GO:0006364	rRNA processing	24	-0.8947513	-1.894244	2.648374e-05	1.430122e-03	RPS27/RPL14/RPL7/NSA2/RPS25/RPS7/RPL26/RPS24/RPL35A/RPL27/NOP56/RPS17/PA2G4/HEATR1/RPL5/NOLC1/DDX21/RPS6/RPL11/RPS16
GO:0002376	immune system process	69	0.7684858	1.790876	7.613914e-05	3.654679e-03	LCN2/CFB/ENSG00000244255/BPIFA1/C3/SLPI/BPIFB1/ATP1B1/IDO1/HLA-B/HLA-C/CD74/SLC15A2/S100A9/ZC3H12A/TNFSF13/B2M/HLA-A/PLD3/SERINC3/SQSTM1/TNFRSF21/LYN/GBP3/TRIM29/PML/S100A8/CSK/CFH/IFITM3/TRAF4/CD46/ADAR/ALCAM/BAG6/NONO
GO:0006281	DNA repair	34	-0.8104264	-1.788807	1.202065e-04	4.720837e-03	MORF4L1/UBE2D3/USP10/MORF4L2/UBE2N/YY1/TRIP12/SFPQ/NUCKS1/RAD21/SUMO1/SMG1/PSME4/RRM1/PDS5A/ASCC3/SSRP1/HMGB1/XRCC6/TAOK1/HUWE1/XRCC5/PRKDC/ERCC1/NPM1
GO:0030593	neutrophil chemotaxis	16	0.9468201	1.718129	1.201057e-04	4.720837e-03	CXCL6/CXCL5/SAA1/CXCL1/CX3CL1/TGFB2/CXCL3/CXCL8/S100A9/IL1B/CCL20/S100A8
GO:0051301	cell division	54	-0.7400143	-1.797617	1.689864e-04	6.083512e-03	MAP4/SEPTIN2/CDK6/RAD21/CDC27/SEPTIN11/TPR/BUB3/CLTC/CKAP5/NUDC/ARPP19/PDS5A/CCNK/USP9X/CLASP1/CCNG2/SEPTIN7/HNRNPU/RB1/CCND2/ANLN/TUBB/TUBA1C/RAN/CCNB1/DYNC1H1/TUBA1B/HMGA2
GO:0045087	innate immune response	57	0.7831326	1.778301	2.744471e-04	9.120087e-03	LCN2/WFDC2/CFB/ENSG00000244255/BPIFA1/C3/SLPI/BPIFB1/ATP1B1/HLA-B/PI3/HLA-C/SLC15A2/S100A9/APOL1/HLA-A/TRIM22/SERINC3/LYN/TRIM29/PML/S100A8/CFH/IFITM3/TRAF4/CD46/ADAR
GO:0051028	mRNA transport	19	-0.8851085	-1.784569	3.884109e-04	1.198525e-02	RANBP2/DDX39B/SRSF3/TPR/ZC3H11A/NUP50/NUTF2/LRPPRC/HNRNPA3/DHX9/KHSRP/IGF2BP2/HNRNPA1/SRSF1/XPO1
GO:0006954	inflammatory response	53	0.7630800	1.717235	5.248094e-04	1.416985e-02	SERPINA3/C3/CXCL6/CXCL5/IDO1/ELF3/CXCL1/CYP26B1/CX3CL1/ITGB6/IL1R1/ALOX15/CXCL3/CXCL8/HSPG2/S100A9/ZC3H12A/PLD3/IL1B/NINJ1/CCL20/CERS6/MAPKAPK2/LYN/IL1RN/STAT3/S100A8
GO:0006952	defense response	16	0.9206088	1.670565	5.100596e-04	1.416985e-02	CXCL6/CXCL5/DUOX2/HLA-B/CXCL1/CX3CL1/CXCL3/CXCL8/CD74/IL32/STAT3
GO:0006457	protein folding	39	-0.7474557	-1.702679	6.146356e-04	1.561897e-02	HSPA5/BAG3/FKBP9/CCT7/STIP1/CANX/RANBP2/HSPA9/PPIA/PDIA6/TCP1/CCT6A/CCT4/NUDC/HSPH1/PPIF/KHSRP/HSP90AA1/CCT5/CCT3/HSP90B1/HSPA8/HSPD1/ERO1A/PTGES3/HSP90AB1/FKBP1A
GO:0021762	substantia nigra development	16	-0.8783423	-1.708044	7.013807e-04	1.683314e-02	RHOA/HSPA5/CALM2/SEC16A/DYNLL1/YWHAH/BASP1/YWHAE/ATP5PB/MAPKAP1/ACTB/CALM3/CALM1/YWHAQ/LDHA
GO:0007186	G protein-coupled receptor signaling pathway	32	0.8140104	1.683028	7.629963e-04	1.734813e-02	C3/GPRC5A/GABBR1/CXCL1/ACKR3/CX3CL1/CXCL8/INSR/GPRC5B/APLP2/AKR1C2/ADGRG1/CCL20/ECE1/GIPC1/CELSR1
GO:0000278	mitotic cell cycle	18	-0.8814832	-1.768249	1.357852e-03	2.932960e-02	TUBA4A/CLTC/ARPP19/SRSF2/NOLC1/TUBB4B/TUBB6/RPS6/TUBB/TUBA1C/RAN/DYNC1H1/TUBA1B
GO:0033138	positive regulation of peptidyl-serine phosphorylation	20	-0.8507256	-1.720891	1.600276e-03	3.291995e-02	PAK1/MIF/MAPKAP1/EIF4G1/VEGFA/ATP2B4/HSP90AA1/DOCK7/TXN/BCAR3/TFRC/HSP90AB1/PTGS2/CD44/CAV1/EGFR
GO:0043484	regulation of RNA splicing	17	-0.8664304	-1.728699	1.835609e-03	3.589883e-02	SF3B3/ESRP1/CELF1/RBM12/GRSF1/FUS/SON/PTBP3/TRA2B/HNRNPL/HNRNPA1/SRSF1/AHNAK2/AHNAK
GO:0010466	negative regulation of peptidase activity	22	0.8589104	1.672122	1.911280e-03	3.589883e-02	SERPINA3/WFDC2/SLPI/SERPINB3/PI3/TIMP2/SPINT1/CSTB/SERPINB7/SERPINB1/APLP2/CTSB
GO:0000226	microtubule cytoskeleton organization	20	-0.8407502	-1.700712	2.344842e-03	3.909078e-02	DYNC1LI2/TUBA4A/MAP4/CAMSAP2/MAP1B/SON/CLASP1/TTL/GAPDH/DOCK7/TAOK1/TUBB4B/TUBB6/TUBB/TUBA1C/TUBA1B
GO:0007049	cell cycle	75	-0.6308387	-1.613302	2.211782e-03	3.909078e-02	CSNK2A2/GNAI2/AJUBA/SEPTIN2/MAPK6/CDK6/RAD21/EP300/SEPTIN11/TPR/RACK1/BUB3/CLTC/CKAP5/NUDC/ARPP19/SON/TFDP1/SPIN1/PDS5A/CCNK/BLCAP/USP9X/PSME3/CLASP1/CCNG2/SEPTIN7/CKAP2/HNRNPU/RB1/CCND2/PTP4A1/ANLN/KRT18/RAN/MKI67/CCNB1/TP63/DYNC1H1/HMGA2
GO:0007601	visual perception	12	0.9179142	1.591580	2.352686e-03	3.909078e-02	EPAS1/RDH10/TACSTD2/COL1A1/DHRS3/CDH3/RDH11/TGFBI/OAT
GO:1902600	proton transmembrane transport	37	0.7767555	1.631457	2.471454e-03	3.954326e-02	ATP1B1/MT-CYB/ATP6AP1/UCP2/MT-CO1/SLC15A2/MT-CO3/MT-ATP6/MT-CO2/MT-ATP8/SLC11A2/UQCR10/ATP6V0C/ATP1A1/COX5B/ATP6V1A/RNASEK/ATP6V0E1

MF

## Picking joint bandwidth of 0.217

## Warning: ggrepel: 227 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

ID	Description	setSize	enrichmentScore	NES	pvalue	p.adjust	geneName
GO:0003723	RNA binding	389	-0.7418193	-2.253921	1.000000e-10	8.250000e-09	ELAVL1/RPL36/EIF4G3/EEF2/PABPC1/PTPN1/PRDX1/LRP1/EEF1A1/RPL27A/EIF4A1/PPP1R10/CNOT6/RPS15/RPS5/USP10/ALDH18A1/STIP1/API5/HNRNPC/YWHAG/EIF3L/SRRM2/SF3B2/RPL24/CAST/ARCN1/PCBP1/CPSF2/RPS12/PAPOLA/HMGB3/RNPS1/UBE2N/HNRNPUL1/SF3B4/RCAN3/CANX/ESRP1/RPS26/YY1/RPS27/RPL3/RPL14/RPL6/TARS1/RPL18/SERBP1/PRRC2A/MAP4/RANBP2/STRAP/HDGF/RPL29/DDX39B/SRPK1/DICER1/EIF3B/RPL7/SFPQ/RBM25/UBA1/RPL15/GOT2/CNBP/RPS20/SMARCA4/NUCKS1/CELF1/SRRM1/VIM/RPS4Y1/RPS21/NSA2/RPS14/SF1/RPL7A/LTA4H/SRSF3/HSPA9/YWHAE/RSL1D1/RPS9/TIAL1/RPS25/PPIA/GTF3A/MRPL3/HNRNPDL/EWSR1/TPR/SYNCRIP/TCP1/ZC3H11A/CCT6A/GDI2/RACK1/ATP5F1C/RPL35/HNRNPAB/RPL19/ILF3/RBM12/RPS7/EIF4G1/GRSF1/RPL26/EPRS1/SUMO1/RTN4/ETF1/CAPRIN1/PRPF8/IMMT/SMG1/RBM3/RPL23/RPL13/RPL31/JUN/CLTC/EIF3A/RPS10/SNRPC/FUS/LRRC59/PABPC4/RPS27A/PFN1/CCT4/TOP1/RPL10/FAU/RPS15A/RPS23/RPS29/HNRNPR/BTF3/DUSP11/RBMX/FSCN1/STXBP1/LRPPRC/ALDOA/S100A16/SON/RPL23A/RPS24/RPL38/U2SURP/RPL18A/HNRNPA3/RPL37/DIAPH1/RPL9/PRRC2C/RPL30/SRSF2/THRAP3/CPNE3/PKM/ASCC3/LSM4/RPS8/SRP9/RPL17/PTBP3/SSRP1/DHX9/RPL32/KHSRP/RPL35A/TRA2B/HNRNPD/RPL27/KPNB1/NCL/HMGB1/RPS4X/RPL7L1/HSP90AA1/RPL36A/FAM120A/EIF5B/IPO5/DUSP14/HNRNPL/RPL10A/XRCC6/GLRX3/PURB/IGF2BP2/BZW1/HNRNPA1/EIF3G/SRSF1/NOP56/CAVIN1/RPL22L1/XPO1/RPS17/PA2G4/SND1/HUWE1/RPL8/SNRPD2/G3BP1/CRKL/CCT3/RPS2/HEATR1/FLNA/HSP90B1/HSPA8/HSPD1/RPS18/MYH9/TNPO1/TXN/EIF3D/CS/XRCC5/HNRNPU/GSPT1/RPL5/NOLC1/FDPS/ANXA2/RPSA/TOP2A/AGO2/EIF5A/PRKDC/DDX21/TFRC/LGALS1/YWHAZ/RPS13/RPS3A/MACF1/RPS6/RPL11/HSP90AB1/RPS16/FLNB/ZFP36L2/HMGA1/KRT18/RPL4/KCTD12/FASN/SUB1/RAN/YBX1/MKI67/ENO1/NAP1L1/PLEC/DSP/DYNC1H1/KPNA2/NPM1/AHNAK
GO:0003735	structural constituent of ribosome	86	-0.8606670	-2.196770	1.000000e-10	8.250000e-09	RPL27A/RPS15/RPS5/RPL24/RPS12/RPS26/RPS27/RPL3/RPL14/RPL6/RPL18/RPL29/UBA52/RPL7/RPL15/RPS20/RPS4Y1/RPS21/RPS14/RPL7A/RPS9/RPS25/MRPL3/ENSG00000260342/RPL35/RPL19/RPS7/RPL26/RPL23/RPL13/RPL31/RPS10/RPS27A/RPL10/FAU/RPS15A/RPS23/RPS29/RPL23A/RPS24/RPL38/RPL18A/RPL37/RPL9/RPL30/RPL36A-HNRNPH2/RPL17-C18orf32/RPS8/RPL17/RPL32/RPL35A/RPL27/RPS4X/RPL7L1/RPL36A/RPL10A/RPL22L1/RPS17/MRPL19/RPL8/RPS2/RPS18/RPL5/RPSA/RPS13/RPS3A/RPS6/RPL11/RPS16/RPL4
GO:0003676	nucleic acid binding	93	-0.7451767	-1.938503	4.111033e-07	1.695801e-05	YBX3/RBMS2/EIF4B/DHX15/UHMK1/KARS1/DDX6/HDLBP/ANKRD17/ELAVL1/PABPC1/EIF4A1/SF3B3/HNRNPC/PCBP1/RNPS1/SF3B4/RCAN3/ESRP1/EHD4/DDX39B/EIF3B/SFPQ/RBM25/CNBP/CELF1/SF1/SRSF3/TIAL1/HNRNPDL/EWSR1/SYNCRIP/HNRNPAB/RBM12/GRSF1/RBM3/NARS1/SNRPC/FUS/PABPC4/HNRNPR/RBMX/SON/U2SURP/HNRNPA3/SRSF2/ASCC3/PTBP3/EHD2/DHX9/KHSRP/TRA2B/HNRNPD/NCL/HNRNPL/IGF2BP2/HNRNPA1/EIF3G/SRSF1/PA2G4/SND1/G3BP1/RPS18/AGO2/DDX21/ETS1/YBX1/NPM1/HMGA2
GO:0000166	nucleotide binding	249	-0.5908301	-1.739421	3.559132e-07	1.695801e-05	EEF1A1/EIF4A1/RAC1/PTK2/CCT7/CHD4/WNK1/UBE2D3/ALDH18A1/CSNK2A2/GNAI2/PFKP/ATL3/HIPK3/AAK1/DYNC1LI2/PAPOLA/RAB6A/UBE2N/MYO1E/EHD4/TUBA4A/VDAC2/TARS1/EHD1/SEPTIN2/PYGL/MAP2K1/LARS1/NME2/HDGF/DDX39B/ATP5F1B/SRPK1/DICER1/PAK1/UBA1/MAPK6/PSMC3/KIF5B/CDK6/STK25/SMARCA4/RAC2/ACACA/GUK1/HINT1/MAPKAPK3/HSPA9/UBE2G1/EPHA2/SEPTIN11/TCP1/ACTB/CCT6A/MYO10/EPRS1/HK1/RRAGA/RAB18/SMG1/NARS1/NRAS/GARS1/VDAC3/AK4/CCT4/UBE2K/MAP2K3/IARS1/RRM1/HSPH1/PAK2/ACSL4/IGF1R/GSK3B/PFKFB3/NAXE/ACTR3/DGKA/THRAP3/ATP2B4/PKM/ASCC3/RAB31/EHD2/OLA1/DHX9/HSP90AA1/ABL2/EIF5B/ABCE1/TTL/XRCC6/ACTR2/EIF2S3/SEPTIN7/IARS2/GAPDH/POMK/TAOK1/TGFBR2/MFN2/CCT5/G3BP1/CCT3/HSP90B1/HSPA8/HSPD1/MYH9/XRCC5/HNRNPU/GSPT1/NOLC1/BMPR2/TOP2A/TUBB4B/PRKDC/DDX21/TUBB6/PAICS/HSP90AB1/TUBB/TUBA1C/RAN/MKI67/PGK1/DYNC1H1/ACLY/ATP13A3/TUBA1B/EGFR/NT5E
GO:0045296	cadherin binding	148	-0.6507749	-1.821781	2.079010e-06	6.860734e-05	EEF2/PTPN1/HSPA5/PRDX1/YKT6/BAG3/VCL/VASP/PFKP/PICALM/RPL24/CAST/PCBP1/RPS26/EHD4/RPL14/RPL6/EHD1/SERBP1/SEPTIN2/PTPN11/RPL29/MPRIP/RPL15/KIF5B/PPFIBP1/LRRFIP1/PRDX6/RPL7A/YWHAE/RSL1D1/EPHA2/YWHAB/RACK1/TJP1/RTN4/CLIC1/CAPZA1/LRRC59/PFN1/CKAP5/NUDC/FSCN1/ALDOA/TLN1/RPL23A/PAK2/ATIC/EEF1G/PKM/CBL/OLA1/PKP2/LIMA1/EIF2S3/BZW1/SEPTIN7/NOP56/ASAP1/SND1/ITGB1/IQGAP1/FXYD5/CRKL/RPS2/FLNA/HSPA8/MYH9/BMPR2/FMNL2/SNX5/TAGLN2/YWHAZ/MACF1/PAICS/ANLN/PKP1/HSP90AB1/FLNB/CDH13/FASN/RAN/ENO1/PLEC/SFN/EGFR/ITGA6/LDHA/AHNAK/NDRG1
GO:0005524	ATP binding	187	-0.5907620	-1.684760	1.591543e-05	4.376743e-04	EIF4A1/PTK2/CCT7/CHD4/WNK1/UBE2D3/ALDH18A1/CSNK2A2/PFKP/HIPK3/AAK1/DYNC1LI2/PAPOLA/UBE2N/MYO1E/EHD4/TARS1/EHD1/PYGL/MAP2K1/LARS1/NME2/DDX39B/ATP5F1B/SRPK1/DICER1/PAK1/UBA1/MAPK6/PSMC3/KIF5B/CDK6/STK25/SMARCA4/ACACA/GUK1/MAPKAPK3/HSPA9/UBE2G1/EPHA2/TCP1/ACTB/CCT6A/MYO10/EIF4G1/EPRS1/HK1/SMG1/NARS1/GARS1/AK4/CCT4/TOP1/UBE2K/MAP2K3/IARS1/RRM1/HSPH1/PAK2/ACSL4/IGF1R/GSK3B/PFKFB3/ACTR3/DGKA/THRAP3/ATP2B4/PKM/ASCC3/EHD2/OLA1/DHX9/HSP90AA1/ABL2/ABCE1/TTL/XRCC6/ACTR2/IARS2/POMK/TAOK1/TGFBR2/CCT5/G3BP1/CCT3/HSP90B1/HSPA8/HSPD1/MYH9/XRCC5/HNRNPU/NOLC1/BMPR2/TOP2A/PRKDC/DDX21/PAICS/HSP90AB1/MKI67/PGK1/DYNC1H1/ACLY/ATP13A3/EGFR
GO:0008233	peptidase activity	53	0.8202711	1.853281	6.719650e-05	1.583918e-03	CFB/ENSG00000244255/CTSD/ENSG00000250644/CTSH/PRSS22/CTSA/TMPRSS4/CAPN13/MMP2/TMPRSS2/CPD/PLAU/MMP14/CTSC/PRSS8/ST14/NCSTN/ECE1/PRSS23/TPP1/BMP1/FAP/ADAM9/CTSB
GO:0004252	serine-type endopeptidase activity	23	0.9147072	1.808740	1.009953e-04	2.083028e-03	CFB/ENSG00000244255/CTSH/PRSS22/TMPRSS4/MMP2/TMPRSS2/PLAU/MMP14/CTSC/PRSS8/RHBDD2/ST14/PRSS23/TPP1/BMP1/FAP
GO:0003697	single-stranded DNA binding	18	-0.9063236	-1.775461	1.653301e-04	3.031052e-03	PCBP1/CNBP/NUCKS1/HNRNPDL/TOP1/LRPPRC/DHX9/HMGB1/PURB/HNRNPA1/HSPD1/HNRNPU/ERCC1/SUB1/YBX1
GO:0003725	double-stranded RNA binding	23	-0.8600451	-1.774193	2.647042e-04	4.367619e-03	DICER1/VIM/LRRFIP1/ILF3/CLTC/DHX9/ACTN1/HSPD1/HNRNPU/AGO2/TUBB4B/DDX21/TFRC/HSP90AB1/TUBA1B/MSN
GO:0019843	rRNA binding	15	-0.9208665	-1.708700	3.864463e-04	5.796695e-03	RPS4Y1/RPS9/RPL23A/RPL37/RPL9/RPS4X/CAVIN1/RPL8/RPS18/RPL5/DDX21/RPL11/NPM1
GO:0008236	serine-type peptidase activity	16	0.9477398	1.766899	5.449999e-04	7.493749e-03	CFB/ENSG00000244255/PRSS22/TMPRSS4/TMPRSS2/PLAU/PRSS8/ST14/PRSS23/TPP1/FAP
GO:0048027	mRNA 5’-UTR binding	13	-0.9179294	-1.637402	1.025865e-03	1.302059e-02	RPS14/RSL1D1/SYNCRIP/RPS7/RPL26/NCL/IGF2BP2/CCT5/RPL5/RPS13/RPS3A
GO:0140662	ATP-dependent protein folding chaperone	15	-0.8887793	-1.649161	1.470854e-03	1.733507e-02	HSPA5/CCT7/HSPA9/TCP1/CCT6A/CCT4/HSPH1/HSP90AA1/CCT5/CCT3/HSP90B1/HSPA8/HSPD1/HSP90AB1
GO:0003729	mRNA binding	70	-0.6464445	-1.623975	2.129410e-03	2.342352e-02	RPS3/STAU1/YTHDF3/DDX6/HDLBP/ELAVL1/EIF4G3/PABPC1/EIF4A1/RPS5/SRRM2/RPL24/PCBP1/ESRP1/RPS26/STRAP/RPL7/RBM25/CNBP/CELF1/SF1/TPR/SYNCRIP/ZC3H11A/RPL35/HNRNPAB/EIF4G1/GRSF1/EIF3A/SNRPC/PABPC4/HNRNPR/RBMX/HNRNPA3/PKM/PTBP3/DHX9/KHSRP/TRA2B/HNRNPD/HNRNPL/PURB/IGF2BP2/SRSF1/G3BP1/RPS2/AGO2/RPS13/ZFP36L2/YBX1/MYC
GO:0005200	structural constituent of cytoskeleton	36	-0.7581917	-1.698192	2.347727e-03	2.421093e-02	VIM/ACTB/ARPC5/TLN1/ACTR3/KRT6B/ACTR2/TUBB4B/TUBB6/TUBB/TUBA1C/PLEC/DSP/TUBA1B/MSN/KRT6A/KRT5/KRT14
GO:0005125	cytokine activity	28	0.8252723	1.681948	3.544953e-03	3.440690e-02	CXCL6/CXCL5/GDF15/CXCL16/CXCL1/CX3CL1/TNFSF10/TGFB2/CXCL3/CXCL8/GRN/TNFSF13/TNFSF12-TNFSF13/IL1B/IL32/CCL20/CSF3/BMP1/IL1RN
GO:0030414	peptidase inhibitor activity	21	0.8721642	1.707911	4.477193e-03	3.742716e-02	SERPINA3/WFDC2/SLPI/SERPINB3/PI3/TIMP2/SPINT1/CSTB/SERPINB7/SERPINB1/APLP2
GO:0004175	endopeptidase activity	12	0.9380566	1.660473	4.925694e-03	3.742716e-02	CTSD/CTSH/MMP2/MMP14/NCSTN/ECE1/TPP1/TMEM59/FAP/CTSB
GO:0003690	double-stranded DNA binding	20	-0.8247057	-1.647610	4.760614e-03	3.742716e-02	HMGB3/HDGF/NUCKS1/HNRNPDL/JUN/TOP1/DHX9/HMGB1/XRCC6/PURB/XRCC5/HNRNPU/PRKDC/SUB1/YBX1/TP63/EGFR
GO:0016887	ATP hydrolysis activity	48	-0.6877584	-1.616073	4.990288e-03	3.742716e-02	PFN2/DHX15/DDX6/ATP5F1A/YME1L1/HSPA5/EIF4A1/CCT7/CHD4/MYO1E/DDX39B/PSMC3/KIF5B/SMARCA4/HSPA9/TCP1/CCT6A/ATP5F1C/CCT4/ATP2B4/ASCC3/OLA1/DHX9/HSP90AA1/CCT5/G3BP1/CCT3/HSP90B1/HSPA8/HSPD1/DDX21/HSP90AB1/ATP13A3
GO:0003779	actin binding	87	-0.6056989	-1.553728	4.112271e-03	3.742716e-02	VCL/PTK2/ENC1/ARPC1A/CAPZA2/TMSB10/VASP/PANX1/MYO1E/HDGF/MPRIP/YWHAH/CNN3/MYO10/MAP1B/ARPC5/CAPZA1/PFN1/FSCN1/ALDOA/TLN1/DIAPH1/GMFB/ACTR3/CAP1/CORO1C/TMOD3/TNS4/LIMA1/ACTR2/ACTN1/PPP1R18/SSH1/ITGB1/FXYD5/FLNA/MYH9/PLS3/TPM3/HNRNPU/FMNL2/COTL1/MACF1/ANLN/FLNB/PLEC/DST/MSN

CC

## Picking joint bandwidth of 0.146

ID	Description	setSize	enrichmentScore	NES	pvalue	p.adjust	geneName
GO:1990904	ribonucleoprotein complex	146	-0.8599946	-2.376753	1.000000e-10	6.633333e-09	ELAVL1/RPL36/EEF2/PABPC1/RPL27A/RPS15/RPS5/HNRNPC/RPL24/PCBP1/RPS12/HNRNPUL1/ESRP1/RPS26/RPS27/RPL3/RPL14/RPL6/RPL18/RPL29/UBA52/RPL7/RPL15/RPS20/CELF1/VIM/RPS4Y1/RPS21/NSA2/RPS14/RPL7A/RPS9/RPS25/MRPL3/HNRNPDL/ENSG00000260342/SYNCRIP/ACTB/RACK1/RPL35/HNRNPAB/RPL19/ILF3/RBM12/RPS7/GRSF1/RPL26/EPRS1/PRPF8/RPL23/RPL13/RPL31/RPS10/SNRPC/PABPC4/RPS27A/RPL10/FAU/RPS15A/RPS23/RPS29/HNRNPR/RBMX/LRPPRC/RPL23A/RPS24/RPL38/RPL18A/HNRNPA3/RPL37/RPL9/RPL30/RPL17-C18orf32/LSM4/RPS8/SRP9/RPL17/DHX9/RPL32/RPL35A/HNRNPD/RPL27/NCL/RPS4X/RPL7L1/CBX5/RPL36A/HNRNPL/RPL10A/HNRNPA1/GAPDH/NOP56/RPL22L1/XPO1/RPS17/PA2G4/MRPL19/IQGAP1/RPL8/SNRPD2/G3BP1/RPS2/HEATR1/HSPA8/RPS18/XRCC5/HNRNPU/RPL5/RPSA/TOP2A/AGO2/RPS13/RPS3A/RPS6/RPL11/RPS16/ZFP36L2/RPL4/YBX1/NPM1
GO:0005840	ribosome	91	-0.8545429	-2.223049	1.000000e-10	6.633333e-09	RPL27A/RPS15/RPS5/RPL24/RPS12/CANX/RPS26/RPS27/RPL3/RPL14/RPL6/RPL18/RPL29/UBA52/RPL7/RPL15/RPS20/RPS4Y1/RPS21/RPS14/SF1/RPL7A/RPS9/RPS25/MRPL3/ENSG00000260342/RACK1/RPL35/RPL19/RPS7/RPL26/RPL23/RPL13/RPL31/RPS10/RPS27A/RPL10/FAU/RPS15A/RPS23/RPS29/RPL23A/RPS24/RPL38/RPL18A/RPL37/RPL9/RPL30/RPL36A-HNRNPH2/RPL17-C18orf32/RPS8/RPL17/RPL32/RPL35A/RPL27/RPS4X/RPL7L1/RPL36A/RPL10A/RPL22L1/RPS17/MRPL19/RPL8/RPS2/RPS18/RPL5/RPSA/RPS13/RPS3A/RPS6/RPL11/RPS16/RPL4
GO:0022626	cytosolic ribosome	74	-0.8610504	-2.162113	1.000000e-10	6.633333e-09	RPL36/RPL27A/RPS15/RPS5/RPL24/RPS12/RPS27/RPL3/RPL14/RPL6/RPL18/RPL29/UBA52/RPL7/RPL15/RPS20/RPS21/RPS14/RPL7A/RPS9/RPS25/RPL35/RPL19/RPS7/RPL26/RPL23/RPL13/RPL31/RPS10/RPS27A/RPL10/FAU/RPS15A/RPS23/RPL23A/RPS24/RPL38/RPL18A/RPL37/RPL9/RPL30/RPS8/RPL17/RPL32/RPL35A/RPL27/RPS4X/RPL36A/RPL10A/RPS17/RPL8/RPS2/RPS18/RPL5/RPSA/RPS13/RPS3A/RPS6/RPL11/RPS16/RPL4
GO:0005615	extracellular space	219	0.7298123	1.941035	1.758343e-10	8.747757e-09	SERPINA3/LCN2/CEACAM6/WFDC2/CFB/PIGR/BPIFA1/C3/MUC4/IGFBP3/CXCL6/RARRES1/SLPI/BPIFB1/CXCL5/GDF15/CTSD/CP/AGR2/CTSH/MUC1/PSAP/PRSS22/CXCL17/SERPINB3/SCGB1A1/TNFAIP2/PI3/HSPB1/CXCL16/GABBR1/FN1/LRRN1/TF/TACSTD2/CXCL1/IGFBP2/FBLN1/TMPRSS4/GSN/ICAM1/TIMP2/SPINT1/CX3CL1/MMP2/CSTB/MUC5B/COL1A1/GOLM1/CPD/ASAH1/TNFSF10/STOM/TINAGL1/TGFB2/VMO1/CXCL3/CXCL8/MFGE8/HSPG2/GRN/SERPINB7/LGALS3BP/VCAN/S100A9/TNFSF13/B2M/TNFSF12-TNFSF13/APOL1/MTUS1/GPRC5B/PLAU/MMP14/IL1B/CCN2/ITM2B/CTSC/IL32/SERPINF1/PRSS8/SERPINB1/PXDN/ST14/CCL20/CSF3/XDH/UBB/QSOX1/GLB1/MAN2B1/BMP1/TGFBI/SPARC/CD63/CREG1/LGALS8/IL1RN/FAP/IGFBP7/ADAM9/SERPINH1/S100A8/CTSB
GO:0005576	extracellular region	296	0.6674799	1.821701	1.781770e-08	7.091443e-07	SERPINA3/LCN2/WFDC2/CFB/ENSG00000244255/PIGR/BPIFA1/C3/MUC4/IGFBP3/CXCL6/SLPI/BPIFB1/S100P/CEACAM5/CXCL5/MUC20/GDF15/SAA2/SAA1/CTSD/PSCA/CP/AGR2/CTSH/MUC1/PSAP/PRSS22/CXCL17/SERPINB3/SCGB1A1/PI3/CXCL16/GABBR1/FN1/TF/CXCL1/IGFBP2/FBLN1/CTSA/TMPRSS4/GSN/NTN1/TIMP2/SPINT1/MDK/CX3CL1/MMP2/TMPRSS2/CSTB/MUC5B/COL1A1/ASAH1/TNFSF10/TINAGL1/TGFB2/IL1R1/VMO1/CXCL3/NOTCH3/CXCL8/MFGE8/CEACAM7/HSPG2/GRN/NTN4/FTH1/LGALS3BP/VCAN/S100A9/TNFSF13/B2M/APOL1/PLAU/IL1B/NINJ1/CCN2/ITM2B/CTSC/IL32/SERPINF1/PRSS8/SERPINB1/PXDN/ST14/ADGRG1/CCL20/CSF3/PRSS23/XDH/CDH1/QSOX1/P4HB/GLB1/SDC4/PDXK/CCN1/EMC10/MAN2B1/BMP1/TGFBI/SPARC/CD63/CREG1/PLBD2/IL1RN/FAP/HEG1/IGFBP7/ADAM9/S100A8/CTSB/GNS
GO:0022625	cytosolic large ribosomal subunit	46	-0.8537428	-1.969380	2.061148e-07	6.836140e-06	RPL36/RPL27A/RPL24/RPL3/RPL14/RPL6/RPL18/RPL29/UBA52/RPL7/RPL15/RPL7A/RPL35/RPL19/RPL26/RPL23/RPL13/RPL31/RPL10/RPL23A/RPL38/RPL18A/RPL37/RPL9/RPL30/RPL17/RPL32/RPL35A/RPL27/RPL7L1/RPL36A/RPL10A/RPL8/RPL5/RPL11/RPL4
GO:0022627	cytosolic small ribosomal subunit	36	-0.8761517	-1.937129	3.383664e-07	9.619274e-06	RPS15/RPS5/RPS12/RPS26/RPS27/UBA52/RPS20/RPS4Y1/RPS21/RPS14/RPS9/RPS25/RACK1/RPS7/RPS10/RPS27A/FAU/RPS15A/RPS23/RPS29/RPS24/RPS8/RPS4X/RPS17/RPS2/RPS18/RPSA/RPS13/RPS3A/RPS6/RPS16
GO:0005730	nucleolus	144	-0.6456737	-1.782424	1.869444e-06	4.650241e-05	EEF1A1/EIF4A1/TTC3/PPP1CB/ENC1/PHB2/SF3B3/MORF4L2/EIF3L/MOB1A/RPL3/RPL18/RPL7/RPS20/SMARCA4/NUCKS1/OSBP/NSA2/RPS14/RPL7A/HSPA9/RSL1D1/RPS9/RPS25/EWSR1/ZFP91/TCP1/ZBED6/RACK1/RPL35/MYO10/RPL19/ILF3/ITPR3/RPS7/RPL26/SUMO1/RPL23/RPL13/EIF3A/BNIP2/RPS10/RPS27A/TOP1/CKAP5/RBMX/S100A16/RPL23A/SPIN1/MACROH2A1/NAA50/CPNE3/RPL17/STON2/NF1/SSRP1/OLA1/DHX9/PAFAH1B2/RPL27/NCL/RPL7L1/CBX5/IPO5/XRCC6/ITGB4/NOP56/XPO1/PA2G4/LRRC8C/HEATR1/FLNA/XPO6/HSPA8/ARNTL2/KLF6/XRCC5/SKP2/RPL5/NOLC1/CCND2/TOP2A/PRKDC/DDX21/RPS13/RPS3A/RPS6/RPL11/KRT18/RPL4/SUB1/RAN/MKI67/MYC/BNC1/PHLDA1/NPM1/SCD
GO:0005681	spliceosomal complex	36	-0.8366763	-1.849851	6.315540e-06	1.396436e-04	PABPC1/API5/SF3B3/HNRNPC/SRRM2/SF3B2/SF3B4/DDX39B/SRRM1/SF1/HNRNPDL/SYNCRIP/PRPF8/RBM3/SNRPC/HNRNPR/RBMX/HNRNPA3/SRSF2/LSM4/TRA2B/NCL/HNRNPA1/SRSF1/SNRPD2/HSPA8/HNRNPU
GO:0005925	focal adhesion	202	-0.5679448	-1.627115	2.726624e-05	5.425982e-04	RPL3/RPL6/RPL18/MAP2K1/MPRIP/PAK1/RPL7/CAV2/CNN3/RAC2/VIM/PPFIBP1/RPS14/RPL7A/HSPA9/YWHAE/RPS9/EPHA2/PPIA/YWHAB/ACTB/GDI2/RPL19/RPS7/FERMT1/RPL23/ANXA1/RPL31/ARPC5/CLTC/RPS10/PFN1/RPS29/SDCBP/TLN1/RPL38/RPL9/RPL30/ACTR3/CD99/CPNE3/RPS8/YWHAQ/CBL/CLASP1/RPL27/ITGA2/CAP1/PXN/CORO1C/MCAM/RPS4X/TNS4/LPP/CD9/FAT1/RPL10A/LIMA1/ACTR2/ACTN1/ITGB4/DOCK7/RPS17/ITGB1/IQGAP1/RPL8/G3BP1/RPS2/FLNA/HSP90B1/HSPA8/RPS18/ITGA5/MYH9/PVR/RPL5/BCAR3/YWHAZ/RPS13/RPS3A/TNC/RPS16/FLNB/CDH13/HMGA1/RPL4/PLEC/DST/CD44/NPM1/MSN/CAV1/EGFR/ITGA6/AHNAK
GO:0005764	lysosome	83	0.7576820	1.785678	3.685353e-05	6.667138e-04	CTSD/CTSH/PSAP/CTSA/CYB561A3/TSPAN1/ASAH1/TINAGL1/LITAF/GRN/CD74/MFSD1/INSR/PLD3/IL1B/CTSC/GABARAP/SERPINB1/ACP2/VAMP8/DRAM1/NCSTN/SLC11A2/GLB1/HGSNAT/TPP1/SQSTM1/TMEM59/HEXA/MAN2B1/CD63/TMEM165/PLBD2/TRIM29/CTSB/GNS/TMEM106B/LAMP1/IFITM3/CALR/ATP6V1A/TPCN1/CD164/LAMP2
GO:0042788	polysomal ribosome	25	-0.8732270	-1.812053	9.128135e-05	1.513749e-03	LARP1/RPL36/RPL24/RPS26/RPL6/RPL18/RPS21/RPL7A/RPL19/RPL31/RPS23/RPS29/BTF3/RPL38/RPL18A/RPL30/DHX9/RPL32/RPL36A/RPL10A/RPL8/RPL11
GO:0015935	small ribosomal subunit	23	-0.8799346	-1.794934	1.333417e-04	1.895357e-03	RPS15/RPS5/RPS26/RPS20/RPS21/RPS9/RPS25/RACK1/RPS27A/FAU/RPS23/RPS29/RPS24/RPS4X/RPS2/RPS18/RPSA/RPS6/RPS16/NPM1
GO:0005874	microtubule	54	-0.7315098	-1.731848	1.314481e-04	1.895357e-03	MAP1LC3B/CCT7/DYNC1I2/DYNLL1/DYNC1LI2/TUBA4A/MAP4/KIF5B/TCP1/CAMSAP2/CCT6A/STMN1/MAP1B/EIF3A/CCT4/NUDC/LRPPRC/HSPH1/FEZ1/CEP170/CLASP1/CKAP2/CCT5/IQGAP1/CCT3/NAV1/TUBB4B/TUBB6/MACF1/TUBB/TUBA1C/DST/DYNC1H1/TUBA1B/NDRG1
GO:0005694	chromosome	42	-0.7812515	-1.767639	1.499906e-04	1.989875e-03	HMGB3/H3-3B/SEPTIN2/SRPK1/PAK1/NUCKS1/RAD21/EP300/RSL1D1/TPR/BUB3/TOP1/CKAP5/PDS5A/ZBTB38/MACROH2A1/SSRP1/CLASP1/NCL/HMGB1/CBX5/XRCC6/SEPTIN7/XRCC5/HNRNPU/DDX21/HMGA1/MKI67
GO:0005794	Golgi apparatus	224	0.5950449	1.586896	1.611959e-04	2.004874e-03	SLPI/GDF15/HLA-B/STEAP4/B4GALT5/ELF3/ID1/COL1A1/GOLM1/ST6GALNAC1/LITAF/GRN/HLA-C/GCNT3/CD74/FUT3/PMEPA1/B2M/HLA-A/MTUS1/TRIM22/FUT2/PLD3/RHOBTB3/ITM2B/CTSC/GABARAP/GABARAPL1/RHBDD2/SLC35C1/NCSTN/SERINC3/NEDD9/GRINA/MGAT4B/ARHGAP32/CDH1/QSOX1/GLB1/TPP1/TMEM59/ERGIC1/RND3/RAB11B/BMP1/SREBF2/CHPF/LYN/CIB1/GBP3/GDI1/LTBR/TMEM132A/YIPF3/TMEM165/GALNT10/TMEM30A/RAB1B/KIAA0319L/ATP1A1/FAM114A1/ERGIC3/ATF6B/AP1B1/DHCR24/LEPROT/GALNT5/GOLM2/CALR/IFNGR2/EXT1/LAPTM4A/GALNT14/PACS1/TM9SF2/NUCB1/COPG1/STK24/KLF5/B4GALT1/AP1G1/NFE2L2/TGOLN2/DNM2/ZDHHC7/CLINT1/TNFRSF1A/SLC35A4/GALNT2
GO:0015630	microtubule cytoskeleton	35	-0.7816922	-1.717326	3.430701e-04	3.911592e-03	DYNLL1/TUBA4A/SEPTIN2/SEPTIN11/CKAP5/EHD2/SEPTIN7/GAPDH/CKAP2/TAOK1/MFN2/IQGAP1/NAV1/TUBB4B/TUBB6/TUBB/TUBA1C/DST/TUBA1B/NDRG1
GO:0000139	Golgi membrane	121	0.6655981	1.652257	3.538123e-04	3.911592e-03	HLA-B/STEAP4/B4GALT5/ATP6AP1/ST6GALNAC1/NOTCH3/LITAF/TAPBP/HLA-C/GCNT3/CD74/FUT3/PMEPA1/B2M/HLA-A/FUT2/PLD3/ITM2B/GABARAP/RHBDD2/SLC35C1/NCSTN/SERINC3/MGAT4B/ARHGAP32/QSOX1/TMEM59/ERGIC1/RND3/SREBF2/CHPF/GBP3/TMEM132A/TMEM165/ATP6V0C/GALNT10/RAB1B/KIAA0319L/ERGIC3/AP1B1/DHCR24/LEPROT/GALNT5/IFNGR2/ATP6V1A/EXT1/GALNT14/RNASEK/COPG1/STK24/B4GALT1/AP1G1/DNM2/ZDHHC7/TNFRSF1A/SLC35A4/GALNT2/SCARB2/AP3D1/GJA1/APH1A/ATP6AP2
GO:0005856	cytoskeleton	227	-0.5208679	-1.495843	3.757794e-04	3.935795e-03	RAC1/VCL/PTK2/MAP1LC3B/ENC1/CHD4/ARPC1A/CALM2/TMSB10/DYNC1I2/VASP/GNAI2/DYNLL1/DYNC1LI2/AJUBA/MYO1E/TUBA4A/MAP4/SEPTIN2/MAP2K1/MPRIP/PAK1/ARHGDIB/KIF5B/CDK6/RAD21/CNN3/RAC2/FGD6/VIM/LRRFIP1/HINT1/CDC27/BASP1/SEPTIN11/TPR/TCP1/ACTB/CAMSAP2/STMN1/CALM3/MYO10/RPS7/MAP1B/FERMT1/CALM1/ARPC5/CLTC/CAPZA1/UBR4/PFN1/CCT4/CKAP5/NUDC/FSCN1/STXBP1/LRPPRC/SDCBP/TLN1/DIAPH1/USP9X/FRMD6/ACTR3/FEZ1/DHX9/CEP170/CLASP1/PXN/CORO1C/TMOD3/TNS4/ABL2/LIMA1/IGF2BP2/ACTR2/SEPTIN7/ACTN1/PPP1R18/SSH1/GAPDH/CKAP2/CCT5/CCT3/FLNA/MYH9/NAV1/TPM3/HNRNPU/TUBB4B/COTL1/TAGLN2/PTP4A1/TUBB6/MACF1/ANLN/FLNB/KRT18/TUBB/PTPN14/TUBA1C/PLEC/CCNB1/DSP/DST/DYNC1H1/TUBA1B/NPM1/MSN/NDRG1/KRT14
GO:0032991	protein-containing complex	147	-0.5573865	-1.540989	9.864377e-04	9.815055e-03	PTPN1/HSPA5/VCL/CHD4/WNK1/CALM2/USP10/PHB2/STIP1/HNRNPC/UGGT1/EIF3L/UBE2N/PANX1/H3-3B/CANX/PSMD11/MYO1E/PSMD3/RPL3/HIGD1A/PTPN11/PAK1/MAPK6/CAV2/SMARCA4/EP300/PPIA/ACTB/STRN/EIF3M/HTT/CALM3/TJP1/RPS7/SDC1/CALM1/RPL23/CLTC/PRELID1/EIF3A/UBQLN1/RPL10/CKAP5/RBMX/STXBP1/HSPH1/SMARCC1/SLC7A1/ATP2B4/LSM4/YWHAQ/DHX9/TRA2B/PRDX3/KPNB1/HSP90AA1/CBX5/UBE2V1/CD9/XRCC6/CAVIN1/XPO1/ARHGAP29/CRKL/XPO6/HSP90B1/HSPD1/MYH9/SET/XRCC5/HNRNPU/RPL5/TOP2A/PRKDC/PTGES3/RPL11/HSP90AB1/PTGS2/TUBB/RAN/MYC/TP63/NPM1/CAV1/EGFR
GO:0016324	apical plasma membrane	57	0.7427206	1.659112	1.790120e-03	1.696352e-02	CEACAM6/CEACAM5/MUC20/SLC6A14/DUOX2/MUC1/SLC44A4/ATP1B1/SLC26A4/FN1/SCNN1A/TF/IGFBP2/CLDN4/SLC34A2/CEACAM7/SLC15A2/PROM2/SLC11A2/SLC9A3R1/CIB1/TMEM30A/ERBB2/CTSB/ATP1A1/OSMR/MAL2/ATP6V1A/JAG1/PRKAA1/AHCYL1/CLDN1
GO:0071013	catalytic step 2 spliceosome	21	-0.8243806	-1.655088	1.876547e-03	1.697422e-02	PABPC1/SF3B3/HNRNPC/SRRM2/SF3B2/SRRM1/SYNCRIP/PRPF8/HNRNPR/RBMX/HNRNPA3/HNRNPA1/SRSF1/SNRPD2/HNRNPU
GO:0031965	nuclear membrane	39	-0.7407478	-1.655065	2.450356e-03	2.120090e-02	ANKRD17/PRNP/ANXA4/EI24/CCNI/RANBP2/PAK1/LYPLA1/TPR/CLCA2/SUMO1/NUP50/OSBPL8/NUTF2/MLX/CLIC1/SDCBP/SPIN1/KPNB1/GAPDH/ITGB4/XPO1/CCND2/LPIN1/EGFR
GO:0005765	lysosomal membrane	71	0.6920416	1.599132	3.018416e-03	2.502770e-02	CTSD/CP/PSAP/CYB561A3/TSPAN1/ATP6AP1/LITAF/GRN/CD74/MFSD1/PLD3/ACP2/VAMP8/DRAM1/NCSTN/SLC11A2/ECE1/HGSNAT/SLC44A2/TMEM59/LYN/CD63/TMEM165/ATP6V0C/TMEM106B/LAMP1/AP1B1/IFITM3/ATP6V1A/LAPTM4A/TPCN1/RNASEK/CD164/AP1G1/ATP6V0E1/LAMP2
GO:0000776	kinetochore	23	-0.8078084	-1.647807	3.508890e-03	2.767522e-02	DYNLL1/DYNC1LI2/SEPTIN2/SMARCA4/TPR/ACTB/BUB3/CKAP5/SMARCC1/CLASP1/CBX5/SEPTIN7/XPO1/HNRNPU/SUMO3
GO:0005815	microtubule organizing center	53	-0.6833060	-1.613573	3.615858e-03	2.767522e-02	PTK2/CHD4/CALM2/GNAI2/DYNLL1/AJUBA/EHBP1/MAP4/MAP2K1/PAK1/CDK6/VIM/TCP1/CALM3/RPS7/CALM1/CCT4/CKAP5/DIAPH1/FEZ1/DHX9/CEP170/CLASP1/CCT5/HNRNPU/KRT18/CCNB1/NPM1/NDRG1
GO:0043202	lysosomal lumen	29	0.8214436	1.679620	3.775464e-03	2.782657e-02	CTSD/PSAP/CTSA/ASAH1/HSPG2/CD74/VCAN/PLD3/ACP2/CSF3/GLB1/SDC4/HGSNAT/TPP1/HEXA/MAN2B1/PLBD2/GNS/LAMP2/IDS/SCARB2/AGRN
GO:0035577	azurophil granule membrane	24	0.8354661	1.670305	4.865691e-03	3.338871e-02	CEACAM6/PIGR/PSAP/STOM/VAMP8/NCSTN/CD63/ATP6V0C/TMEM30A/LAMP1/B4GALT1/LAMP2
GO:0062023	collagen-containing extracellular matrix	67	0.6914547	1.577152	4.798476e-03	3.338871e-02	SERPINA3/SLPI/GDF15/CTSD/CTSH/PSAP/FN1/FBLN1/ICAM1/TIMP2/MDK/MMP2/CSTB/COL1A1/TINAGL1/TGFB2/MFGE8/HSPG2/LGALS3BP/VCAN/S100A9/CCN2/CTSC/SERPINF1/SERPINB1/PXDN/ANXA11/CCN1/TGFBI/SPARC/IGFBP7/SERPINH1/S100A8/CTSB
GO:0031410	cytoplasmic vesicle	138	0.5923770	1.490639	5.594158e-03	3.710791e-02	LCN2/GPRC5A/SERPINB3/SCNN1A/TF/RAB11FIP1/IGFBP2/ATP6AP1/STOM/MFGE8/GPNMB/PIGT/TP53INP2/GPRC5B/MMP14/RHOBTB3/GABARAP/GABARAPL1/PROM2/VAMP8/NCSTN/SLC11A2/PACSIN2/GDE1/SQSTM1/RND3/GIPC1/RAB11B/SREBF2/GBP3/LGALS8/ATP6V0C/TMEM30A/ERBB2/KIAA0319L/SYNGR2/CDK16/TBC1D2/AP1B1/CALR/IFNGR2/ATP6V1A/RNASEK/COPG1/CD164/PAM/CD46/AP1G1/DNM2/LAMP2/BCL2L1/MYO1C/CLINT1

MetaCore

Metacore

Metacore is a commercial software that performs gene-set based analysis using a manually curated, proprietary database. It takes as input a subset of genes passing certain p-value/fold-change thresholds (i.e., differentially expressed genes). It is recommended for the analysis of human, mouse, and rat data. It is best used to gain drug/disease-related information and comprehensive pathway map figures.

Registration

Using MetaCore requires an account. One can be obtained by emailing sequencing@fgcz.ethz.ch.

How to use Metacore: quick start

Right Click and Save File to Download Expression File for MetaCore (p <= 0.01)
Go to the MetaCore website
Upload the Expression File to MetaCore, selecting three columns: Gene ID, log ratio, and p-value
Select Pathway Maps from the One-click Analysis tab.

Important notes

When uploading the data into MetaCore, select three columns:

A gene identifier, pick one of:
- Ensembl Gene IDs – ENSEMBL IDs
- Entrez Gene IDs – EntrezGene (LocusLink) IDs
Log fold changes of the genes – log ratio
P values

You must ensure that the data type drop-down menu above each column is correct.

Select ---ignore--- from the drop down for all other columns in the table that are not to be used.

Please refer to the FGCZ Wiki for a more comprehensive guide to using MetaCore.

MetaCore has numerous tutorials online, including a useful YouTube page: https://www.youtube.com/watch?v=_J_ViIw9wIM&list=PL2tDZtDsVy5xqUibWp-mfl9xuZP4Bhi-v&index=2

MetaCore Compatibility

MetaCore currently has full pathway support for three core species: Human; mouse, and; rat. Additionally, it can use Entrez IDs as orthologs to analyse a series of non-core species:

Cow
Chimpanzee
Dog
Zebra fish
Chicken
Fly
Mosquito
Worm
Arabidopsis
Rice
Blast of rice (fungal species)
Macaca mulatta
Mold
Bread mold
Candida sphaerica
Fission yeast
Baker’s yeast

Technical bias

We define 4 gene sets

high GC: the 5% of the genes with the highest GC content
low GC: the 5% of the genes with the lowest GC content
long genes: the 5% of the genes with the biggest length
short genes: the 5% of the genes with the smalles length

And we test if the up- or down-regulated genes are associated with one of those gene sets. If there is a significant association, some of the significant genes are potentially false positives due to a technical bias.

Tests where the association p-value is below 0.001 are highlighted in red. The column “overlapping/total genes” shows the number of overlapping genes and the total number of genes in that category.

Association test: 241 up-regulated and 154 down-regulated genes
	overlapping/total genes	odds ratio	p-value
low GC – Up-regulation	6/92	0.445	9.88e-01
low GC – Down-regulation	15/92	2.234	8.26e-03
high GC – Up-regulation	22/92	2.173	2.91e-03
high GC – Down-regulation	6/92	0.748	8.05e-01
short genes – Up-regulation	15/92	1.300	2.23e-01
short genes – Down-regulation	5/92	0.611	9.02e-01
long genes – Up-regulation	10/92	0.794	7.95e-01
long genes – Down-regulation	19/92	3.080	1.36e-04

Input dataset

SessionInfo

## ezRun tag: c374ec67050e41361e171788c4b5e55b055634c9 
## ezRun github link: https://github.com/uzh/ezRun/tree/c374ec67050e41361e171788c4b5e55b055634c9 
##  
## R version 4.3.2 (2023-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 10 (buster)
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so;  LAPACK version 3.8.0
## 
## 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       
## 
## time zone: Europe/Zurich
## tzcode source: system (glibc)
## 
## attached base packages:
##  [1] parallel  tools     stats4    stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] gplots_3.1.3                annotate_1.80.0            
##  [3] XML_3.99-0.15               GOstats_2.68.0             
##  [5] graph_1.80.0                Category_2.68.0            
##  [7] pheatmap_1.0.12             RColorBrewer_1.1-3         
##  [9] ggrepel_0.9.4               htmltools_0.5.7            
## [11] SingleCellExperiment_1.24.0 Matrix_1.6-1.1             
## [13] tidyselect_1.2.0            writexl_1.4.2              
## [15] DT_0.30                     DOSE_3.28.0                
## [17] BiocParallel_1.36.0         readxl_1.4.3               
## [19] htmlwidgets_1.6.2           webshot_0.5.5              
## [21] plotly_4.10.3               kableExtra_1.3.4           
## [23] knitr_1.45                  clusterProfiler_4.10.0     
## [25] GO.db_3.18.0                AnnotationDbi_1.64.1       
## [27] edgeR_4.0.1                 limma_3.58.1               
## [29] rtracklayer_1.62.0          SummarizedExperiment_1.32.0
## [31] Biobase_2.62.0              MatrixGenerics_1.14.0      
## [33] matrixStats_1.1.0           withr_2.5.2                
## [35] ezRun_3.18.1                lubridate_1.9.3            
## [37] forcats_1.0.0               stringr_1.5.1              
## [39] dplyr_1.1.4                 purrr_1.0.2                
## [41] readr_2.1.4                 tidyr_1.3.0                
## [43] tibble_3.2.1                ggplot2_3.5.0              
## [45] tidyverse_2.0.0             GenomicRanges_1.54.1       
## [47] Biostrings_2.70.1           GenomeInfoDb_1.38.1        
## [49] XVector_0.42.0              IRanges_2.36.0             
## [51] S4Vectors_0.40.2            BiocGenerics_0.48.1        
## [53] data.table_1.14.8          
## 
## loaded via a namespace (and not attached):
##   [1] fs_1.6.3                      bitops_1.0-7                 
##   [3] enrichplot_1.22.0             HDO.db_0.99.1                
##   [5] httr_1.4.7                    Rgraphviz_2.46.0             
##   [7] utf8_1.2.4                    R6_2.5.1                     
##   [9] lazyeval_0.2.2                mgcv_1.9-0                   
##  [11] prettyunits_1.2.0             gridExtra_2.3                
##  [13] cli_3.6.1                     scatterpie_0.2.1             
##  [15] labeling_0.4.3                sass_0.4.7                   
##  [17] genefilter_1.84.0             ggridges_0.5.4               
##  [19] goseq_1.54.0                  Rsamtools_2.18.0             
##  [21] systemfonts_1.0.5             yulab.utils_0.1.0            
##  [23] gson_0.1.0                    svglite_2.1.2                
##  [25] AnnotationForge_1.44.0        rstudioapi_0.15.0            
##  [27] RSQLite_2.3.3                 generics_0.1.3               
##  [29] gridGraphics_0.5-1            BiocIO_1.12.0                
##  [31] gtools_3.9.4                  crosstalk_1.2.0              
##  [33] vroom_1.6.4                   zip_2.3.0                    
##  [35] fansi_1.0.5                   abind_1.4-5                  
##  [37] lifecycle_1.0.4               yaml_2.3.7                   
##  [39] qvalue_2.34.0                 SparseArray_1.2.2            
##  [41] BiocFileCache_2.10.1          grid_4.3.2                   
##  [43] blob_1.2.4                    promises_1.2.1               
##  [45] crayon_1.5.2                  lattice_0.22-5               
##  [47] cowplot_1.1.1                 GenomicFeatures_1.54.1       
##  [49] KEGGREST_1.42.0               pillar_1.9.0                 
##  [51] fgsea_1.28.0                  rjson_0.2.21                 
##  [53] codetools_0.2-19              fastmatch_1.1-4              
##  [55] glue_1.6.2                    ggfun_0.1.3                  
##  [57] vctrs_0.6.4                   png_0.1-8                    
##  [59] treeio_1.26.0                 cellranger_1.1.0             
##  [61] gtable_0.3.4                  cachem_1.0.8                 
##  [63] openxlsx_4.2.5.2              xfun_0.41                    
##  [65] S4Arrays_1.2.0                mime_0.12                    
##  [67] tidygraph_1.2.3               survival_3.5-7               
##  [69] statmod_1.5.0                 interactiveDisplayBase_1.40.0
##  [71] ellipsis_0.3.2                nlme_3.1-163                 
##  [73] ggtree_3.10.0                 bit64_4.0.5                  
##  [75] progress_1.2.2                filelock_1.0.2               
##  [77] bslib_0.5.1                   KernSmooth_2.23-22           
##  [79] colorspace_2.1-0              DBI_1.1.3                    
##  [81] bit_4.0.5                     compiler_4.3.2               
##  [83] curl_5.1.0                    rvest_1.0.3                  
##  [85] BiasedUrn_2.0.11              xml2_1.3.5                   
##  [87] DelayedArray_0.28.0           shadowtext_0.1.2             
##  [89] caTools_1.18.2                scales_1.3.0                 
##  [91] RBGL_1.78.0                   rappdirs_0.3.3               
##  [93] digest_0.6.33                 rmarkdown_2.25               
##  [95] pkgconfig_2.0.3               highr_0.10                   
##  [97] dbplyr_2.4.0                  fastmap_1.1.1                
##  [99] rlang_1.1.3                   shiny_1.7.5.1                
## [101] farver_2.1.1                  jquerylib_0.1.4              
## [103] jsonlite_1.8.7                GOSemSim_2.28.0              
## [105] RCurl_1.98-1.13               magrittr_2.0.3               
## [107] GenomeInfoDbData_1.2.11       ggplotify_0.1.2              
## [109] patchwork_1.2.0               munsell_0.5.0                
## [111] Rcpp_1.0.11                   ggnewscale_0.4.9             
## [113] ape_5.7-1                     viridis_0.6.4                
## [115] stringi_1.8.2                 ggraph_2.1.0                 
## [117] zlibbioc_1.48.0               MASS_7.3-60                  
## [119] AnnotationHub_3.10.0          plyr_1.8.9                   
## [121] HPO.db_0.99.2                 graphlayouts_1.0.2           
## [123] splines_4.3.2                 hms_1.1.3                    
## [125] geneLenDataBase_1.38.0        locfit_1.5-9.8               
## [127] igraph_1.5.1                  reshape2_1.4.4               
## [129] biomaRt_2.58.0                BiocVersion_3.18.0           
## [131] evaluate_0.23                 BiocManager_1.30.22          
## [133] tzdb_0.4.0                    tweenr_2.0.2                 
## [135] httpuv_1.6.12                 polyclip_1.10-6              
## [137] ggforce_0.4.1                 xtable_1.8-4                 
## [139] restfulr_0.0.15               tidytree_0.4.5               
## [141] MPO.db_0.99.7                 later_1.3.1                  
## [143] viridisLite_0.4.2             aplot_0.2.2                  
## [145] memoise_2.0.1                 GenomicAlignments_1.38.0     
## [147] timechange_0.2.0              GSEABase_1.64.0