diff–over–undiff

Settings

2025-11-25 16:18:45

	Setting
Analysis:	NGS two group analysis
Reference:	Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Release_48-2025-07-03
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.p14/Annotation/Release_48-2025-07-03
Number of features:	21077
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	781	0.2324000	781	639	286	122	67	22	16
p < 0.05	636	0.1431000	636	599	286	122	67	22	16
p < 0.01	416	0.0434300	416	416	282	122	67	22	16
p < 0.001	275	0.0063590	275	275	236	122	67	22	16
p < 1e-04	200	0.0009087	200	200	194	118	67	22	16
p < 1e-05	156	0.0001077	156	156	154	106	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:	416

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!)

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:	416

Cluster plot

GO categories of feature clusters

	BP	MF	CC	Enrichr
Cluster 1	Cluster-BP-1.html	Cluster-MF-1.html	Cluster-CC-1.html	Enrichr
Cluster 2				Enrichr
Cluster 3	Cluster-BP-3.html			Enrichr
Cluster 4				Enrichr
Cluster 5		Cluster-MF-5.html	Cluster-CC-5.html	Enrichr
Cluster 6			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	250	Analyse at Enrichr website	Not run	p <= 0.01 , log2 ratio > 0
downGenes	166	Analyse at Enrichr website	Not run	p <= 0.01 , log2 ratio < 0
bothGenes	416	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	24
BP: downGenes	1
BP: bothGenes	18
MF: upGenes	5
MF: downGenes	0
MF: bothGenes	2
CC: upGenes	12
CC: downGenes	1
CC: bothGenes	8

BP

upGenes

ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	geneName
GO:0006955	immune response	29/239	46/1763	3.050470e-15	1.009706e-12	PXDN/IL1R1/IL1B/ITGB6/CCL20/ACKR3/TNFSF10/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/CD74/HLA-A/HLA-C/HLA-B/ITGB8/TRIM22/FTH1/CTSC/B2M/SMAD3/CTSH/IL32/CX3CL1/TNFSF13/C3/SLPI/XBP1
GO:0006954	inflammatory response	24/239	60/1763	1.955725e-07	3.236725e-05	HSPG2/ZC3H12A/TXNIP/S100A9/ELF3/FOSL2/CYP26B1/IL1R1/IL1B/ITGB6/CCL20/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/AGR2/IDO1/NINJ1/SERPINA3/CX3CL1/ALOX15/C3/PLD3
GO:0006935	chemotaxis	12/239	21/1763	2.824133e-06	3.115960e-04	S100A9/CCL20/ACKR3/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/PLAU/CX3CL1/CXCL16/CXCL17
GO:0006952	defense response	10/239	16/1763	6.673326e-06	5.522177e-04	CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/CD74/HLA-B/DUOX2/IL32/CX3CL1
GO:0030593	neutrophil chemotaxis	9/239	14/1763	1.449640e-05	9.596619e-04	S100A9/TGFB2/IL1B/CXCL8/CXCL6/CXCL5/CXCL3/SAA1/CX3CL1
GO:0006508	proteolysis	21/239	61/1763	1.994148e-05	1.100105e-03	ECE1/TINAGL1/CAPN13/UBD/ENSG00000244255/CFB/PLAU/ENSG00000250644/CTSD/CTSC/TMPRSS4/ST14/MMP14/CTSH/PRSS22/PRSS8/MMP2/CPD/WFDC2/CTSA/TMPRSS2
GO:0001525	angiogenesis	20/239	58/1763	3.094629e-05	1.463317e-03	HSPG2/ZC3H12A/GLUL/PXDN/CYP1B1/EPAS1/FN1/ACKR3/CXCL8/CCN2/NINJ1/MMP14/TNFAIP2/MFGE8/MMP2/CXCL17/EMC10/ID1/XBP1/SAT1
GO:0006629	lipid metabolic process	22/239	68/1763	3.836324e-05	1.587279e-03	ERRFI1/DHRS3/HSPG2/EPHX1/CYP1B1/CYP26B1/SGPP2/IP6K2/ASAH1/RDH10/PSAP/PNPLA2/LRP10/HEXA/ALDH1A3/ALOX15/GPX4/FUT3/PLD3/FUT2/GPCPD1/XBP1
GO:0001666	response to hypoxia	15/239	38/1763	5.314443e-05	1.954534e-03	TGFB2/FOSL2/EPAS1/SOD2/PLAU/UCP2/SLC11A2/MMP14/SMAD3/MMP2/MT-ND2/MT-CO1/MT-ND4/MT-ND5/MT-CYB
GO:0006979	response to oxidative stress	13/239	31/1763	8.145161e-05	2.696048e-03	TXNIP/PXDN/EPAS1/NCOA7/SOD2/RBPMS/TXNRD1/MMP14/DUOX2/MMP2/GPX4/RCAN1/MT-CO1
GO:0045766	positive regulation of angiogenesis	13/239	32/1763	1.208174e-04	3.635506e-03	ZC3H12A/CYP1B1/IL1B/CXCL8/ITGB8/HSPB1/NINJ1/CTSH/CX3CL1/GRN/C3/EMC10/XBP1
GO:0032496	response to lipopolysaccharide	11/239	25/1763	1.758652e-04	4.850949e-03	FOSL2/IL1B/CXCL6/SOD2/IDO1/SCGB1A1/IRAK3/NFKBIA/LITAF/GPX4/SLPI
GO:0030335	positive regulation of cell migration	19/239	64/1763	4.707053e-04	1.198488e-02	IL1B/NEDD9/SOD2/GPNMB/CLDN4/PLAU/MDK/MMP14/SMAD3/CTSH/MMP2/CX3CL1/CXCL16/GRN/COL1A1/SERPINB3/INSR/CEACAM6/XBP1
GO:0060326	cell chemotaxis	7/239	13/1763	6.419320e-04	1.517711e-02	CCL20/ACKR3/CXCL8/CXCL6/CXCL1/CXCL5/CX3CL1
GO:0045087	innate immune response	17/239	56/1763	7.087458e-04	1.563966e-02	GBP3/S100A9/ATP1B1/FOSL2/SLC15A2/HLA-A/HLA-C/HLA-B/LCN2/TRIM22/BPIFA1/BPIFB1/SERINC3/PI3/SLPI/WFDC2/APOL1
GO:0007267	cell-cell signaling	10/239	25/1763	8.808527e-04	1.822264e-02	S100A9/IL1B/CCL20/TNFSF10/CXCL6/CXCL5/PCDH1/GPNMB/CX3CL1/GDF15
GO:0061844	antimicrobial humoral immune response mediated by antimicrobial peptide	6/239	11/1763	1.489304e-03	2.889616e-02	S100A9/CXCL8/CXCL6/CXCL5/CX3CL1/BPIFA1
GO:0007186	G protein-coupled receptor signaling pathway	11/239	31/1763	1.571392e-03	2.889616e-02	ECE1/ACKR3/CXCL8/CXCL1/GABBR1/AKR1C2/GPRC5A/GPRC5B/CX3CL1/C3/INSR
GO:0007165	signal transduction	36/239	170/1763	2.595344e-03	3.646478e-02	CRABP2/PIGR/EPAS1/IL1R1/IL1B/CCL20/TNFSF10/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/NEDD9/CCN2/IFNGR1/GPNMB/PTGES/PLAU/MDK/SCGB1A1/ARHGAP32/GPRC5A/IRAK3/TXNRD1/PRKAB1/IL32/CX3CL1/ABR/CXCL16/TNFSF13/GRN/LGALS3BP/C3/GDF15/CEACAM7/NECTIN2
GO:0007601	visual perception	6/239	12/1763	2.643972e-03	3.646478e-02	DHRS3/TACSTD2/EPAS1/RDH10/CDH3/COL1A1
GO:0010718	positive regulation of epithelial to mesenchymal transition	6/239	12/1763	2.643972e-03	3.646478e-02	TGFB2/IL1B/MDK/SMAD3/COL1A1/SERPINB3
GO:0050727	regulation of inflammatory response	6/239	12/1763	2.643972e-03	3.646478e-02	IL1R1/PTGES/SCGB1A1/DUOXA2/ALOX15/GRN
GO:0060348	bone development	6/239	12/1763	2.643972e-03	3.646478e-02	FOSL2/ITGB6/SH3PXD2B/LRP5/MMP14/TTC9
GO:0071333	cellular response to glucose stimulus	6/239	12/1763	2.643972e-03	3.646478e-02	UCP2/SMAD3/SERPINF1/COL1A1/ICAM1/XBP1

downGenes

ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	geneName
GO:0008544	epidermis development	9/161	22/1763	6.231055e-05	0.01925396	YBX1/LAMC2/TP63/DSP/EGFR/KRT5/BNC1/KRT14/LAMA3

bothGenes

ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	geneName
GO:0006955	immune response	31/400	46/1763	6.711854e-11	2.523657e-08	PXDN/IL1R1/IL1B/ITGB6/CCL20/ACKR3/TNFSF10/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/CD74/HLA-A/HLA-C/HLA-B/ITGB8/TRIM22/FTH1/CTSC/B2M/SMAD3/CTSH/IL32/CX3CL1/TNFSF13/C3/SLPI/XBP1/ETS1/PNP
GO:0006935	chemotaxis	14/400	21/1763	1.861219e-05	3.286605e-03	S100A9/CCL20/ACKR3/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/PLAU/CX3CL1/CXCL16/CXCL17/FOSL1/PLP2
GO:0006954	inflammatory response	28/400	60/1763	2.622291e-05	3.286605e-03	HSPG2/ZC3H12A/TXNIP/S100A9/ELF3/FOSL2/CYP26B1/IL1R1/IL1B/ITGB6/CCL20/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/AGR2/IDO1/NINJ1/SERPINA3/CX3CL1/ALOX15/C3/PLD3/CD44/FOSL1/ACER3/FASN
GO:0008544	epidermis development	14/400	22/1763	4.069555e-05	3.825381e-03	CRABP2/CDKN1A/CCN2/SPINT1/INSR/YBX1/LAMC2/TP63/DSP/EGFR/KRT5/BNC1/KRT14/LAMA3
GO:0009611	response to wounding	11/400	16/1763	1.034735e-04	7.781210e-03	TGFB2/ITGB6/FN1/CCN2/MDK/TMPRSS4/ZFP36L2/SERPINE2/DST/TNC/FOSL1
GO:0006629	lipid metabolic process	29/400	68/1763	1.464532e-04	8.081822e-03	ERRFI1/DHRS3/HSPG2/EPHX1/CYP1B1/CYP26B1/SGPP2/IP6K2/ASAH1/RDH10/PSAP/PNPLA2/LRP10/HEXA/ALDH1A3/ALOX15/GPX4/FUT3/PLD3/FUT2/GPCPD1/XBP1/SLC16A1/TMEM43/INPP4B/HMGCS1/ACAT2/SQLE/ACLY
GO:0045766	positive regulation of angiogenesis	17/400	32/1763	1.504595e-04	8.081822e-03	ZC3H12A/CYP1B1/IL1B/CXCL8/ITGB8/HSPB1/NINJ1/CTSH/CX3CL1/GRN/C3/EMC10/XBP1/F3/AGO2/ETS1/HMGA2
GO:0001666	response to hypoxia	19/400	38/1763	1.767186e-04	8.305773e-03	TGFB2/FOSL2/EPAS1/SOD2/PLAU/UCP2/SLC11A2/MMP14/SMAD3/MMP2/MT-ND2/MT-CO1/MT-ND4/MT-ND5/MT-CYB/SLC2A1/PLOD2/TFRC/CAV1
GO:0030335	positive regulation of cell migration	27/400	64/1763	3.101223e-04	1.295622e-02	IL1B/NEDD9/SOD2/GPNMB/CLDN4/PLAU/MDK/MMP14/SMAD3/CTSH/MMP2/CX3CL1/CXCL16/GRN/COL1A1/SERPINB3/INSR/CEACAM6/XBP1/F3/LAMC2/ITGA6/PTP4A1/EGFR/CAV1/SNAI2/CDH13
GO:0006979	response to oxidative stress	16/400	31/1763	3.668579e-04	1.379386e-02	TXNIP/PXDN/EPAS1/NCOA7/SOD2/RBPMS/TXNRD1/MMP14/DUOX2/MMP2/GPX4/RCAN1/MT-CO1/PTGS2/ERO1A/ERCC1
GO:0007165	signal transduction	57/400	170/1763	4.341157e-04	1.483886e-02	CRABP2/PIGR/EPAS1/IL1R1/IL1B/CCL20/TNFSF10/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/NEDD9/CCN2/IFNGR1/GPNMB/PTGES/PLAU/MDK/SCGB1A1/ARHGAP32/GPRC5A/IRAK3/TXNRD1/PRKAB1/IL32/CX3CL1/ABR/CXCL16/TNFSF13/GRN/LGALS3BP/C3/GDF15/CEACAM7/NECTIN2/SFN/BCAR3/ARHGAP29/S100A6/ABL2/PKP1/DUSP7/FLNB/TFRC/FGFBP1/INPP4B/FBN2/TENM2/NPM1/FAM83B/EGFR/NRG1/NDRG1/PTGES3/GPI/PVR
GO:0006952	defense response	10/400	16/1763	6.878251e-04	2.155185e-02	CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/CD74/HLA-B/DUOX2/IL32/CX3CL1
GO:0010628	positive regulation of gene expression	28/400	71/1763	9.007800e-04	2.445765e-02	ZC3H12A/CYP26B1/IL1B/FN1/CXCL8/CD74/IFNGR1/AGR2/ITGB8/GSN/SMAD3/CTSH/IL32/CDH3/FBLN1/RPL11/F3/PKP1/BMPR2/TFRC/CAV1/MYC/AGO2/TNC/DKK1/ETS1/HMGA2/MSN
GO:0030593	neutrophil chemotaxis	9/400	14/1763	9.757043e-04	2.445765e-02	S100A9/TGFB2/IL1B/CXCL8/CXCL6/CXCL5/CXCL3/SAA1/CX3CL1
GO:0048146	positive regulation of fibroblast proliferation	9/400	14/1763	9.757043e-04	2.445765e-02	FOSL2/FN1/CD74/CDKN1A/FBLN1/S100A6/CCNB1/EGFR/MYC
GO:0008285	negative regulation of cell population proliferation	26/400	65/1763	1.071060e-03	2.516991e-02	TGFB2/CYP1B1/IL1B/ACKR3/RARRES1/CXCL8/CXCL1/CDKN1A/SOD2/GPNMB/IGFBP3/PTGES/FTH1/SMAD3/NUPR1/PTPN14/SERPINE2/FGFBP1/NPM1/HMGA1/CAV1/NDRG1/ETS1/RB1/CDH13/ADAMTS1
GO:0042060	wound healing	14/400	28/1763	1.296804e-03	2.848050e-02	TGFB2/ITGB6/FN1/CDKN1A/TPM1/SMAD3/CX3CL1/ALOX15/MACF1/DSP/DST/NRG1/PLEC/KRT6A
GO:0050727	regulation of inflammatory response	8/400	12/1763	1.363428e-03	2.848050e-02	IL1R1/PTGES/SCGB1A1/DUOXA2/ALOX15/GRN/PTGS2/TNC

MF

upGenes

ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	geneName
GO:0005125	cytokine activity	15/245	27/1786	2.875392e-07	3.910534e-05	TGFB2/IL1B/CCL20/TNFSF10/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/IL32/CX3CL1/CXCL16/TNFSF13/GRN/GDF15
GO:0004252	serine-type endopeptidase activity	13/245	23/1786	1.443717e-06	9.817277e-05	ENSG00000244255/CFB/RHBDD2/PLAU/CTSC/TMPRSS4/ST14/MMP14/CTSH/PRSS22/PRSS8/MMP2/TMPRSS2
GO:0008236	serine-type peptidase activity	8/245	15/1786	3.031341e-04	1.374208e-02	ENSG00000244255/CFB/PLAU/TMPRSS4/ST14/PRSS22/PRSS8/TMPRSS2
GO:0020037	heme binding	7/245	14/1786	1.223686e-03	3.952749e-02	PXDN/CYP1B1/CYP26B1/STEAP4/IDO1/DUOX2/MT-CO1
GO:0004867	serine-type endopeptidase inhibitor activity	9/245	22/1786	1.453217e-03	3.952749e-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	17/408	27/1786	7.884289e-06	0.001466478	TGFB2/IL1B/CCL20/TNFSF10/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/IL32/CX3CL1/CXCL16/TNFSF13/GRN/GDF15/NRG1/GPI
GO:0004252	serine-type endopeptidase activity	14/408	23/1786	8.981636e-05	0.008352922	ENSG00000244255/CFB/RHBDD2/PLAU/CTSC/TMPRSS4/ST14/MMP14/CTSH/PRSS22/PRSS8/MMP2/TMPRSS2/F3

CC

upGenes

ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	geneName
GO:0005615	extracellular space	85/247	221/1801	1.120745e-23	1.737155e-21	HSPG2/TINAGL1/TACSTD2/S100A9/MUC1/PIGR/TGFB2/PXDN/XDH/IL1B/FN1/IGFBP2/CCL20/LRRN1/TF/CP/RARRES1/TNFSF10/MUC4/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/VCAN/SERPINB1/HLA-A/HLA-C/HLA-B/CFB/CCN2/AGR2/IGFBP3/HSPB1/MTUS1/ASAH1/GOLM1/GSN/STOM/LCN2/PSAP/PLAU/MUC5B/CTSD/SCGB1A1/CTSC/TMPRSS4/ST14/MMP14/SERPINA3/TNFAIP2/SPINT1/B2M/CTSH/MFGE8/PRSS22/IL32/GPRC5B/PRSS8/MMP2/CX3CL1/SERPINF1/CXCL16/VMO1/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	88/247	301/1801	3.070883e-15	2.379934e-13	HSPG2/TINAGL1/S100A9/MUC1/PIGR/TGFB2/PXDN/XDH/IL1R1/IL1B/FN1/IGFBP2/CCL20/TF/CP/RARRES1/TNFSF10/MUC20/MUC4/S100P/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/VCAN/CD74/SERPINB1/GABBR1/ENSG00000244255/CFB/CCN2/AGR2/IGFBP3/ASAH1/PSCA/NINJ1/GSN/LCN2/PSAP/PLAU/MUC5B/CTSD/SAA2/SAA1/MDK/FTH1/SCGB1A1/CTSC/TMPRSS4/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	27/247	70/1801	1.028200e-07	5.312364e-06	HSPG2/TINAGL1/S100A9/TGFB2/PXDN/FN1/VCAN/SERPINB1/CCN2/PSAP/ANXA11/CTSD/MDK/CTSC/SERPINA3/CTSH/MFGE8/MMP2/SERPINF1/COL1A1/TIMP2/LGALS3BP/ICAM1/GDF15/SLPI/CSTB/FBLN1
GO:0031012	extracellular matrix	13/247	27/1801	1.508618e-05	5.845894e-04	PXDN/FN1/LRRN1/MUC4/VCAN/CCN2/MUC5B/MMP14/MMP2/COL1A1/TIMP2/PI3/FBLN1
GO:0005764	lysosome	26/247	91/1801	1.046453e-04	3.244003e-03	TINAGL1/TSPAN1/TMEM59/VAMP8/IL1B/MFSD1/CD74/SERPINB1/ASAH1/PSAP/ENSG00000250644/CTSD/ACP2/CYB561A3/FTH1/CTSC/SLC11A2/DRAM1/HEXA/CTSH/LITAF/GABARAP/GRN/INSR/PLD3/CTSA
GO:0016324	apical plasma membrane	20/247	64/1801	1.810435e-04	4.676958e-03	PDZK1IP1/MUC1/ATP1B1/PROM2/FN1/IGFBP2/SLC15A2/TF/MUC20/SLC34A2/SLC44A4/CLDN4/SLC26A4/SCNN1A/SLC11A2/DUOX2/CEACAM7/CEACAM5/CEACAM6/SLC6A14
GO:0072562	blood microparticle	10/247	22/1801	2.805803e-04	6.212850e-03	FN1/TF/CP/CFB/GSN/STOM/SERPINA3/LGALS3BP/C3/APOL1
GO:0009897	external side of plasma membrane	16/247	52/1801	9.897786e-04	1.917696e-02	ECE1/ANTXR1/IL1R1/ITGB6/ACKR3/CD74/HLA-A/HLA-C/HLA-B/PLAU/ST14/SCNN1A/B2M/MFGE8/INSR/ICAM1
GO:0005796	Golgi lumen	7/247	14/1801	1.222476e-03	2.105376e-02	HSPG2/MUC1/MUC20/MUC4/VCAN/MUC5B/MMP14
GO:1904724	tertiary granule lumen	8/247	18/1801	1.416597e-03	2.195726e-02	CXCL1/ASAH1/CTSD/FTH1/B2M/CTSH/TIMP2/CSTB
GO:0031901	early endosome membrane	12/247	36/1801	2.003220e-03	2.822719e-02	VAMP8/HLA-A/HLA-C/HLA-B/TMEM63B/GPNMB/STEAP4/SLC11A2/B2M/LITAF/PLD3/PMEPA1
GO:0043202	lysosomal lumen	10/247	29/1801	3.585717e-03	4.631551e-02	HSPG2/VCAN/CD74/ASAH1/PSAP/CTSD/ACP2/HEXA/PLD3/CTSA

downGenes

ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	geneName
GO:0005882	intermediate filament	9/165	19/1801	1.520155e-05	0.00244745	MACF1/PKP1/DSP/DST/PLEC/KRT6A/KRT5/KRT18/KRT14

bothGenes

ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	geneName
GO:0005615	extracellular space	110/412	221/1801	3.712015e-21	6.904349e-19	HSPG2/TINAGL1/TACSTD2/S100A9/MUC1/PIGR/TGFB2/PXDN/XDH/IL1B/FN1/IGFBP2/CCL20/LRRN1/TF/CP/RARRES1/TNFSF10/MUC4/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/VCAN/SERPINB1/HLA-A/HLA-C/HLA-B/CFB/CCN2/AGR2/IGFBP3/HSPB1/MTUS1/ASAH1/GOLM1/GSN/STOM/LCN2/PSAP/PLAU/MUC5B/CTSD/SCGB1A1/CTSC/TMPRSS4/ST14/MMP14/SERPINA3/TNFAIP2/SPINT1/B2M/CTSH/MFGE8/PRSS22/IL32/GPRC5B/PRSS8/MMP2/CX3CL1/SERPINF1/CXCL16/VMO1/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/PLOD2/TFRC/FGFBP1/FST/EGFR/NRG1/TNC/DKK1/SORL1/ERO1A/LTBP2/CDH13/SERPINB5/SERPINB2/GPI/PVR/MSN/PGK1
GO:0005576	extracellular region	120/412	301/1801	2.065772e-13	1.921168e-11	HSPG2/TINAGL1/S100A9/MUC1/PIGR/TGFB2/PXDN/XDH/IL1R1/IL1B/FN1/IGFBP2/CCL20/TF/CP/RARRES1/TNFSF10/MUC20/MUC4/S100P/CXCL8/CXCL6/CXCL1/CXCL5/CXCL3/VCAN/CD74/SERPINB1/GABBR1/ENSG00000244255/CFB/CCN2/AGR2/IGFBP3/ASAH1/PSCA/NINJ1/GSN/LCN2/PSAP/PLAU/MUC5B/CTSD/SAA2/SAA1/MDK/FTH1/SCGB1A1/CTSC/TMPRSS4/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/TUBB/HSP90AB1/EGFR/NRG1/TNC/DKK1/CD44/SORL1/PNP/ERO1A/LTBP2/DYNC1H1/CDH13/COTL1/ACLY/LAMA3/SERPINB5/SERPINB2/GPI/PVR/ADAMTS1
GO:0062023	collagen-containing extracellular matrix	38/412	70/1801	5.816065e-09	3.605960e-07	HSPG2/TINAGL1/S100A9/TGFB2/PXDN/FN1/VCAN/SERPINB1/CCN2/PSAP/ANXA11/CTSD/MDK/CTSC/SERPINA3/CTSH/MFGE8/MMP2/SERPINF1/COL1A1/TIMP2/LGALS3BP/ICAM1/GDF15/SLPI/CSTB/FBLN1/F3/S100A6/LAMC2/SERPINE2/PLOD2/FBN2/TNC/LTBP2/CDH13/LAMA3/ADAMTS1
GO:0031012	extracellular matrix	16/412	27/1801	4.471294e-05	2.079152e-03	PXDN/FN1/LRRN1/MUC4/VCAN/CCN2/MUC5B/MMP14/MMP2/COL1A1/TIMP2/PI3/FBLN1/FBN2/LTBP2/ADAMTS1
GO:0016324	apical plasma membrane	28/412	64/1801	1.309888e-04	4.872782e-03	PDZK1IP1/MUC1/ATP1B1/PROM2/FN1/IGFBP2/SLC15A2/TF/MUC20/SLC34A2/SLC44A4/CLDN4/SLC26A4/SCNN1A/SLC11A2/DUOX2/CEACAM7/CEACAM5/CEACAM6/SLC6A14/SLC2A1/SLC16A1/SEPTIN7/CAV1/NRG1/PALM2AKAP2/CD44/MSN
GO:0072562	blood microparticle	13/412	22/1801	2.516054e-04	7.799767e-03	FN1/TF/CP/CFB/GSN/STOM/SERPINA3/LGALS3BP/C3/APOL1/SLC2A1/TFRC/MSN
GO:0031901	early endosome membrane	18/412	36/1801	2.949044e-04	7.836032e-03	VAMP8/HLA-A/HLA-C/HLA-B/TMEM63B/GPNMB/STEAP4/SLC11A2/B2M/LITAF/PLD3/PMEPA1/ATP13A3/EGFR/CAV1/DKK1/SORL1/SNX5
GO:0009986	cell surface	41/412	119/1801	1.949907e-03	4.533535e-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/CEACAM7/CEACAM5/CEACAM6/NECTIN2/PLXNB2/ENO1/F3/HNRNPU/ITGA6/HSPD1/BMPR2/TFRC/FGFBP1/HSP90AB1/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

[1] “<table class="table table-striped" style="width: auto !important; "> GSEA: Number of Significant Pathways BP 21 MF 19 CC 30

”

BP

## Picking joint bandwidth of 0.238

## Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

ID	Description	setSize	enrichmentScore	NES	pvalue	p.adjust	geneName
GO:0006412	translation	133	-0.8118885	-2.214434	1.000000e-10	1.950000e-08	RPS3/SARS1/EIF3I/EIF3K/KARS1/RPLP0/EIF3E/LARP1/HARS1/RPL36/EEF2/EIF4G3/RPL27A/EIF4A1/RPS15/RPS5/EEF1A1/EIF3L/RPL24/RPS12/RPS26/RPS27/RPL3/RPL14/RPL6/RPL18/TARS1/LARS1/RPL29/UBA52/EIF3B/RPL7/RPL15/RPS20/RPS4Y1/RPS21/RPS14/RPL7A/RPS9/RPS25/MRPL3/EIF3M/RPL23/ENSG00000260342/RACK1/RPL35/RPL19/EIF4G1/RPS7/RPL26/EPRS1/EEF1B2/ETF1/RPL13/NARS1/RPL31/GARS1/EIF3A/RPS10/RPS27A/PABPC4/FAU/RPL10/RPS23/RPS15A/RPS29/RPL38/IARS1/RPL23A/RPS24/RPL18A/RPL37/RPL9/RPL30/NACA/EEF1G/RPL17-C18orf32/RPL36A-HNRNPH2/RPS8/RPL17/RPL32/RPL35A/RPL27/RPS4X/RPL36A/EIF5B/RPL10A/EIF2S3/IARS2/EIF3G/RPS17/RPL22L1/RPL8/MRPL19/RPS2/RPS18/EIF3D/GSPT1/RPL5/RPSA/AGO2/EIF5A/RPS13/RPS3A/RPS6/RPL11/RPS16/RPL4
GO:0002181	cytoplasmic translation	80	-0.8573077	-2.172272	1.000000e-10	1.950000e-08	RPL27A/RPS15/RPS5/RPL24/RPS12/RPS26/RPS27/RPL3/RPL14/RPL6/RPL18/RPL29/UBA52/RPL7/RPL15/RPS20/RPS21/RPS14/RPL7A/RPS9/RPS25/RPL23/RACK1/RPL35/RPL19/RPS7/RPL26/RPL13/RPL31/RPS10/RPS27A/FAU/RPL10/RPS23/RPS15A/RPS29/RPL38/RPL23A/RPS24/RPL18A/RPL37/RPL9/RPL30/RPS8/RPL17/RPL32/RPL35A/RPL27/RPS4X/RPL36A/RPL10A/RPS17/RPL22L1/RPL8/RPS2/RPS18/RPL5/RPSA/RPS13/RPS3A/RPS6/RPL11/RPS16/RPL4
GO:0008380	RNA splicing	51	-0.8311608	-1.997661	2.012997e-07	2.616897e-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/DHX9/KHSRP/TRA2B/PTBP3/HNRNPA1/SRSF1/SNRPD2/HSPA8/HNRNPU/YBX1
GO:0006397	mRNA processing	55	-0.8242746	-1.992156	3.390780e-07	3.306010e-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/DHX9/KHSRP/TRA2B/PTBP3/HNRNPL/HNRNPA1/SRSF1/SNRPD2/HSPA8/HNRNPU/YBX1
GO:0006508	proteolysis	61	0.8290805	1.873764	3.316022e-06	2.586497e-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:0006955	immune response	46	0.8731192	1.886618	5.341334e-06	3.471867e-04	C3/CXCL6/SLPI/CXCL5/CTSH/HLA-B/XBP1/CXCL1/ACKR3/CX3CL1/ITGB6/TNFSF10/ITGB8/IL1R1/CXCL3/CXCL8/HLA-C/CD74/FTH1/TNFSF13/B2M/HLA-A/TRIM22/IL1B/IL32/CTSC/SMAD3/PXDN/CCL20/CSF3/LTBR/IL1RN
GO:0006364	rRNA processing	24	-0.8944891	-1.821371	5.492821e-05	3.060286e-03	RPS27/RPL14/RPL7/NSA2/RPS25/RPS7/RPL26/RPS24/RPL35A/RPL27/NOP56/RPS17/PA2G4/HEATR1/RPL5/NOLC1/DDX21/RPS6/RPL11/RPS16
GO:0042274	ribosomal small subunit biogenesis	25	-0.8746549	-1.804921	8.954040e-05	4.365094e-03	RPS15/RPS5/RPS12/RPS27/RPS14/RPS9/RPS25/RPS7/RPS23/RPS15A/RPS24/RPS8/RPS4X/NOP56/RPS17/HEATR1/RPS13/RPS3A/RPS6/RPS16/NPM1
GO:0051301	cell division	51	-0.7480385	-1.797879	1.050937e-04	4.554061e-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:0000398	mRNA splicing, via spliceosome	31	-0.8310937	-1.807860	1.448643e-04	5.133465e-03	PABPC1/SF3B3/HNRNPC/SRRM2/SF3B2/RNPS1/SF3B4/DDX39B/SRRM1/SF1/SYNCRIP/PRPF8/SNRPC/HNRNPR/RBMX/HNRNPA3/LSM4/TRA2B/HNRNPA1/SRSF1/SNRPD2/HSPA8/HNRNPU
GO:0006954	inflammatory response	60	0.7773788	1.746754	1.444984e-04	5.133465e-03	SERPINA3/C3/CXCL6/CXCL5/AGR2/IDO1/ELF3/CXCL1/CYP26B1/CX3CL1/ITGB6/TXNIP/ALOX15/IL1R1/CXCL3/CXCL8/HSPG2/S100A9/ZC3H12A/PLD3/IL1B/NINJ1/FOSL2/CCL20/CERS6/MAPKAPK2/LYN/IL1RN/STAT3/S100A8/FAM114A1
GO:0051028	mRNA transport	17	-0.9210099	-1.743967	1.579528e-04	5.133465e-03	RANBP2/DDX39B/SRSF3/TPR/ZC3H11A/NUP50/NUTF2/LRPPRC/DHX9/KHSRP/IGF2BP2/HNRNPA1/SRSF1/XPO1
GO:0006281	DNA repair	36	-0.7928440	-1.770671	4.523903e-04	1.357171e-02	MORF4L1/UBE2D3/USP10/MORF4L2/UBE2N/YY1/TRIP12/SFPQ/NUCKS1/RAD21/SMG1/SUMO1/PSME4/RRM1/PDS5A/MACROH2A1/ASCC3/SSRP1/HMGB1/XRCC6/TAOK1/HUWE1/XRCC5/ERCC1/PRKDC/NPM1
GO:0030593	neutrophil chemotaxis	14	0.9430983	1.652380	6.602164e-04	1.839174e-02	CXCL6/CXCL5/SAA1/CX3CL1/TGFB2/CXCL3/CXCL8/S100A9/IL1B/S100A8
GO:0006952	defense response	16	0.9206039	1.646451	8.818244e-04	2.292743e-02	CXCL6/CXCL5/DUOX2/HLA-B/CXCL1/CX3CL1/CXCL3/CXCL8/CD74/IL32/STAT3
GO:0021762	substantia nigra development	16	-0.8776725	-1.640823	9.474912e-04	2.309510e-02	RHOA/HSPA5/CALM2/SEC16A/DYNLL1/YWHAH/BASP1/YWHAE/ATP5PB/MAPKAP1/ACTB/CALM3/CALM1/YWHAQ/LDHA
GO:0045087	innate immune response	56	0.7420090	1.648771	1.467199e-03	3.263952e-02	LCN2/WFDC2/BPIFA1/SLPI/BPIFB1/ATP1B1/HLA-B/PI3/HLA-C/SLC15A2/S100A9/APOL1/HLA-A/TRIM22/FOSL2/SERINC3/GBP3/LYN/TRIM29/PML/S100A8/IFITM3/TRAF4/CD46/ADAR
GO:0000226	microtubule cytoskeleton organization	20	-0.8406205	-1.640337	1.506439e-03	3.263952e-02	DYNC1LI2/TUBA4A/MAP4/CAMSAP2/MAP1B/SON/CLASP1/TTL/GAPDH/DOCK7/TAOK1/TUBB4B/TUBB6/TUBB/TUBA1C/TUBA1B
GO:1902600	proton transmembrane transport	45	0.7741185	1.669705	1.991636e-03	3.981481e-02	ATP1B1/ATP6AP1/MT-CO1/UCP2/MT-ND5/MT-ND2/SLC15A2/MT-ND4/MT-CO3/MT-ATP6/MT-CO2/MT-ND4L/MT-ND1/MT-ATP8/SLC11A2/UQCR10/ATP6V0C/ATP1A1/COX5B/MT-ND3/ATP6V1A/RNASEK/NDUFB4/ATP6V0E1
GO:0007186	G protein-coupled receptor signaling pathway	31	0.8059038	1.650221	2.041785e-03	3.981481e-02	C3/GPRC5A/GABBR1/CXCL1/ACKR3/CX3CL1/CXCL8/INSR/GPRC5B/APLP2/AKR1C2/ADGRG1/ECE1/GIPC1/CELSR1
GO:0043484	regulation of RNA splicing	17	-0.8651165	-1.638131	2.211934e-03	4.107877e-02	SF3B3/ESRP1/CELF1/RBM12/GRSF1/FUS/SON/TRA2B/PTBP3/HNRNPL/HNRNPA1/SRSF1/AHNAK2/AHNAK

MF

## Picking joint bandwidth of 0.181

## Warning: ggrepel: 233 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

ID	Description	setSize	enrichmentScore	NES	pvalue	p.adjust	geneName
GO:0003723	RNA binding	388	-0.7384469	-2.273742	1.000000e-10	9.600000e-09	ELAVL1/EEF2/EIF4G3/PABPC1/LRP1/PTPN1/PRDX1/RPL27A/PPP1R10/EIF4A1/RPS15/RPS5/CNOT6/EEF1A1/USP10/STIP1/ALDH18A1/API5/HNRNPC/YWHAG/EIF3L/SRRM2/SF3B2/RPL24/CAST/CPSF2/RPS12/ARCN1/PCBP1/HMGB3/PAPOLA/RNPS1/UBE2N/HNRNPUL1/SF3B4/CANX/RCAN3/ESRP1/RPS26/YY1/RPS27/RPL3/RPL14/RPL6/PRRC2A/RPL18/SERBP1/MAP4/RANBP2/HDGF/STRAP/RPL29/DDX39B/DICER1/SRPK1/EIF3B/RPL7/UBA1/SFPQ/RPL15/RBM25/GOT2/CNBP/RPS20/SMARCA4/NUCKS1/CELF1/SRRM1/VIM/RPS4Y1/RPS21/RPS14/SF1/RPL7A/NSA2/LTA4H/YWHAE/RPS9/HSPA9/SRSF3/RSL1D1/TIAL1/RPS25/GTF3A/PPIA/MRPL3/EWSR1/HNRNPDL/RPL23/SYNCRIP/TPR/ZC3H11A/TCP1/RACK1/CCT6A/GDI2/ATP5F1C/RPL35/RPL19/HNRNPAB/ILF3/SMG1/RBM12/EIF4G1/RPS7/RPL26/GRSF1/EPRS1/SUMO1/RTN4/CAPRIN1/PRPF8/FUS/ETF1/IMMT/RBM3/RPL13/RPL31/JUN/CLTC/EIF3A/SNRPC/RPS10/LRRC59/PFN1/RPS27A/PABPC4/FAU/RPL10/TOP1/CCT4/RPS23/RPS15A/RPS29/BTF3/HNRNPR/RBMX/DUSP11/ALDOA/FSCN1/STXBP1/LRPPRC/S100A16/SON/RPL38/RPL23A/RPS24/RPL18A/U2SURP/RPL37/HNRNPA3/DIAPH1/RPL9/PRRC2C/RPL30/SRSF2/THRAP3/CPNE3/PKM/ASCC3/LSM4/RPS8/RPL17/SRP9/SSRP1/DHX9/RPL32/KHSRP/RPL35A/TRA2B/PTBP3/HNRNPD/RPL27/KPNB1/NCL/HMGB1/RPS4X/RPL7L1/HSP90AA1/FAM120A/RPL36A/IPO5/EIF5B/RPL10A/HNRNPL/DUSP14/XRCC6/GLRX3/PURB/IGF2BP2/BZW1/HNRNPA1/EIF3G/SRSF1/NOP56/CAVIN1/RPS17/XPO1/RPL22L1/PA2G4/SND1/RPL8/HUWE1/SNRPD2/G3BP1/CRKL/CCT3/RPS2/FLNA/HEATR1/HSP90B1/RPS18/HSPA8/HSPD1/MYH9/TNPO1/TXN/EIF3D/CS/XRCC5/HNRNPU/GSPT1/RPL5/NOLC1/FDPS/ANXA2/RPSA/TOP2A/AGO2/EIF5A/PRKDC/DDX21/LGALS1/TFRC/YWHAZ/RPS13/RPS3A/MACF1/RPS6/RPL11/PKP1/HSP90AB1/RPS16/FLNB/HMGA1/KRT18/ZFP36L2/RPL4/FASN/KCTD12/SUB1/RAN/YBX1/MKI67/ENO1/NAP1L1/PLEC/DSP/DYNC1H1/KPNA2/NPM1/AHNAK
GO:0003735	structural constituent of ribosome	86	-0.8602085	-2.205477	1.000000e-10	9.600000e-09	RPL27A/RPS15/RPS5/RPL24/RPS12/RPS26/RPS27/RPL3/RPL14/RPL6/RPL18/RPL29/UBA52/RPL7/RPL15/RPS20/RPS4Y1/RPS21/RPS14/RPL7A/RPS9/RPS25/MRPL3/RPL23/ENSG00000260342/RPL35/RPL19/RPS7/RPL26/RPL13/RPL31/RPS10/RPS27A/FAU/RPL10/RPS23/RPS15A/RPS29/RPL38/RPL23A/RPS24/RPL18A/RPL37/RPL9/RPL30/RPL17-C18orf32/RPL36A-HNRNPH2/RPS8/RPL17/RPL32/RPL35A/RPL27/RPS4X/RPL7L1/RPL36A/RPL10A/RPS17/RPL22L1/RPL8/MRPL19/RPS2/RPS18/RPL5/RPSA/RPS13/RPS3A/RPS6/RPL11/RPS16/RPL4
GO:0003676	nucleic acid binding	94	-0.7465038	-1.937369	8.540063e-08	5.465640e-06	SF3B3/HNRNPC/PCBP1/RNPS1/SF3B4/RCAN3/ESRP1/EHD4/DDX39B/DICER1/EIF3B/SFPQ/RBM25/CNBP/CELF1/SF1/SRSF3/TIAL1/EWSR1/HNRNPDL/SYNCRIP/HNRNPAB/RBM12/GRSF1/FUS/RBM3/NARS1/SNRPC/PABPC4/HNRNPR/RBMX/SON/U2SURP/HNRNPA3/SRSF2/ASCC3/EHD2/DHX9/KHSRP/TRA2B/PTBP3/HNRNPD/NCL/HNRNPL/IGF2BP2/HNRNPA1/EIF3G/SRSF1/PA2G4/SND1/G3BP1/RPS18/AGO2/DDX21/ETS1/YBX1/NPM1/HMGA2
GO:0045296	cadherin binding	148	-0.6491101	-1.769749	2.308255e-06	1.107962e-04	BAG3/VASP/PFKP/RPL24/PICALM/CAST/PCBP1/RPS26/EHD4/RPL14/RPL6/EHD1/SERBP1/PTPN11/RPL29/SEPTIN2/MPRIP/RPL15/KIF5B/PPFIBP1/PRDX6/LRRFIP1/RPL7A/YWHAE/RSL1D1/YWHAB/EPHA2/RACK1/TJP1/RTN4/CLIC1/LRRC59/CAPZA1/PFN1/CKAP5/NUDC/ALDOA/FSCN1/TLN1/RPL23A/PAK2/ATIC/EEF1G/PKM/CBL/OLA1/PKP2/LIMA1/EIF2S3/BZW1/SEPTIN7/NOP56/ASAP1/SND1/IQGAP1/FXYD5/CRKL/RPS2/FLNA/HSPA8/MYH9/ITGB1/BMPR2/FMNL2/SNX5/TAGLN2/YWHAZ/PAICS/MACF1/ANLN/PKP1/HSP90AB1/FLNB/CDH13/FASN/RAN/ENO1/PLEC/SFN/EGFR/ITGA6/LDHA/AHNAK/NDRG1
GO:0005524	ATP binding	191	-0.5985035	-1.701735	5.526242e-06	2.122077e-04	EIF4A1/PTK2/CCT7/CHD4/WNK1/UBE2D3/ALDH18A1/CSNK2A2/PFKP/HIPK3/AAK1/DYNC1LI2/PAPOLA/UBE2N/MYO1E/EHD4/VDAC2/EHD1/TARS1/PYGL/NME2/MAP2K1/LARS1/ATP5F1B/DDX39B/DICER1/SRPK1/UBA1/PAK1/PSMC3/MAPK6/KIF5B/CDK6/SMARCA4/STK25/ACACA/GUK1/MAPKAPK3/HSPA9/UBE2G1/EPHA2/ACTB/TCP1/CCT6A/MYO10/ITPR3/SMG1/EIF4G1/HK1/EPRS1/CAPRIN1/NARS1/GARS1/AK4/TOP1/CCT4/UBE2K/MAP2K3/IARS1/RRM1/PAK2/HSPH1/IGF1R/ACSL4/GSK3B/PFKFB3/DGKA/ACTR3/THRAP3/PKM/ATP2B4/ASCC3/EHD2/DHX9/OLA1/HSP90AA1/ABL2/ABCE1/TTL/XRCC6/ACTR2/IARS2/POMK/TGFBR2/TAOK1/CCT5/G3BP1/CCT3/HSP90B1/HSPA8/HSPD1/MYH9/XRCC5/HNRNPU/NOLC1/BMPR2/TOP2A/PRKDC/DDX21/PAICS/HSP90AB1/MKI67/PGK1/VDAC1/DYNC1H1/ACLY/ATP13A3/EGFR
GO:0004252	serine-type endopeptidase activity	23	0.9150157	1.753027	3.858240e-05	1.234637e-03	CFB/ENSG00000244255/CTSH/PRSS22/TMPRSS4/MMP2/TMPRSS2/PLAU/MMP14/CTSC/PRSS8/RHBDD2/ST14/PRSS23/TPP1/BMP1/FAP
GO:0003725	double-stranded RNA binding	23	-0.8603786	-1.736653	1.749631e-04	4.798987e-03	DICER1/VIM/LRRFIP1/ILF3/CLTC/DHX9/ACTN1/HSPD1/HNRNPU/AGO2/TUBB4B/DDX21/TFRC/HSP90AB1/TUBA1B/MSN
GO:0008236	serine-type peptidase activity	15	0.9497988	1.706281	2.183100e-04	5.239439e-03	CFB/ENSG00000244255/PRSS22/TMPRSS4/TMPRSS2/PLAU/PRSS8/ST14/PRSS23/TPP1/FAP
GO:0019843	rRNA binding	15	-0.9216137	-1.715669	2.545518e-04	5.430437e-03	RPS4Y1/RPS9/RPL23A/RPL37/RPL9/RPS4X/CAVIN1/RPL8/RPS18/RPL5/DDX21/RPL11/NPM1
GO:0003697	single-stranded DNA binding	16	-0.9079714	-1.707624	6.798848e-04	1.305379e-02	PCBP1/NUCKS1/HNRNPDL/TOP1/LRPPRC/DHX9/HMGB1/PURB/HNRNPA1/HSPD1/HNRNPU/ERCC1/SUB1/YBX1
GO:0140662	ATP-dependent protein folding chaperone	15	-0.8887804	-1.654546	1.297366e-03	1.916109e-02	HSPA5/CCT7/HSPA9/TCP1/CCT6A/CCT4/HSPH1/HSP90AA1/CCT5/CCT3/HSP90B1/HSPA8/HSPD1/HSP90AB1
GO:0003729	mRNA binding	73	-0.6446746	-1.622885	1.134491e-03	1.916109e-02	RPS3/STAU1/YTHDF3/DDX6/HDLBP/ELAVL1/EIF4G3/PABPC1/EIF4A1/RPS5/SRRM2/RPL24/PCBP1/ESRP1/RPS26/STRAP/DDX39B/RPL7/RBM25/CNBP/CELF1/SF1/SRSF3/TIAL1/TPR/RPL35/HNRNPAB/EIF4G1/GRSF1/CAPRIN1/EIF3A/SNRPC/HNRNPR/RBMX/PKM/DHX9/KHSRP/TRA2B/PTBP3/HNRNPD/HSP90AA1/HNRNPL/PURB/SRSF1/G3BP1/RPS2/AGO2/DDX21/RPS13/ZFP36L2/YBX1/MYC
GO:0004175	endopeptidase activity	13	0.9304763	1.621368	1.270378e-03	1.916109e-02	CTSD/CTSH/MMP2/MMP14/NCSTN/ECE1/TPP1/TMEM59/FAP/CTSB
GO:0003779	actin binding	87	-0.6134234	-1.570656	1.679175e-03	2.302868e-02	PTK2/VCL/ENC1/ARPC1A/TMSB10/CAPZA2/VASP/PANX1/MYO1E/HDGF/MPRIP/YWHAH/CNN3/MYO10/MAP1B/ARPC5/CAPZA1/PFN1/ALDOA/FSCN1/TLN1/DIAPH1/GMFB/ACTR3/CAP1/CORO1C/TMOD3/TNS4/LIMA1/ACTR2/ACTN1/PPP1R18/SSH1/FXYD5/FLNA/MYH9/ITGB1/PLS3/TPM3/HNRNPU/FMNL2/COTL1/MACF1/ANLN/FLNB/PLEC/DST/MSN
GO:0016887	ATP hydrolysis activity	56	-0.6895083	-1.673269	2.567654e-03	3.081185e-02	DDX6/ATP5F1A/YME1L1/HSPA5/EIF4A1/CCT7/CHD4/MYO1E/ATP5F1B/DDX39B/PSMC3/KIF5B/HSPA9/ACTB/TCP1/CCT6A/ATP5F1C/CCT4/ATP2B4/ASCC3/DHX9/OLA1/HSP90AA1/ABCE1/XRCC6/CCT5/G3BP1/CCT3/HSP90B1/HSPA8/HSPD1/NAV1/XRCC5/DDX21/HSP90AB1/DYNC1H1/ATP13A3
GO:0003690	double-stranded DNA binding	17	-0.8632317	-1.661243	2.453026e-03	3.081185e-02	HMGB3/NUCKS1/HNRNPDL/JUN/TOP1/DHX9/HMGB1/XRCC6/PURB/XRCC5/HNRNPU/PRKDC/SUB1/YBX1/TP63/EGFR
GO:0048027	mRNA 5’-UTR binding	13	-0.9177107	-1.642019	2.786742e-03	3.130113e-02	RPS14/RSL1D1/SYNCRIP/RPS7/RPL26/NCL/IGF2BP2/CCT5/RPL5/RPS13/RPS3A
GO:0005125	cytokine activity	27	0.8203071	1.614508	2.934481e-03	3.130113e-02	CXCL6/CXCL5/GDF15/CXCL16/CXCL1/CX3CL1/TNFSF10/TGFB2/CXCL3/CXCL8/GRN/TNFSF13/IL1B/IL32/CCL20/CSF3/BMP1/IL1RN
GO:0019900	kinase binding	20	-0.8245150	-1.632026	4.048258e-03	4.090871e-02	HTT/UBQLN1/LDHB/FLNA/BCAR3/RB1/HSP90AB1/SLC2A1/EGFR

CC

## Picking joint bandwidth of 0.145

## Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

ID	Description	setSize	enrichmentScore	NES	pvalue	p.adjust	geneName
GO:1990904	ribonucleoprotein complex	142	-0.8544448	-2.326128	1.000000e-10	6.600000e-09	RPL36/ELAVL1/EEF2/PABPC1/RPL27A/RPS15/RPS5/HNRNPC/RPL24/RPS12/PCBP1/HNRNPUL1/ESRP1/RPS26/RPS27/RPL3/RPL14/RPL6/RPL18/RPL29/UBA52/RPL7/RPL15/RPS20/CELF1/RPS4Y1/RPS21/RPS14/RPL7A/NSA2/RPS9/RPS25/MRPL3/HNRNPDL/RPL23/ENSG00000260342/ACTB/SYNCRIP/RACK1/RPL35/RPL19/HNRNPAB/ILF3/RBM12/RPS7/RPL26/GRSF1/EPRS1/RPL13/RPL31/SNRPC/RPS10/RPS27A/PABPC4/FAU/RPL10/RPS23/RPS15A/RPS29/HNRNPR/RBMX/LRPPRC/RPL38/RPL23A/RPS24/RPL18A/RPL37/HNRNPA3/RPL9/RPL30/RPL17-C18orf32/RPL36A-HNRNPH2/RPS8/RPL17/DHX9/RPL32/RPL35A/HNRNPD/RPL27/NCL/RPS4X/RPL7L1/CBX5/RPL36A/RPL10A/HNRNPL/HNRNPA1/GAPDH/NOP56/RPS17/XPO1/RPL22L1/PA2G4/RPL8/MRPL19/IQGAP1/SNRPD2/RPS2/HEATR1/RPS18/HSPA8/XRCC5/HNRNPU/RPL5/RPSA/TOP2A/AGO2/RPS13/RPS3A/RPS6/RPL11/RPS16/ZFP36L2/RPL4/YBX1/NPM1
GO:0005840	ribosome	95	-0.8395558	-2.170304	1.000000e-10	6.600000e-09	SERP1/RPL36/EEF2/RPL27A/RPS15/RPS5/EEF1A1/RPL24/RPS12/RPS26/RPS27/RPL3/RPL14/RPL6/RPL18/RPL29/UBA52/RPL7/RPL15/RPS20/RPS4Y1/RPS21/RPS14/SF1/RPL7A/RPS9/RPS25/MRPL3/RPL23/ENSG00000260342/RACK1/RPL35/RPL19/EIF4G1/RPS7/RPL26/RPL13/RPL31/RPS10/RPS27A/FAU/RPL10/RPS23/RPS15A/RPS29/RPL38/RPL23A/RPS24/RPL18A/RPL37/RPL9/RPL30/RPL17-C18orf32/RPL36A-HNRNPH2/RPS8/RPL17/RPL32/RPL35A/RPL27/RPS4X/RPL7L1/RPL36A/RPL10A/RPS17/RPL22L1/RPL8/MRPL19/RPS2/RPS18/RPL5/RPSA/RPS13/RPS3A/RPS6/RPL11/RPS16/RPL4
GO:0022626	cytosolic ribosome	85	-0.8460235	-2.149742	1.000000e-10	6.600000e-09	RPL27A/RPS15/RPS5/EEF1A1/USP10/RPL24/RPS12/RPS26/RPS27/RPL3/RPL14/RPL6/RPL18/RPL29/UBA52/RPL7/RPL15/RPS20/RPS21/RPS14/RPL7A/RPS9/RPS25/RPL23/RPL35/RPL19/RPS7/RPL26/ETF1/RPL13/RPL31/RPS10/RPS27A/FAU/RPL10/RPS23/RPS15A/RPS29/RPL38/RPL23A/RPS24/RPL18A/RPL37/RPL9/RPL30/ASCC3/RPS8/RPL17/RPL32/RPL35A/RPL27/RPS4X/RPL36A/ABCE1/RPL10A/RPS17/RPL8/RPS2/RPS18/GSPT1/RPL5/RPSA/RPS13/RPS3A/RPS6/RPL11/RPS16/RPL4
GO:0005615	extracellular space	221	0.7314207	1.921139	6.806135e-10	3.369037e-08	SERPINA3/LCN2/CEACAM6/WFDC2/CFB/PIGR/BPIFA1/C3/MUC4/IGFBP3/CXCL6/RARRES1/SLPI/BPIFB1/CXCL5/GDF15/CTSD/CP/AGR2/CTSH/MUC1/PSAP/PRSS22/CXCL17/HLA-B/SERPINB3/SCGB1A1/TNFAIP2/PI3/HSPB1/CXCL16/FN1/LRRN1/TF/TACSTD2/CXCL1/IGFBP2/FBLN1/GSN/TMPRSS4/ICAM1/TIMP2/SPINT1/CX3CL1/MMP2/CSTB/MUC5B/COL1A1/GOLM1/ASAH1/CPD/TNFSF10/STOM/TINAGL1/TGFB2/VMO1/CXCL3/CXCL8/GRN/HSPG2/MFGE8/HLA-C/SERPINB7/LGALS3BP/VCAN/S100A9/TNFSF13/B2M/APOL1/HLA-A/MTUS1/GPRC5B/PLAU/MMP14/IL1B/CCN2/ITM2B/IL32/CTSC/PRSS8/SERPINF1/SERPINB1/PXDN/ST14/CCL20/CSF3/XDH/UBB/QSOX1/GLB1/CCN1/BMP1/TGFBI/MAN2B1/CD63/SPARC/CREG1/PLOD1/LGALS8/IL1RN/FAP/IGFBP7/ADAM9/SERPINH1/S100A8/CTSB
GO:0005576	extracellular region	301	0.6669680	1.812637	6.424027e-09	2.543915e-07	SERPINA3/LCN2/WFDC2/CFB/ENSG00000244255/PIGR/BPIFA1/C3/MUC4/IGFBP3/CXCL6/RARRES1/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/GSN/TMPRSS4/NTN1/TIMP2/SPINT1/MDK/CX3CL1/MMP2/TMPRSS2/CSTB/MUC5B/COL1A1/ASAH1/TNFSF10/TINAGL1/TGFB2/IL1R1/VMO1/CXCL3/NOTCH3/CXCL8/GRN/HSPG2/MFGE8/CEACAM7/CD74/FTH1/NTN4/LGALS3BP/VCAN/S100A9/TNFSF13/B2M/APOL1/PLAU/IL1B/NINJ1/CCN2/ITM2B/IL32/CTSC/PRSS8/SERPINF1/SERPINB1/PXDN/ADGRG1/CCL20/CSF3/PRSS23/XDH/CDH1/QSOX1/P4HB/GLB1/SDC4/PDXK/CCN1/EMC10/BMP1/TGFBI/MAN2B1/CD63/SPARC/CREG1/PLBD2/IL1RN/FAP/HEG1/IGFBP7/ADAM9/S100A8/CTSB/GNS
GO:0005730	nucleolus	157	-0.6637912	-1.825960	3.018705e-07	9.961725e-06	RPS5/PPP1CB/EEF1A1/POLR1D/PHB2/POLR2L/SF3B3/MORF4L2/EIF3L/RPS12/RPS27/RPL3/RPL18/RPL7/RPS20/SMARCA4/NUCKS1/OSBP/RPS14/RPL7A/NSA2/RPS9/HSPA9/RSL1D1/RPS25/EWSR1/ZFP91/RPL23/RACK1/ZBED6/RPL35/MYO10/ITPR3/RPL19/ILF3/RPS7/RPL26/SUMO1/RPL13/EIF3A/RPS10/BNIP2/RPS27A/TOP1/RPS23/RPS15A/CKAP5/RBMX/S100A16/RPL23A/RPS24/SPIN1/IGF1R/MACROH2A1/NAA50/CPNE3/RPS8/NF1/RPL17/STON2/SSRP1/DHX9/OLA1/PAFAH1B2/RPL27/NCL/RPS4X/RPL7L1/CBX5/IPO5/XRCC6/ITGB4/NOP56/CKAP2/RPS17/XPO1/PA2G4/LRRC8C/FLNA/XPO6/HEATR1/HSPA8/BMAL2/TNPO1/KLF6/XRCC5/SKP2/RPL5/NOLC1/CCND2/TOP2A/PRKDC/DDX21/RPS13/RPS3A/RPS6/RPL11/RPS16/KRT18/RPL4/SUB1/RAN/MKI67/BNC1/PHLDA1/MYC/NPM1/SCD
GO:0022625	cytosolic large ribosomal subunit	46	-0.8530371	-1.956552	3.670300e-07	1.038170e-05	RPL36/RPL27A/RPL24/RPL3/RPL14/RPL6/RPL18/RPL29/UBA52/RPL7/RPL15/RPL7A/RPL23/RPL35/RPL19/RPL26/RPL13/RPL31/RPL10/RPL38/RPL23A/RPL18A/RPL37/RPL9/RPL30/RPL17/RPL32/RPL35A/RPL27/RPL7L1/RPL36A/RPL10A/RPL8/RPL5/RPL11/RPL4
GO:0022627	cytosolic small ribosomal subunit	35	-0.8739451	-1.926362	1.996625e-06	4.941647e-05	RPS15/RPS5/RPS12/RPS26/RPS27/RPS20/RPS4Y1/RPS21/RPS14/RPS9/RPS25/RACK1/RPS7/RPS10/RPS27A/FAU/RPS23/RPS15A/RPS29/RPS24/RPS8/RPS4X/RPS17/RPS2/RPS18/RPSA/RPS13/RPS3A/RPS6/RPS16
GO:0005764	lysosome	91	0.7635279	1.831787	2.050660e-05	4.511452e-04	CTSD/ENSG00000250644/CTSH/PSAP/CTSA/CYB561A3/TSPAN1/ASAH1/TINAGL1/LITAF/GRN/CD74/MFSD1/FTH1/INSR/PLD3/IL1B/CTSC/GABARAP/SERPINB1/ACP2/VAMP8/NCOA4/DRAM1/NCSTN/SLC11A2/GLB1/HGSNAT/TPP1/SQSTM1/TMEM59/HEXA/MAN2B1/CD63/CREG1/PLBD2/TRIM29/CTSB/GNS/TMEM106B/LAMP1/CALR/IFITM3/ATP6V1A/TPCN1/CD164
GO:0005681	spliceosomal complex	35	-0.8343925	-1.839180	3.501765e-05	6.933495e-04	PABPC1/API5/SF3B3/HNRNPC/SRRM2/SF3B2/SF3B4/DDX39B/SRRM1/SF1/HNRNPDL/SYNCRIP/PRPF8/RBM3/SNRPC/HNRNPR/RBMX/HNRNPA3/LSM4/TRA2B/NCL/HNRNPA1/SRSF1/SNRPD2/HSPA8/HNRNPU
GO:0005925	focal adhesion	203	-0.5700708	-1.627686	4.074223e-05	7.333602e-04	RPL3/RPL6/RPL18/MAP2K1/MPRIP/RPL7/PAK1/CAV2/RAC2/CNN3/VIM/PPFIBP1/RPS14/RPL7A/YWHAE/RPS9/HSPA9/YWHAB/EPHA2/PPIA/RPL23/ACTB/GDI2/RPL19/RPS7/FERMT1/RPL31/ANXA1/CLTC/ARPC5/RPS10/PFN1/RPS29/SDCBP/TLN1/RPL38/PAK2/RPL9/RPL30/ACTR3/CPNE3/RPS8/YWHAQ/CBL/CLASP1/RPL27/CAP1/ITGA2/PXN/MCAM/CORO1C/RPS4X/TNS4/LPP/FAT1/CD9/RPL10A/LIMA1/ACTR2/ACTN1/ITGB4/DOCK7/RPS17/RPL8/IQGAP1/G3BP1/RPS2/FLNA/HSP90B1/RPS18/HSPA8/ITGA5/MYH9/ITGB1/SHC1/RPL5/BCAR3/PVR/YWHAZ/RPS13/RPS3A/TNC/RPS16/FLNB/CDH13/HMGA1/RPL4/PLEC/DST/CD44/NPM1/MSN/CAV1/EGFR/ITGA6/AHNAK
GO:0032040	small-subunit processome	25	-0.8749625	-1.815650	7.502993e-05	1.237994e-03	RPS5/RPS12/RPS27/RPS14/RPS9/RPS7/RPS27A/RPS23/RPS15A/RPS24/RPS8/RPS4X/NOP56/RPS17/HEATR1/XRCC5/PRKDC/RPS13/RPS3A/RPS6/RPS16
GO:0005874	microtubule	52	-0.7372184	-1.732587	1.543414e-04	2.350738e-03	CCT7/MAP1LC3B/DYNC1I2/DYNLL1/DYNC1LI2/TUBA4A/MAP4/KIF5B/LUZP1/TCP1/CAMSAP2/CCT6A/STMN1/MAP1B/CCT4/NUDC/LRPPRC/HSPH1/FEZ1/CLASP1/CKAP2/CCT5/IQGAP1/CCT3/NAV1/TUBB4B/TUBB6/MACF1/TUBB/TUBA1C/DST/DYNC1H1/TUBA1B/NDRG1
GO:0005694	chromosome	54	-0.7251289	-1.721094	1.722282e-04	2.435799e-03	DYNLL1/HMGB3/H3-3B/SEPTIN2/SRPK1/PAK1/SMARCA4/NUCKS1/RAD21/EP300/RSL1D1/TPR/LUZP1/BUB3/CARM1/TOP1/CKAP5/PDS5A/ZBTB38/MACROH2A1/SSRP1/CLASP1/NCL/HMGB1/CBX5/XRCC6/SEPTIN7/XRCC5/HNRNPU/DDX21/HMGA1/MKI67
GO:0005856	cytoskeleton	223	-0.5282981	-1.516893	2.427410e-04	3.204181e-03	PTK2/RAC1/VCL/CHD4/MAP1LC3B/ENC1/WNK1/ARPC1A/TMSB10/CALM2/DYNC1I2/VASP/GNAI2/DYNLL1/DYNC1LI2/AJUBA/MYO1E/TUBA4A/MAP4/MAP2K1/SEPTIN2/MPRIP/ARHGDIB/PAK1/KIF5B/CDK6/RAC2/RAD21/FGD6/VIM/HINT1/LRRFIP1/BASP1/CDC27/SEPTIN11/ACTB/TPR/LUZP1/TCP1/CAMSAP2/STMN1/CALM3/MYO10/RPS7/MAP1B/FERMT1/CALM1/CLTC/ARPC5/UBR4/CAPZA1/PFN1/CCT4/CKAP5/NUDC/FSCN1/LRPPRC/SDCBP/TLN1/DIAPH1/USP9X/FRMD6/ACTR3/FEZ1/DHX9/CLASP1/PXN/CORO1C/TMOD3/TNS4/ABL2/LIMA1/ACTR2/IGF2BP2/ACTN1/SEPTIN7/PPP1R18/SSH1/GAPDH/CKAP2/CCT5/CCT3/FLNA/MYH9/NAV1/TPM3/HNRNPU/TUBB4B/COTL1/PTP4A1/TUBB6/MACF1/ANLN/FLNB/KRT18/TUBB/PTPN14/TUBA1C/PLEC/CCNB1/DSP/DST/DYNC1H1/TUBA1B/NPM1/MSN/NDRG1/KRT14
GO:0015935	small ribosomal subunit	22	-0.8722628	-1.778127	3.056067e-04	3.781883e-03	RPS15/RPS5/RPS26/RPS20/RPS21/RPS14/RPS9/RPS25/RACK1/FAU/RPS23/RPS29/RPS24/RPS4X/RPS2/RPS18/RPSA/RPS6/RPS16
GO:0031965	nuclear membrane	43	-0.7736134	-1.763607	4.554164e-04	5.304261e-03	ANKRD17/PRNP/ANXA4/EI24/CCNI/CANX/RANBP2/PAK1/KIF5B/LYPLA1/TPR/CLCA2/SUMO1/NUP50/OSBPL8/NUTF2/MLX/CLIC1/SDCBP/SPIN1/KPNB1/IPO5/GAPDH/ITGB4/XPO1/CCND2/LPIN1/HMGA1/KPNA2/EGFR
GO:0000139	Golgi membrane	130	0.6522863	1.636010	5.351672e-04	5.886839e-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/GRINA/MGAT4B/ARHGAP32/QSOX1/TMEM59/ERGIC1/RND3/SREBF2/CHPF/GBP3/TMEM132A/TMEM165/ATP6V0C/GALNT10/RAB1B/KIAA0319L/ERGIC3/ATF6B/DHCR24/AP1B1/LEPROT/GALNT5/IFNGR2/ATP6V1A/EXT1/GALNT14/NUCB1/RNASEK/COPG1/B4GALT1/AP1G1/DNM2/ZDHHC7/TNFRSF1A/SLC35A4/GALNT2/AP3D1/SCARB2/GJA1/APH1A/ATP6AP2
GO:0015630	microtubule cytoskeleton	37	-0.7745305	-1.711230	8.400058e-04	8.753745e-03	DYNLL1/TUBA4A/MAP4/SEPTIN2/SEPTIN11/CKAP5/CLASP1/SEPTIN7/GAPDH/CKAP2/TAOK1/MFN2/IQGAP1/NAV1/TUBB4B/TUBB6/TUBB/TUBA1C/DST/TUBA1B/NDRG1
GO:0032991	protein-containing complex	146	-0.5547027	-1.509184	1.399202e-03	1.385210e-02	HSPA5/PTPN1/VCL/CHD4/WNK1/CALM2/USP10/PHB2/STIP1/HNRNPC/UGGT1/EIF3L/UBE2N/PANX1/H3-3B/PSMD11/PSMD3/RPL3/HIGD1A/PLEKHA2/PTPN11/PAK1/MAPK6/SMARCA4/CAV2/EP300/PPIA/EIF3M/RPL23/ACTB/CALM3/HTT/TJP1/RPS7/EPRS1/EEF1B2/CALM1/CLTC/PRELID1/EIF3A/RPL10/UBQLN1/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/TUBB/RAN/MYC/TP63/NPM1/CAV1/EGFR
GO:0005765	lysosomal membrane	72	0.7125772	1.666919	1.645246e-03	1.480722e-02	CTSD/CP/PSAP/CYB561A3/TSPAN1/ATP6AP1/LITAF/GRN/CD74/MFSD1/B2M/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/ARL8B/AP3D1/SCARB2/ATP6AP2
GO:0005794	Golgi apparatus	231	0.5724600	1.514812	1.637631e-03	1.480722e-02	SLPI/GDF15/HLA-B/STEAP4/B4GALT5/ELF3/GOLM1/ST6GALNAC1/LITAF/GRN/HLA-C/GCNT3/CD74/FUT3/PMEPA1/B2M/HLA-A/MTUS1/TRIM22/FUT2/PLD3/RHOBTB3/CCN2/ITM2B/GABARAP/GABARAPL1/RHBDD2/SLC35C1/NCSTN/SERINC3/NEDD9/GRINA/SLC11A2/MGAT4B/ARHGAP32/CDH1/QSOX1/GLB1/TPP1/TMEM59/ERGIC1/RND3/RAB11B/BMP1/SREBF2/CHPF/GBP3/CIB1/LYN/LTBR/PLOD1/GDI1/YIPF3/TMEM132A/TMEM165/GALNT10/TMEM30A/RAB1B/KIAA0319L/ATP1A1/FAM114A1/ERGIC3/ATF6B/DHCR24/AP1B1/LEPROT/GALNT5/GOLM2/CTNNA1/IFNGR2/EXT1/LAPTM4A/GALNT14/PACS1/TM9SF2/NUCB1/COPG1/STK24/KLF5/B4GALT1/AP1G1/TGOLN2/DNM2/NFE2L2/ZDHHC7/CLINT1/TNFRSF1A/SLC35A4/GALNT2
GO:0043202	lysosomal lumen	29	0.8227671	1.681956	2.316199e-03	1.993945e-02	CTSD/PSAP/CTSA/ASAH1/HSPG2/CD74/VCAN/PLD3/ACP2/CSF3/GLB1/SDC4/HGSNAT/TPP1/HEXA/MAN2B1/PLBD2/GNS/LAMP2/IDS/SCARB2/AGRN
GO:0016324	apical plasma membrane	64	0.7086301	1.619634	3.457938e-03	2.852799e-02	CEACAM6/CEACAM5/MUC20/SLC6A14/DUOX2/MUC1/SLC44A4/ATP1B1/SLC26A4/FN1/PDZK1IP1/SCNN1A/TF/IGFBP2/CLDN4/SLC34A2/CEACAM7/SLC15A2/PROM2/SLC11A2/NHERF1/CIB1/TMEM30A/ERBB2/CTSB/ATP1A1/OSMR/MAL2/ATP6V1A/JAG1/PRKAA1/AHCYL1/CLDN1
GO:0031410	cytoplasmic vesicle	117	0.6154723	1.525959	3.715234e-03	2.942465e-02	LCN2/GPRC5A/SERPINB3/SCNN1A/TF/ATP6AP1/STOM/MFGE8/GPNMB/FTH1/SLC15A2/PIGT/TP53INP2/GPRC5B/MMP14/GABARAP/GABARAPL1/PROM2/NCOA4/NCSTN/SLC11A2/GDE1/GIPC1/SREBF2/GBP3/LGALS8/ATP6V0C/TMEM30A/ERBB2/KIAA0319L/SYNGR2/LAMP1/CDK16/TBC1D2/AP1B1/CALR/IFNGR2/ATP6V1A/RNASEK/COPG1/PAM/CD46/AP1G1/BCL2L1/MYO1C/LAMP2/CLINT1
GO:0005813	centrosome	77	-0.6158066	-1.540220	4.550046e-03	3.465035e-02	PTK2/CHD4/CALM2/DYNC1I2/GNAI2/DYNLL1/DYNC1LI2/AJUBA/MAP2K1/PAK1/MDH1/CDK6/CDC27/LUZP1/TCP1/CAMSAP2/CALM3/RPS7/CALM1/MARCHF7/UBR4/CCT4/CKAP5/DIAPH1/GSK3B/USP9X/FEZ1/DHX9/OLA1/CLASP1/CKAP2/CCT5/HNRNPU/SLC16A1/CCNB1/DYNC1H1/NPM1/NDRG1
GO:0071013	catalytic step 2 spliceosome	20	-0.8340422	-1.675624	4.832377e-03	3.543743e-02	PABPC1/SF3B3/HNRNPC/SRRM2/SF3B2/SRRM1/SYNCRIP/PRPF8/HNRNPR/RBMX/HNRNPA3/HNRNPA1/SRSF1/SNRPD2/HNRNPU
GO:1904724	tertiary granule lumen	18	0.8557789	1.587396	6.559059e-03	4.638192e-02	CTSD/CTSH/CXCL1/TIMP2/CSTB/ASAH1/FTH1/B2M/QSOX1/YPEL5
GO:0035577	azurophil granule membrane	24	0.8355374	1.673308	7.039442e-03	4.646032e-02	CEACAM6/PIGR/PSAP/STOM/VAMP8/NCSTN/CD63/ATP6V0C/TMEM30A/LAMP1/B4GALT1/LAMP2/CKAP4/LAMTOR1/BRI3/DDOST
GO:0035580	specific granule lumen	14	0.8954180	1.580039	6.991324e-03	4.646032e-02	LCN2/SLPI/CTSD/CXCL1/TIMP2/B2M/QSOX1/PDXK

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: 250 up-regulated and 166 down-regulated genes

	overlapping/total genes	odds ratio	p-value
low GC – Up-regulation	6/92	0.426	9.92e-01
low GC – Down-regulation	15/92	2.041	1.62e-02
high GC – Up-regulation	24/92	2.354	8.54e-04
high GC – Down-regulation	6/92	0.686	8.59e-01
short genes – Up-regulation	16/92	1.349	1.81e-01
short genes – Down-regulation	7/92	0.816	7.48e-01
long genes – Up-regulation	9/92	0.672	9.04e-01
long genes – Down-regulation	21/92	3.238	3.76e-05

Input dataset

SessionInfo

## ezRun tag: 28496712ee737d3a120e054f95c1bc9b6b30a722 
## ezRun github link: https://github.com/uzh/ezRun/tree/28496712ee737d3a120e054f95c1bc9b6b30a722 
##  
## R version 4.5.0 (2025-04-11)
## Platform: x86_64-pc-linux-gnu
## Running under: Debian GNU/Linux 12 (bookworm)
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0  LAPACK version 3.11.0
## 
## 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_3.2.0                annotate_1.86.0            
##  [3] XML_3.99-0.18               GOstats_2.74.0             
##  [5] graph_1.86.0                Category_2.74.0            
##  [7] pheatmap_1.0.13             RColorBrewer_1.1-3         
##  [9] ggrepel_0.9.6               htmltools_0.5.8.1          
## [11] SingleCellExperiment_1.30.1 Matrix_1.7-3               
## [13] tidyselect_1.2.1            writexl_1.5.4              
## [15] DT_0.33                     DOSE_4.2.0                 
## [17] BiocParallel_1.42.2         readxl_1.4.5               
## [19] htmlwidgets_1.6.4           webshot_0.5.5              
## [21] plotly_4.11.0               kableExtra_1.4.0           
## [23] knitr_1.50                  qs2_0.1.5                  
## [25] clusterProfiler_4.16.0      GO.db_3.21.0               
## [27] AnnotationDbi_1.70.0        edgeR_4.6.3                
## [29] limma_3.64.3                rtracklayer_1.68.0         
## [31] SummarizedExperiment_1.38.1 Biobase_2.68.0             
## [33] MatrixGenerics_1.20.0       matrixStats_1.5.0          
## [35] withr_3.0.2                 ezRun_3.21.1               
## [37] lubridate_1.9.4             forcats_1.0.1              
## [39] stringr_1.5.2               dplyr_1.1.4                
## [41] purrr_1.1.0                 readr_2.1.5                
## [43] tidyr_1.3.1                 tibble_3.3.0               
## [45] ggplot2_4.0.0               tidyverse_2.0.0            
## [47] GenomicRanges_1.60.0        Biostrings_2.76.0          
## [49] GenomeInfoDb_1.44.3         XVector_0.48.0             
## [51] IRanges_2.42.0              S4Vectors_0.46.0           
## [53] BiocGenerics_0.54.1         generics_0.1.4             
## [55] data.table_1.17.8          
## 
## loaded via a namespace (and not attached):
##   [1] splines_4.5.0            BiocIO_1.18.0            filelock_1.0.3          
##   [4] bitops_1.0-9             ggplotify_0.1.3          BiasedUrn_2.0.12        
##   [7] R.oo_1.27.1              cellranger_1.1.0         httr2_1.1.2             
##  [10] lifecycle_1.0.4          lattice_0.22-7           vroom_1.6.5             
##  [13] crosstalk_1.2.1          magrittr_2.0.4           openxlsx_4.2.8          
##  [16] sass_0.4.10              rmarkdown_2.29           jquerylib_0.1.4         
##  [19] yaml_2.3.10              ggtangle_0.0.6           zip_2.3.3               
##  [22] cowplot_1.2.0            DBI_1.2.3                abind_1.4-8             
##  [25] R.utils_2.13.0           RCurl_1.98-1.17          yulab.utils_0.2.1       
##  [28] rappdirs_0.3.3           GenomeInfoDbData_1.2.14  enrichplot_1.28.2       
##  [31] AnnotationForge_1.50.0   tidytree_0.4.6           genefilter_1.90.0       
##  [34] svglite_2.2.1            codetools_0.2-20         DelayedArray_0.34.1     
##  [37] xml2_1.3.8               aplot_0.2.9              UCSC.utils_1.4.0        
##  [40] farver_2.1.2             goseq_1.60.0             BiocFileCache_2.16.0    
##  [43] GenomicAlignments_1.44.0 jsonlite_2.0.0           ggridges_0.5.6          
##  [46] survival_3.8-3           systemfonts_1.2.3        progress_1.2.3          
##  [49] treeio_1.32.0            Rcpp_1.1.0               glue_1.8.0              
##  [52] SparseArray_1.8.1        mgcv_1.9-3               geneLenDataBase_1.44.0  
##  [55] xfun_0.52                qvalue_2.40.0            fastmap_1.2.0           
##  [58] caTools_1.18.3           digest_0.6.37            timechange_0.3.0        
##  [61] R6_2.6.1                 gridGraphics_0.5-1       textshaping_1.0.1       
##  [64] gtools_3.9.5             biomaRt_2.64.0           dichromat_2.0-0.1       
##  [67] RSQLite_2.3.11           R.methodsS3_1.8.2        prettyunits_1.2.0       
##  [70] httr_1.4.7               S4Arrays_1.8.1           pkgconfig_2.0.3         
##  [73] gtable_0.3.6             blob_1.2.4               S7_0.2.0                
##  [76] fgsea_1.34.2             RBGL_1.84.0              GSEABase_1.70.0         
##  [79] scales_1.4.0             png_0.1-8                ggfun_0.2.0             
##  [82] rstudioapi_0.17.1        tzdb_0.5.0               reshape2_1.4.4          
##  [85] rjson_0.2.23             nlme_3.1-168             curl_6.2.3              
##  [88] cachem_1.1.0             KernSmooth_2.23-26       restfulr_0.0.15         
##  [91] pillar_1.11.1            grid_4.5.0               vctrs_0.6.5             
##  [94] stringfish_0.16.0        dbplyr_2.5.0             xtable_1.8-4            
##  [97] Rgraphviz_2.52.0         evaluate_1.0.3           GenomicFeatures_1.60.0  
## [100] cli_3.6.5                locfit_1.5-9.12          compiler_4.5.0          
## [103] Rsamtools_2.24.0         rlang_1.1.6              crayon_1.5.3            
## [106] labeling_0.4.3           plyr_1.8.9               fs_1.6.6                
## [109] stringi_1.8.7            viridisLite_0.4.2        txdbmaker_1.4.1         
## [112] lazyeval_0.2.2           GOSemSim_2.34.0          hms_1.1.3               
## [115] patchwork_1.3.2          bit64_4.6.0-1            KEGGREST_1.48.0         
## [118] statmod_1.5.1            igraph_2.2.0             memoise_2.0.1           
## [121] RcppParallel_5.1.11-1    bslib_0.9.0              ggtree_3.16.3           
## [124] fastmatch_1.1-6          bit_4.6.0                ape_5.8-1               
## [127] gson_0.1.0