Schematic overview of the cellular and molecular mechanisms involved in the cancer progression, including the proposed cellular and molecular mechanisms in cancer cells trajectory. AT1: alveolar type 1 cells; AT2: alveolar type 2 cells; AAH: atypical adenomatous hyperplasia; AIS: adenocarcinoma in situ; MIA: minimally invasive adenocarcinoma; IA: invasive adenocarcinoma; EMT: epithelial-mesenchymal transition

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	Gene summary
	Malignant transformation analysis
	Malignant transformation related pathway analysis
	Cell-cell communication analysis
	Single-cell gene regulatory network inference analysis
	Somatic mutation of malignant transformation related genes
	Related drugs of malignant transformation related genes

Gene: PSME2

Gene summary for PSME2

Gene summary.

Gene information	Species	Human
	Gene symbol	PSME2
	Gene ID	5721
	Gene name	proteasome activator subunit 2
	Gene Alias	PA28B
	Cytomap	14q12
	Gene Type	protein-coding
	GO ID	GO:0000082
	UniProtAcc	Q86SZ7

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Malignant transformation analysis

Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells

Malignant transformation involving gene list.

Entrez ID	Symbol	Replicates	Species	Organ	Tissue	Adj P-value	Log2FC	Malignancy
5721	PSME2	GSM5276934	Human	Endometrium	EEC	1.32e-06	2.02e-01	-0.0913
5721	PSME2	GSM6177620_NYU_UCEC1_lib1_lib1	Human	Endometrium	EEC	4.58e-29	6.65e-02	-0.1869
5721	PSME2	GSM6177620_NYU_UCEC1_lib2_lib2	Human	Endometrium	EEC	1.53e-29	6.41e-02	-0.1875
5721	PSME2	GSM6177620_NYU_UCEC1_lib3_lib3	Human	Endometrium	EEC	9.46e-28	-9.10e-02	-0.1883
5721	PSME2	GSM6177621_NYU_UCEC2_lib1_lib1	Human	Endometrium	EEC	1.78e-29	-3.34e-01	-0.1934
5721	PSME2	GSM6177622_NYU_UCEC3_lib1_lib1	Human	Endometrium	EEC	6.25e-53	-2.53e-01	-0.1917
5721	PSME2	GSM6177622_NYU_UCEC3_lib2_lib2	Human	Endometrium	EEC	1.61e-30	-3.06e-01	-0.1916
5721	PSME2	GSM6177623_NYU_UCEC3_Vis	Human	Endometrium	EEC	1.01e-19	3.36e-01	-0.1269
5721	PSME2	LZE2T	Human	Esophagus	ESCC	2.45e-02	1.30e+00	0.082
5721	PSME2	LZE4T	Human	Esophagus	ESCC	7.91e-24	1.16e+00	0.0811
5721	PSME2	LZE5T	Human	Esophagus	ESCC	1.71e-12	1.78e+00	0.0514
5721	PSME2	LZE7T	Human	Esophagus	ESCC	1.26e-07	7.56e-01	0.0667
5721	PSME2	LZE8T	Human	Esophagus	ESCC	1.26e-19	1.38e+00	0.067
5721	PSME2	LZE20T	Human	Esophagus	ESCC	1.42e-08	9.46e-01	0.0662
5721	PSME2	LZE22T	Human	Esophagus	ESCC	1.23e-04	1.04e+00	0.068
5721	PSME2	LZE24D1	Human	Esophagus	HGIN	1.50e-02	2.21e+00	0.054
5721	PSME2	LZE24T	Human	Esophagus	ESCC	5.84e-45	1.99e+00	0.0596
5721	PSME2	LZE22D3	Human	Esophagus	HGIN	2.17e-07	5.11e-01	0.0653
5721	PSME2	LZE21T	Human	Esophagus	ESCC	1.02e-10	1.47e+00	0.0655
5721	PSME2	LZE6T	Human	Esophagus	ESCC	8.92e-25	1.77e+00	0.0845

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Breast		IDC: Invasive ductal carcinoma
		DCIS: Ductal carcinoma in situ
		Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
Cervix		CC: Cervix cancer
		HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
		N_HPV: HPV-infected normal cervix
Colorectum (GSE201348)		FAP: Familial adenomatous polyposis
		CRC: Colorectal cancer
Colorectum (HTA11)		AD: Adenomas
		SER: Sessile serrated lesions
		MSI-H: Microsatellite-high colorectal cancer
		MSS: Microsatellite stable colorectal cancer
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
GC		CAG: Chronic atrophic gastritis
		CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
		CSG: Chronic superficial gastritis
		GC: Gastric cancer
		SIM: Severe intestinal metaplasia
		WIM: Wild intestinal metaplasia
Liver		HCC: Hepatocellular carcinoma
		NAFLD: Non-alcoholic fatty liver disease
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
Prostate		BPH: Benign Prostatic Hyperplasia
Skin		AK: Actinic keratosis
		cSCC: Cutaneous squamous cell carcinoma
		SCCIS:squamous cell carcinoma in situ
Thyroid		ATC: Anaplastic thyroid cancer
		HT: Hashimoto's thyroiditis
		PTC: Papillary thyroid cancer

∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.

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Malignant transformation related pathway analysis

Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer

Figure of enriched GO biological processes.

Tissue	Disease Stage	Enriched GO biological Processes
Colorectum	AD
Colorectum	SER
Colorectum	MSS
Colorectum	MSI-H
Colorectum	FAP

∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).

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Enriched GO biological processes.

GO ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	Count
GO:00525479	Breast	Precancer	regulation of peptidase activity	71/1080	461/18723	2.72e-14	6.94e-12	71
GO:00525489	Breast	Precancer	regulation of endopeptidase activity	67/1080	432/18723	1.06e-13	2.36e-11	67
GO:00458629	Breast	Precancer	positive regulation of proteolysis	51/1080	372/18723	7.77e-09	5.70e-07	51
GO:00109529	Breast	Precancer	positive regulation of peptidase activity	33/1080	197/18723	3.01e-08	1.89e-06	33
GO:00104989	Breast	Precancer	proteasomal protein catabolic process	58/1080	490/18723	1.54e-07	8.05e-06	58
GO:00109509	Breast	Precancer	positive regulation of endopeptidase activity	29/1080	179/18723	4.23e-07	1.90e-05	29
GO:19033629	Breast	Precancer	regulation of cellular protein catabolic process	36/1080	255/18723	6.03e-07	2.55e-05	36
GO:00421769	Breast	Precancer	regulation of protein catabolic process	47/1080	391/18723	1.50e-06	5.58e-05	47
GO:19030509	Breast	Precancer	regulation of proteolysis involved in cellular protein catabolic process	31/1080	221/18723	4.10e-06	1.27e-04	31
GO:00611369	Breast	Precancer	regulation of proteasomal protein catabolic process	24/1080	187/18723	1.99e-04	3.14e-03	24
GO:005254714	Breast	IDC	regulation of peptidase activity	96/1434	461/18723	7.58e-20	6.15e-17	96
GO:005254814	Breast	IDC	regulation of endopeptidase activity	88/1434	432/18723	1.20e-17	4.85e-15	88
GO:004586214	Breast	IDC	positive regulation of proteolysis	66/1434	372/18723	9.76e-11	1.29e-08	66
GO:001049814	Breast	IDC	proteasomal protein catabolic process	75/1434	490/18723	5.59e-09	4.41e-07	75
GO:001095214	Breast	IDC	positive regulation of peptidase activity	40/1434	197/18723	1.04e-08	7.67e-07	40
GO:004217614	Breast	IDC	regulation of protein catabolic process	63/1434	391/18723	1.32e-08	9.61e-07	63
GO:190336214	Breast	IDC	regulation of cellular protein catabolic process	46/1434	255/18723	4.00e-08	2.68e-06	46
GO:190305014	Breast	IDC	regulation of proteolysis involved in cellular protein catabolic process	41/1434	221/18723	9.77e-08	5.84e-06	41
GO:001095013	Breast	IDC	positive regulation of endopeptidase activity	35/1434	179/18723	2.24e-07	1.17e-05	35
GO:006113614	Breast	IDC	regulation of proteasomal protein catabolic process	33/1434	187/18723	5.24e-06	1.75e-04	33

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0305010	Breast	Precancer	Proteasome	25/684	46/8465	4.35e-16	9.81e-15	7.52e-15	25
hsa0461218	Breast	Precancer	Antigen processing and presentation	19/684	78/8465	9.61e-06	1.12e-04	8.62e-05	19
hsa0305013	Breast	Precancer	Proteasome	25/684	46/8465	4.35e-16	9.81e-15	7.52e-15	25
hsa0461219	Breast	Precancer	Antigen processing and presentation	19/684	78/8465	9.61e-06	1.12e-04	8.62e-05	19
hsa0305023	Breast	IDC	Proteasome	26/867	46/8465	9.89e-15	2.47e-13	1.85e-13	26
hsa0461223	Breast	IDC	Antigen processing and presentation	24/867	78/8465	4.61e-07	8.33e-06	6.23e-06	24
hsa0305033	Breast	IDC	Proteasome	26/867	46/8465	9.89e-15	2.47e-13	1.85e-13	26
hsa0461233	Breast	IDC	Antigen processing and presentation	24/867	78/8465	4.61e-07	8.33e-06	6.23e-06	24
hsa0305042	Breast	DCIS	Proteasome	26/846	46/8465	5.46e-15	1.36e-13	9.99e-14	26
hsa0461242	Breast	DCIS	Antigen processing and presentation	25/846	78/8465	6.75e-08	1.28e-06	9.45e-07	25
hsa0305052	Breast	DCIS	Proteasome	26/846	46/8465	5.46e-15	1.36e-13	9.99e-14	26
hsa0461252	Breast	DCIS	Antigen processing and presentation	25/846	78/8465	6.75e-08	1.28e-06	9.45e-07	25
hsa0461220	Cervix	CC	Antigen processing and presentation	34/1267	78/8465	1.06e-09	2.14e-08	1.26e-08	34
hsa0305014	Cervix	CC	Proteasome	16/1267	46/8465	6.69e-04	3.09e-03	1.83e-03	16
hsa04612110	Cervix	CC	Antigen processing and presentation	34/1267	78/8465	1.06e-09	2.14e-08	1.26e-08	34
hsa0305015	Cervix	CC	Proteasome	16/1267	46/8465	6.69e-04	3.09e-03	1.83e-03	16
hsa0461243	Cervix	N_HPV	Antigen processing and presentation	20/349	78/8465	2.61e-11	1.42e-09	1.11e-09	20
hsa0461253	Cervix	N_HPV	Antigen processing and presentation	20/349	78/8465	2.61e-11	1.42e-09	1.11e-09	20
hsa03050	Colorectum	AD	Proteasome	29/2092	46/8465	3.87e-08	6.18e-07	3.94e-07	29
hsa030501	Colorectum	AD	Proteasome	29/2092	46/8465	3.87e-08	6.18e-07	3.94e-07	29

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Cell-cell communication analysis

Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states

Ligand

Receptor

LRpair

Pathway

Tissue

Disease Stage

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Single-cell gene regulatory network inference analysis

Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states

Cell Type

Tissue

Disease Stage

Target Gene

RSS

Regulon Activity

∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.

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Somatic mutation of malignant transformation related genes

Annotation of somatic variants for genes involved in malignant transformation

Hugo Symbol

Variant Class

Variant Classification

dbSNP RS

HGVSc

HGVSp

HGVSp Short

SWISSPROT

BIOTYPE

SIFT

PolyPhen

Tumor Sample Barcode

Tissue

Histology

Sex

Age

Stage

Therapy Types

Drugs

Outcome

PSME2

SNV

Missense_Mutation

novel

c.512N>A

p.Arg171His

p.R171H

Q9UL46

protein_coding

tolerated(0.06)

benign(0.36)

TCGA-AO-A0J3-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

cyclophosphamide

PSME2

insertion

Nonsense_Mutation

novel

c.98_99insTCGTGATTCTATCAGTTACCTAGCTGGTAGCCTTAAGTAAGT

p.Arg34_Phe35insAspSerIleSerTyrLeuAlaGlySerLeuLysTerValArg

p.R34_F35insDSISYLAGSLK*VR

Q9UL46

protein_coding

TCGA-A2-A0ER-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

PSME2

SNV

Missense_Mutation

novel

c.229G>A

p.Glu77Lys

p.E77K

Q9UL46

protein_coding

tolerated(0.78)

benign(0.059)

TCGA-VS-A958-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

PSME2

SNV

Missense_Mutation

rs150829665

c.511C>T

p.Arg171Cys

p.R171C

Q9UL46

protein_coding

deleterious(0)

possibly_damaging(0.673)

TCGA-A6-3809-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

PSME2

SNV

Missense_Mutation

c.105C>A

p.Phe35Leu

p.F35L

Q9UL46

protein_coding

deleterious(0.04)

possibly_damaging(0.577)

TCGA-AP-A056-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

PSME2

SNV

Missense_Mutation

novel

c.631N>A

p.Ala211Thr

p.A211T

Q9UL46

protein_coding

tolerated(0.18)

benign(0.001)

TCGA-AX-A06F-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

carboplatin

PSME2

SNV

Missense_Mutation

novel

c.358N>A

p.Leu120Met

p.L120M

Q9UL46

protein_coding

tolerated(0.11)

probably_damaging(0.981)

TCGA-AX-A2HC-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

paclitaxel

PSME2

SNV

Missense_Mutation

rs1136581

c.181N>T

p.Arg61Trp

p.R61W

Q9UL46

protein_coding

deleterious(0)

probably_damaging(0.91)

TCGA-AX-A3G8-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

PSME2

SNV

Missense_Mutation

c.101G>T

p.Arg34Ile

p.R34I

Q9UL46

protein_coding

tolerated(0.11)

benign(0.029)

TCGA-B5-A0JY-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

doxorubicin

PSME2

SNV

Missense_Mutation

novel

c.557N>G

p.Asp186Gly

p.D186G

Q9UL46

protein_coding

deleterious(0)

possibly_damaging(0.899)

TCGA-B5-A3FA-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

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Related drugs of malignant transformation related genes

Identification of chemicals and drugs interact with genes involved in malignant transfromation

(DGIdb 4.0)

Entrez ID	Symbol	Category	Interaction Types	Drug Claim Name	Drug Name	PMIDs
5721	PSME2	NA	inhibitor	CARFILZOMIB	CARFILZOMIB
5721	PSME2	NA	inhibitor	BORTEZOMIB	BORTEZOMIB

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