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: USP34

Gene summary for USP34

Gene summary.

Gene information	Species	Human
	Gene symbol	USP34
	Gene ID	9736
	Gene name	ubiquitin specific peptidase 34
	Gene Alias	USP34
	Cytomap	2p15
	Gene Type	protein-coding
	GO ID	GO:0006464
	UniProtAcc	Q70CQ2

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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
9736	USP34	CA_HPV_1	Human	Cervix	CC	4.95e-02	-5.58e-02	0.0264
9736	USP34	CCI_1	Human	Cervix	CC	1.89e-03	1.36e+00	0.528
9736	USP34	CCI_2	Human	Cervix	CC	5.57e-12	1.59e+00	0.5249
9736	USP34	CCI_3	Human	Cervix	CC	6.87e-16	1.24e+00	0.516
9736	USP34	HTA11_3410_2000001011	Human	Colorectum	AD	6.89e-11	-5.44e-01	0.0155
9736	USP34	HTA11_2951_2000001011	Human	Colorectum	AD	1.35e-04	-7.23e-01	0.0216
9736	USP34	HTA11_347_2000001011	Human	Colorectum	AD	3.15e-03	3.33e-01	-0.1954
9736	USP34	HTA11_83_2000001011	Human	Colorectum	SER	1.13e-02	-2.69e-01	-0.1526
9736	USP34	HTA11_7862_2000001011	Human	Colorectum	AD	1.35e-03	-4.18e-01	-0.0179
9736	USP34	HTA11_866_3004761011	Human	Colorectum	AD	4.83e-11	-6.28e-01	0.096
9736	USP34	HTA11_8622_2000001021	Human	Colorectum	SER	3.19e-02	-6.28e-01	0.0528
9736	USP34	HTA11_10711_2000001011	Human	Colorectum	AD	1.14e-03	-4.33e-01	0.0338
9736	USP34	HTA11_7696_3000711011	Human	Colorectum	AD	3.87e-13	-5.25e-01	0.0674
9736	USP34	HTA11_7469_2000001011	Human	Colorectum	AD	5.74e-05	-7.54e-01	-0.0124
9736	USP34	HTA11_99999971662_82457	Human	Colorectum	MSS	1.05e-05	-3.26e-01	0.3859
9736	USP34	HTA11_99999973899_84307	Human	Colorectum	MSS	1.24e-03	-6.04e-01	0.2585
9736	USP34	HTA11_99999974143_84620	Human	Colorectum	MSS	7.26e-07	-4.02e-01	0.3005
9736	USP34	F007	Human	Colorectum	FAP	2.47e-04	-3.79e-01	0.1176
9736	USP34	A001-C-207	Human	Colorectum	FAP	5.76e-05	-1.82e-01	0.1278
9736	USP34	A015-C-203	Human	Colorectum	FAP	1.81e-36	-4.60e-01	-0.1294

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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
Liver		HCC: Hepatocellular carcinoma
		NAFLD: Non-alcoholic fatty liver disease
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
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:00160557	Cervix	CC	Wnt signaling pathway	98/2311	444/18723	4.82e-09	4.65e-07	98
GO:01987387	Cervix	CC	cell-cell signaling by wnt	98/2311	446/18723	6.16e-09	5.58e-07	98
GO:00301117	Cervix	CC	regulation of Wnt signaling pathway	76/2311	328/18723	3.05e-08	2.08e-06	76
GO:00608287	Cervix	CC	regulation of canonical Wnt signaling pathway	58/2311	253/18723	1.83e-06	5.89e-05	58
GO:00600707	Cervix	CC	canonical Wnt signaling pathway	66/2311	303/18723	2.47e-06	7.35e-05	66
GO:00301776	Cervix	CC	positive regulation of Wnt signaling pathway	31/2311	140/18723	8.01e-04	7.02e-03	31
GO:00711083	Cervix	CC	protein K48-linked deubiquitination	10/2311	35/18723	7.99e-03	4.18e-02	10
GO:00902636	Cervix	CC	positive regulation of canonical Wnt signaling pathway	22/2311	106/18723	9.52e-03	4.72e-02	22
GO:0030111	Colorectum	AD	regulation of Wnt signaling pathway	102/3918	328/18723	8.51e-06	2.03e-04	102
GO:0016055	Colorectum	AD	Wnt signaling pathway	130/3918	444/18723	1.60e-05	3.37e-04	130
GO:0198738	Colorectum	AD	cell-cell signaling by wnt	130/3918	446/18723	2.02e-05	4.10e-04	130
GO:0060070	Colorectum	AD	canonical Wnt signaling pathway	90/3918	303/18723	1.76e-04	2.38e-03	90
GO:0060828	Colorectum	AD	regulation of canonical Wnt signaling pathway	77/3918	253/18723	2.19e-04	2.87e-03	77
GO:0030177	Colorectum	AD	positive regulation of Wnt signaling pathway	45/3918	140/18723	1.23e-03	1.09e-02	45
GO:00160551	Colorectum	SER	Wnt signaling pathway	97/2897	444/18723	2.02e-04	3.68e-03	97
GO:01987381	Colorectum	SER	cell-cell signaling by wnt	97/2897	446/18723	2.39e-04	4.11e-03	97
GO:00301111	Colorectum	SER	regulation of Wnt signaling pathway	75/2897	328/18723	2.47e-04	4.20e-03	75
GO:00600701	Colorectum	SER	canonical Wnt signaling pathway	66/2897	303/18723	2.10e-03	2.06e-02	66
GO:00608281	Colorectum	SER	regulation of canonical Wnt signaling pathway	56/2897	253/18723	3.03e-03	2.67e-02	56
GO:0090263	Colorectum	SER	positive regulation of canonical Wnt signaling pathway	27/2897	106/18723	5.12e-03	3.92e-02	27

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Enriched KEGG pathways.

Pathway ID

Tissue

Disease Stage

Description

Gene Ratio

Bg Ratio

pvalue

p.adjust

qvalue

Count

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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

USP34

SNV

Missense_Mutation

c.3479G>T

p.Ser1160Ile

p.S1160I

Q70CQ2

protein_coding

deleterious(0)

probably_damaging(0.962)

TCGA-AP-A059-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

USP34

SNV

Missense_Mutation

c.7045N>T

p.Arg2349Cys

p.R2349C

Q70CQ2

protein_coding

tolerated(0.07)

benign(0.075)

TCGA-AP-A0LM-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

cisplatin

USP34

SNV

Missense_Mutation

rs770690878

c.1928N>A

p.Arg643Gln

p.R643Q

Q70CQ2

protein_coding

tolerated_low_confidence(0.2)

benign(0)

TCGA-AP-A0LM-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

cisplatin

USP34

SNV

Missense_Mutation

novel

c.9914N>A

p.Pro3305His

p.P3305H

Q70CQ2

protein_coding

deleterious(0.01)

possibly_damaging(0.478)

TCGA-AP-A1DK-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

USP34

SNV

Missense_Mutation

novel

c.6508N>G

p.Arg2170Gly

p.R2170G

Q70CQ2

protein_coding

deleterious(0)

probably_damaging(0.959)

TCGA-AP-A1DK-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

USP34

SNV

Missense_Mutation

c.10063N>T

p.Arg3355Trp

p.R3355W

Q70CQ2

protein_coding

deleterious(0)

probably_damaging(0.973)

TCGA-AP-A1DV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

USP34

SNV

Missense_Mutation

novel

c.8117N>A

p.Ser2706Tyr

p.S2706Y

Q70CQ2

protein_coding

deleterious(0.04)

probably_damaging(0.974)

TCGA-AP-A1DV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

USP34

SNV

Missense_Mutation

c.7045N>T

p.Arg2349Cys

p.R2349C

Q70CQ2

protein_coding

tolerated(0.07)

benign(0.075)

TCGA-AP-A1DV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

USP34

SNV

Missense_Mutation

rs769491541

c.6712N>T

p.Arg2238Cys

p.R2238C

Q70CQ2

protein_coding

deleterious(0.01)

probably_damaging(0.986)

TCGA-AP-A1DV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

USP34

SNV

Missense_Mutation

novel

c.3784N>G

p.Phe1262Val

p.F1262V

Q70CQ2

protein_coding

tolerated(0.47)

possibly_damaging(0.879)

TCGA-AP-A1DV-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

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