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: USP47

Gene summary for USP47

Gene summary.

Gene information	Species	Human
	Gene symbol	USP47
	Gene ID	55031
	Gene name	ubiquitin specific peptidase 47
	Gene Alias	TRFP
	Cytomap	11p15.3
	Gene Type	protein-coding
	GO ID	GO:0000086
	UniProtAcc	Q68D97

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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
55031	USP47	CCI_2	Human	Cervix	CC	5.49e-03	5.13e-01	0.5249
55031	USP47	CCI_3	Human	Cervix	CC	1.60e-03	5.47e-01	0.516
55031	USP47	HTA11_3410_2000001011	Human	Colorectum	AD	7.18e-16	-6.56e-01	0.0155
55031	USP47	HTA11_2487_2000001011	Human	Colorectum	SER	3.48e-03	-5.42e-01	-0.1808
55031	USP47	HTA11_3361_2000001011	Human	Colorectum	AD	2.20e-08	-7.41e-01	-0.1207
55031	USP47	HTA11_696_2000001011	Human	Colorectum	AD	7.07e-18	-5.53e-01	-0.1464
55031	USP47	HTA11_866_2000001011	Human	Colorectum	AD	9.10e-15	-4.79e-01	-0.1001
55031	USP47	HTA11_1391_2000001011	Human	Colorectum	AD	1.35e-02	-4.22e-01	-0.059
55031	USP47	HTA11_5212_2000001011	Human	Colorectum	AD	5.25e-03	-7.51e-01	-0.2061
55031	USP47	HTA11_546_2000001011	Human	Colorectum	AD	2.27e-02	-4.79e-01	-0.0842
55031	USP47	HTA11_866_3004761011	Human	Colorectum	AD	2.98e-12	-6.71e-01	0.096
55031	USP47	HTA11_8622_2000001021	Human	Colorectum	SER	1.83e-02	-6.95e-01	0.0528
55031	USP47	HTA11_10711_2000001011	Human	Colorectum	AD	9.32e-07	-6.27e-01	0.0338
55031	USP47	HTA11_7696_3000711011	Human	Colorectum	AD	2.14e-21	-5.54e-01	0.0674
55031	USP47	HTA11_6818_2000001021	Human	Colorectum	AD	3.64e-04	-6.33e-01	0.0588
55031	USP47	HTA11_99999970781_79442	Human	Colorectum	MSS	6.31e-06	-3.74e-01	0.294
55031	USP47	HTA11_99999971662_82457	Human	Colorectum	MSS	1.52e-09	-4.39e-01	0.3859
55031	USP47	HTA11_99999973899_84307	Human	Colorectum	MSS	5.62e-05	-6.66e-01	0.2585
55031	USP47	HTA11_99999974143_84620	Human	Colorectum	MSS	1.58e-25	-6.47e-01	0.3005
55031	USP47	A015-C-203	Human	Colorectum	FAP	6.69e-28	-2.14e-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
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:2001020112	Thyroid	PTC	regulation of response to DNA damage stimulus	113/5968	219/18723	9.37e-10	2.77e-08	113
GO:0071214111	Thyroid	PTC	cellular response to abiotic stimulus	158/5968	331/18723	9.90e-10	2.89e-08	158
GO:0104004111	Thyroid	PTC	cellular response to environmental stimulus	158/5968	331/18723	9.90e-10	2.89e-08	158
GO:2001243113	Thyroid	PTC	negative regulation of intrinsic apoptotic signaling pathway	60/5968	98/18723	2.05e-09	5.77e-08	60
GO:0001558111	Thyroid	PTC	regulation of cell growth	188/5968	414/18723	4.13e-09	1.09e-07	188
GO:0060828110	Thyroid	PTC	regulation of canonical Wnt signaling pathway	123/5968	253/18723	1.83e-08	4.26e-07	123
GO:0060070110	Thyroid	PTC	canonical Wnt signaling pathway	141/5968	303/18723	5.71e-08	1.21e-06	141
GO:19019908	Thyroid	PTC	regulation of mitotic cell cycle phase transition	138/5968	299/18723	1.44e-07	2.78e-06	138
GO:007147819	Thyroid	PTC	cellular response to radiation	93/5968	186/18723	1.90e-07	3.51e-06	93
GO:0009314111	Thyroid	PTC	response to radiation	195/5968	456/18723	5.10e-07	8.27e-06	195
GO:00094117	Thyroid	PTC	response to UV	76/5968	149/18723	8.97e-07	1.36e-05	76
GO:003017719	Thyroid	PTC	positive regulation of Wnt signaling pathway	72/5968	140/18723	1.16e-06	1.69e-05	72
GO:0043281113	Thyroid	PTC	regulation of cysteine-type endopeptidase activity involved in apoptotic process	99/5968	209/18723	1.93e-06	2.64e-05	99
GO:00457867	Thyroid	PTC	negative regulation of cell cycle	166/5968	385/18723	1.93e-06	2.64e-05	166
GO:0008630112	Thyroid	PTC	intrinsic apoptotic signaling pathway in response to DNA damage	54/5968	99/18723	2.46e-06	3.22e-05	54
GO:19019878	Thyroid	PTC	regulation of cell cycle phase transition	167/5968	390/18723	2.97e-06	3.87e-05	167
GO:2000116113	Thyroid	PTC	regulation of cysteine-type endopeptidase activity	108/5968	235/18723	3.99e-06	4.99e-05	108
GO:00346447	Thyroid	PTC	cellular response to UV	49/5968	90/18723	7.58e-06	8.77e-05	49
GO:0052547113	Thyroid	PTC	regulation of peptidase activity	191/5968	461/18723	7.82e-06	9.02e-05	191
GO:009026319	Thyroid	PTC	positive regulation of canonical Wnt signaling pathway	55/5968	106/18723	1.45e-05	1.55e-04	55

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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

USP47

SNV

Missense_Mutation

rs754155092

c.2314N>T

p.Arg772Cys

p.R772C

Q96K76

protein_coding

deleterious(0)

probably_damaging(0.965)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

USP47

SNV

Missense_Mutation

c.3127N>C

p.Glu1043Gln

p.E1043Q

Q96K76

protein_coding

tolerated(0.25)

benign(0.047)

TCGA-AR-A0U0-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

USP47

SNV

Missense_Mutation

novel

c.81N>C

p.Met27Ile

p.M27I

Q96K76

protein_coding

tolerated_low_confidence(0.19)

benign(0)

TCGA-BH-A0B6-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

USP47

SNV

Missense_Mutation

c.4046G>A

p.Arg1349His

p.R1349H

Q96K76

protein_coding

tolerated(0.09)

benign(0)

TCGA-BH-A18F-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

USP47

SNV

Missense_Mutation

c.3865C>T

p.His1289Tyr

p.H1289Y

Q96K76

protein_coding

deleterious(0.01)

benign(0.101)

TCGA-C8-A12Q-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

USP47

SNV

Missense_Mutation

c.2879N>G

p.Asp960Gly

p.D960G

Q96K76

protein_coding

tolerated(0.06)

probably_damaging(0.971)

TCGA-D8-A27I-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adrimycin+cyclophosphamide

USP47

SNV

Missense_Mutation

c.1726N>C

p.Asp576His

p.D576H

Q96K76

protein_coding

tolerated(0.1)

benign(0)

TCGA-EW-A1P4-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

docetaxel

USP47

SNV

Missense_Mutation

novel

c.3742G>C

p.Glu1248Gln

p.E1248Q

Q96K76

protein_coding

deleterious(0.04)

probably_damaging(0.954)

TCGA-LD-A74U-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

taxotere

USP47

insertion

Frame_Shift_Ins

novel

c.3125_3126insGTCCCTC

p.Asp1042GlufsTer4

p.D1042Efs*4

Q96K76

protein_coding

TCGA-AR-A0U0-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

USP47

SNV

Missense_Mutation

novel

c.1153N>A

p.Leu385Met

p.L385M

Q96K76

protein_coding

deleterious(0)

probably_damaging(0.996)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

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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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