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: PKP4

Gene summary for PKP4

Gene summary.

Gene information	Species	Human
	Gene symbol	PKP4
	Gene ID	8502
	Gene name	plakophilin 4
	Gene Alias	p0071
	Cytomap	2q24.1
	Gene Type	protein-coding
	GO ID	GO:0000910
	UniProtAcc	Q99569

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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
8502	PKP4	CA_HPV_1	Human	Cervix	CC	5.56e-04	-1.78e-01	0.0264
8502	PKP4	CCI_1	Human	Cervix	CC	2.79e-09	1.12e+00	0.528
8502	PKP4	CCI_2	Human	Cervix	CC	1.89e-12	1.48e+00	0.5249
8502	PKP4	CCI_3	Human	Cervix	CC	8.04e-14	1.22e+00	0.516
8502	PKP4	HTA11_3410_2000001011	Human	Colorectum	AD	3.02e-10	-4.88e-01	0.0155
8502	PKP4	HTA11_83_2000001011	Human	Colorectum	SER	1.16e-03	-2.54e-01	-0.1526
8502	PKP4	HTA11_866_3004761011	Human	Colorectum	AD	2.83e-02	-3.74e-01	0.096
8502	PKP4	HTA11_99999973899_84307	Human	Colorectum	MSS	3.98e-03	-5.09e-01	0.2585
8502	PKP4	A015-C-203	Human	Colorectum	FAP	1.17e-28	-5.08e-01	-0.1294
8502	PKP4	A015-C-204	Human	Colorectum	FAP	3.19e-06	-2.40e-01	-0.0228
8502	PKP4	A014-C-040	Human	Colorectum	FAP	4.47e-07	-5.82e-01	-0.1184
8502	PKP4	A002-C-201	Human	Colorectum	FAP	1.24e-13	-3.03e-01	0.0324
8502	PKP4	A001-C-119	Human	Colorectum	FAP	1.61e-07	-4.21e-01	-0.1557
8502	PKP4	A001-C-108	Human	Colorectum	FAP	9.67e-12	-7.68e-02	-0.0272
8502	PKP4	A002-C-205	Human	Colorectum	FAP	5.11e-26	-5.17e-01	-0.1236
8502	PKP4	A015-C-006	Human	Colorectum	FAP	8.31e-16	-7.29e-02	-0.0994
8502	PKP4	A015-C-106	Human	Colorectum	FAP	7.24e-10	-1.73e-01	-0.0511
8502	PKP4	A002-C-114	Human	Colorectum	FAP	1.14e-18	-3.54e-01	-0.1561
8502	PKP4	A015-C-104	Human	Colorectum	FAP	3.22e-28	-4.72e-01	-0.1899
8502	PKP4	A001-C-014	Human	Colorectum	FAP	6.62e-08	-1.84e-01	0.0135

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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
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:004578714	Prostate	Tumor	positive regulation of cell cycle	81/3246	313/18723	8.45e-05	8.46e-04	81
GO:004308713	Prostate	Tumor	regulation of GTPase activity	88/3246	348/18723	1.04e-04	1.00e-03	88
GO:000704317	Prostate	Tumor	cell-cell junction assembly	39/3246	146/18723	2.93e-03	1.58e-02	39
GO:004354713	Prostate	Tumor	positive regulation of GTPase activity	60/3246	255/18723	6.87e-03	3.11e-02	60
GO:009006813	Prostate	Tumor	positive regulation of cell cycle process	56/3246	236/18723	7.35e-03	3.28e-02	56
GO:003432919	Skin	AK	cell junction assembly	86/1910	420/18723	1.95e-10	2.68e-08	86
GO:004521626	Skin	AK	cell-cell junction organization	51/1910	200/18723	4.51e-10	5.24e-08	51
GO:000704319	Skin	AK	cell-cell junction assembly	36/1910	146/18723	3.88e-07	1.47e-05	36
GO:004578716	Skin	AK	positive regulation of cell cycle	58/1910	313/18723	5.08e-06	1.19e-04	58
GO:000091017	Skin	AK	cytokinesis	36/1910	173/18723	2.48e-05	4.47e-04	36
GO:009006810	Skin	AK	positive regulation of cell cycle process	43/1910	236/18723	1.20e-04	1.50e-03	43
GO:004308716	Skin	AK	regulation of GTPase activity	54/1910	348/18723	1.17e-03	8.98e-03	54
GO:0034329110	Skin	SCCIS	cell junction assembly	52/919	420/18723	7.89e-10	5.23e-07	52
GO:004308717	Skin	SCCIS	regulation of GTPase activity	39/919	348/18723	1.38e-06	8.71e-05	39
GO:0045216110	Skin	SCCIS	cell-cell junction organization	26/919	200/18723	5.65e-06	2.29e-04	26
GO:004354710	Skin	SCCIS	positive regulation of GTPase activity	27/919	255/18723	1.48e-04	3.00e-03	27
GO:0007043110	Skin	SCCIS	cell-cell junction assembly	18/919	146/18723	2.94e-04	5.23e-03	18
GO:000091018	Skin	SCCIS	cytokinesis	18/919	173/18723	2.16e-03	2.18e-02	18
GO:000091021	Skin	cSCC	cytokinesis	84/4864	173/18723	1.36e-10	6.04e-09	84
GO:004578717	Skin	cSCC	positive regulation of cell cycle	120/4864	313/18723	8.95e-07	1.64e-05	120

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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

PKP4

SNV

Missense_Mutation

c.1141N>C

p.Asp381His

p.D381H

Q99569

protein_coding

deleterious(0.02)

probably_damaging(0.959)

TCGA-A8-A09G-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

PKP4

SNV

Missense_Mutation

rs766638824

c.754N>A

p.Asp252Asn

p.D252N

Q99569

protein_coding

tolerated(0.08)

benign(0.205)

TCGA-A8-A09N-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

PKP4

SNV

Missense_Mutation

rs750000750

c.1837N>A

p.Val613Ile

p.V613I

Q99569

protein_coding

deleterious(0)

benign(0.245)

TCGA-AC-A3QQ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

PKP4

SNV

Missense_Mutation

novel

c.923C>A

p.Thr308Asn

p.T308N

Q99569

protein_coding

deleterious(0.01)

benign(0.033)

TCGA-AC-A3W7-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

femara

PKP4

SNV

Missense_Mutation

novel

c.521N>T

p.Asn174Ile

p.N174I

Q99569

protein_coding

tolerated(0.44)

benign(0.003)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

PKP4

SNV

Missense_Mutation

rs375821441

c.1961N>A

p.Arg654Gln

p.R654Q

Q99569

protein_coding

tolerated(0.96)

benign(0.055)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

PKP4

SNV

Missense_Mutation

c.3175N>T

p.Arg1059Cys

p.R1059C

Q99569

protein_coding

deleterious(0)

possibly_damaging(0.549)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

PKP4

SNV

Missense_Mutation

c.2645G>A

p.Arg882Lys

p.R882K

Q99569

protein_coding

deleterious(0)

possibly_damaging(0.801)

TCGA-AN-A0FV-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

PKP4

SNV

Missense_Mutation

c.2032G>A

p.Asp678Asn

p.D678N

Q99569

protein_coding

deleterious(0.03)

benign(0.019)

TCGA-AR-A0TT-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

doxorubicin

PKP4

SNV

Missense_Mutation

c.2799N>C

p.Glu933Asp

p.E933D

Q99569

protein_coding

tolerated(1)

benign(0.003)

TCGA-AR-A24Q-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

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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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