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: PKP1

Gene summary for PKP1

Gene summary.

Gene information	Species	Human
	Gene symbol	PKP1
	Gene ID	5317
	Gene name	plakophilin 1
	Gene Alias	B6P
	Cytomap	1q32.1
	Gene Type	protein-coding
	GO ID	GO:0006139
	UniProtAcc	Q13835

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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
5317	PKP1	CA_HPV_1	Human	Cervix	CC	3.82e-10	-3.23e-01	0.0264
5317	PKP1	CA_HPV_3	Human	Cervix	CC	4.59e-11	4.19e-01	0.0414
5317	PKP1	HSIL_HPV_1	Human	Cervix	HSIL_HPV	7.11e-04	-3.17e-01	0.0116
5317	PKP1	HSIL_HPV_2	Human	Cervix	HSIL_HPV	2.44e-03	-2.77e-01	0.0208
5317	PKP1	N_HPV_2	Human	Cervix	N_HPV	5.12e-06	3.95e-01	-0.0131
5317	PKP1	CCI_1	Human	Cervix	CC	1.36e-11	1.08e+00	0.528
5317	PKP1	CCI_3	Human	Cervix	CC	2.38e-10	1.05e+00	0.516
5317	PKP1	Tumor	Human	Cervix	CC	4.39e-32	7.30e-01	0.1241
5317	PKP1	sample3	Human	Cervix	CC	4.47e-38	6.63e-01	0.1387
5317	PKP1	T3	Human	Cervix	CC	2.01e-37	6.86e-01	0.1389
5317	PKP1	LZE2T	Human	Esophagus	ESCC	9.78e-07	1.68e+00	0.082
5317	PKP1	LZE4T	Human	Esophagus	ESCC	3.00e-22	9.42e-01	0.0811
5317	PKP1	LZE5T	Human	Esophagus	ESCC	2.34e-02	-1.12e-01	0.0514
5317	PKP1	LZE7T	Human	Esophagus	ESCC	1.55e-13	1.38e+00	0.0667
5317	PKP1	LZE8T	Human	Esophagus	ESCC	1.75e-08	4.25e-01	0.067
5317	PKP1	LZE20T	Human	Esophagus	ESCC	1.10e-06	2.21e-01	0.0662
5317	PKP1	LZE21D1	Human	Esophagus	HGIN	5.70e-03	8.88e-01	0.0632
5317	PKP1	LZE22D1	Human	Esophagus	HGIN	7.87e-05	2.17e-02	0.0595
5317	PKP1	LZE22T	Human	Esophagus	ESCC	7.16e-03	7.79e-01	0.068
5317	PKP1	LZE24T	Human	Esophagus	ESCC	2.48e-08	7.42e-01	0.0596

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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
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
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:00451045	Skin	AK	intermediate filament cytoskeleton organization	14/1910	51/18723	4.29e-04	4.05e-03	14
GO:00451036	Skin	AK	intermediate filament-based process	14/1910	52/18723	5.32e-04	4.84e-03	14
GO:004670019	Skin	AK	heterocycle catabolic process	64/1910	445/18723	3.01e-03	1.88e-02	64
GO:004427020	Skin	AK	cellular nitrogen compound catabolic process	64/1910	451/18723	4.11e-03	2.41e-02	64
GO:001943919	Skin	AK	aromatic compound catabolic process	65/1910	467/18723	5.99e-03	3.24e-02	65
GO:190136119	Skin	AK	organic cyclic compound catabolic process	67/1910	495/18723	9.91e-03	4.80e-02	67
GO:190331126	Skin	cSCC	regulation of mRNA metabolic process	162/4864	288/18723	5.90e-28	2.46e-25	162
GO:0006401111	Skin	cSCC	RNA catabolic process	133/4864	278/18723	2.71e-15	2.23e-13	133
GO:0006402111	Skin	cSCC	mRNA catabolic process	115/4864	232/18723	9.01e-15	6.57e-13	115
GO:0034655111	Skin	cSCC	nucleobase-containing compound catabolic process	172/4864	407/18723	4.11e-13	2.43e-11	172
GO:0046700110	Skin	cSCC	heterocycle catabolic process	178/4864	445/18723	4.45e-11	2.13e-09	178
GO:0044270110	Skin	cSCC	cellular nitrogen compound catabolic process	179/4864	451/18723	8.34e-11	3.79e-09	179
GO:0019439110	Skin	cSCC	aromatic compound catabolic process	183/4864	467/18723	1.76e-10	7.68e-09	183
GO:003133028	Skin	cSCC	negative regulation of cellular catabolic process	115/4864	262/18723	2.03e-10	8.72e-09	115
GO:000989527	Skin	cSCC	negative regulation of catabolic process	133/4864	320/18723	6.99e-10	2.77e-08	133
GO:0061013110	Skin	cSCC	regulation of mRNA catabolic process	79/4864	166/18723	1.57e-09	5.92e-08	79
GO:1901361110	Skin	cSCC	organic cyclic compound catabolic process	188/4864	495/18723	1.92e-09	7.01e-08	188
GO:190331228	Skin	cSCC	negative regulation of mRNA metabolic process	47/4864	92/18723	2.24e-07	4.77e-06	47
GO:190236918	Skin	cSCC	negative regulation of RNA catabolic process	33/4864	75/18723	5.35e-04	3.97e-03	33
GO:004510423	Skin	cSCC	intermediate filament cytoskeleton organization	24/4864	51/18723	9.43e-04	6.42e-03	24

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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

PKP1

SNV

Missense_Mutation

c.1309N>A

p.Ala437Thr

p.A437T

Q13835

protein_coding

deleterious(0.01)

possibly_damaging(0.505)

TCGA-A8-A09Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

PKP1

SNV

Missense_Mutation

c.1600N>C

p.Glu534Gln

p.E534Q

Q13835

protein_coding

tolerated(0.18)

benign(0.424)

TCGA-BH-A0DZ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

docetaxel

PKP1

SNV

Missense_Mutation

c.1738N>T

p.Gly580Trp

p.G580W

Q13835

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-BH-A0E9-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

PKP1

SNV

Missense_Mutation

c.547N>T

p.Arg183Cys

p.R183C

Q13835

protein_coding

deleterious(0)

benign(0.306)

TCGA-BH-A0HA-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

PKP1

SNV

Missense_Mutation

rs781340038

c.548N>A

p.Arg183His

p.R183H

Q13835

protein_coding

deleterious(0.03)

benign(0)

TCGA-BH-A0HA-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

PKP1

SNV

Missense_Mutation

rs751817941

c.1454G>A

p.Arg485His

p.R485H

Q13835

protein_coding

tolerated(0.06)

benign(0.067)

TCGA-E9-A1NC-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

PKP1

insertion

In_Frame_Ins

novel

c.1880_1881insAGGGGAAATGAGACTTCCCTCTCTCCACCCATCTGG

p.Leu627_Leu628insGlyGluMetArgLeuProSerLeuHisProSerGly

p.L627_L628insGEMRLPSLHPSG

Q13835

protein_coding

TCGA-AN-A0FK-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

PKP1

deletion

Frame_Shift_Del

novel

c.1740delG

p.Leu581Ter

p.L581*

Q13835

protein_coding

TCGA-D8-A27V-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

PKP1

deletion

Frame_Shift_Del

novel

c.2172delA

p.Gly725ValfsTer10

p.G725Vfs*10

Q13835

protein_coding

TCGA-D8-A27V-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

PKP1

SNV

Missense_Mutation

novel

c.97A>G

p.Thr33Ala

p.T33A

Q13835

protein_coding

tolerated(0.12)

benign(0.437)

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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