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: EDN3

Gene summary for EDN3

Gene summary.

Gene information	Species	Human
	Gene symbol	EDN3
	Gene ID	1908
	Gene name	endothelin 3
	Gene Alias	ET-3
	Cytomap	20q13.32
	Gene Type	protein-coding
	GO ID	GO:0000165
	UniProtAcc	P14138

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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
1908	EDN3	SYSMH6	Human	Oral cavity	OSCC	2.33e-05	1.63e-01	0.1275

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma

∗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:01400145	Oral cavity	OSCC	mitotic nuclear division	191/7305	287/18723	1.99e-21	3.70e-19	191
GO:00073469	Oral cavity	OSCC	regulation of mitotic cell cycle	266/7305	457/18723	3.87e-17	3.41e-15	266
GO:00482852	Oral cavity	OSCC	organelle fission	265/7305	488/18723	3.22e-12	1.27e-10	265
GO:007190010	Oral cavity	OSCC	regulation of protein serine/threonine kinase activity	201/7305	359/18723	3.90e-11	1.27e-09	201
GO:00002801	Oral cavity	OSCC	nuclear division	237/7305	439/18723	9.62e-11	2.90e-09	237
GO:00457879	Oral cavity	OSCC	positive regulation of cell cycle	173/7305	313/18723	3.28e-09	7.44e-08	173
GO:00434054	Oral cavity	OSCC	regulation of MAP kinase activity	101/7305	177/18723	8.13e-07	1.12e-05	101
GO:00070882	Oral cavity	OSCC	regulation of mitotic nuclear division	68/7305	110/18723	1.05e-06	1.41e-05	68
GO:004586016	Oral cavity	OSCC	positive regulation of protein kinase activity	194/7305	386/18723	3.90e-06	4.59e-05	194
GO:00900688	Oral cavity	OSCC	positive regulation of cell cycle process	126/7305	236/18723	4.75e-06	5.44e-05	126
GO:000268714	Oral cavity	OSCC	positive regulation of leukocyte migration	78/7305	135/18723	7.43e-06	8.08e-05	78
GO:003367418	Oral cavity	OSCC	positive regulation of kinase activity	228/7305	467/18723	8.31e-06	8.90e-05	228
GO:00719028	Oral cavity	OSCC	positive regulation of protein serine/threonine kinase activity	107/7305	200/18723	2.12e-05	2.02e-04	107
GO:0051783	Oral cavity	OSCC	regulation of nuclear division	78/7305	139/18723	3.13e-05	2.86e-04	78
GO:000166719	Oral cavity	OSCC	ameboidal-type cell migration	228/7305	475/18723	3.46e-05	3.10e-04	228
GO:000268510	Oral cavity	OSCC	regulation of leukocyte migration	108/7305	210/18723	1.63e-04	1.13e-03	108
GO:00321037	Oral cavity	OSCC	positive regulation of response to external stimulus	203/7305	427/18723	1.79e-04	1.22e-03	203
GO:00509216	Oral cavity	OSCC	positive regulation of chemotaxis	76/7305	141/18723	2.30e-04	1.49e-03	76
GO:005090010	Oral cavity	OSCC	leukocyte migration	176/7305	369/18723	3.80e-04	2.31e-03	176
GO:00026908	Oral cavity	OSCC	positive regulation of leukocyte chemotaxis	53/7305	94/18723	4.71e-04	2.79e-03	53

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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
EDN3	EDNRA	EDN3_EDNRA	EDN	Cervix	ADJ
EDN3	EDNRB	EDN3_EDNRB	EDN	CRC	AD
EDN3	EDNRA	EDN3_EDNRA	EDN	Endometrium	Healthy
EDN3	EDNRB	EDN3_EDNRB	EDN	Endometrium	Healthy
EDN3	EDNRA	EDN3_EDNRA	EDN	HNSCC	ADJ
EDN3	EDNRB	EDN3_EDNRB	EDN	HNSCC	ADJ

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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

EDN3

SNV

Missense_Mutation

novel

c.685N>A

p.Pro229Thr

p.P229T

P14138

protein_coding

deleterious_low_confidence(0)

benign(0.222)

TCGA-A1-A0SO-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

EDN3

SNV

Missense_Mutation

rs776028645

c.256G>A

p.Glu86Lys

p.E86K

P14138

protein_coding

tolerated(0.49)

benign(0)

TCGA-E2-A10C-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

EDN3

deletion

Frame_Shift_Del

c.684delN

p.Arg230AlafsTer40

p.R230Afs*40

P14138

protein_coding

TCGA-A1-A0SO-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

EDN3

insertion

In_Frame_Ins

novel

c.402_403insGGTGTGGAGAGGGCGGGGTGTGGAGAGGGTGGGGTGTGG

p.Gly134_Ser135insGlyValGluArgAlaGlyCysGlyGluGlyGlyValTrp

p.G134_S135insGVERAGCGEGGVW

P14138

protein_coding

TCGA-AR-A0TW-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

doxorubicin

EDN3

SNV

Missense_Mutation

novel

c.10N>T

p.Gly4Trp

p.G4W

P14138

protein_coding

deleterious(0)

probably_damaging(0.995)

TCGA-MU-A8JM-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

EDN3

SNV

Missense_Mutation

c.265N>A

p.Pro89Thr

p.P89T

P14138

protein_coding

deleterious(0.02)

possibly_damaging(0.718)

TCGA-AA-3966-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

EDN3

SNV

Missense_Mutation

rs778461734

c.478G>A

p.Ala160Thr

p.A160T

P14138

protein_coding

tolerated(0.32)

benign(0.003)

TCGA-AA-3984-01

Colorectum

colon adenocarcinoma

Female

<65

I/II

Unknown

EDN3

SNV

Missense_Mutation

c.286N>T

p.Arg96Cys

p.R96C

P14138

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AZ-4315-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

EDN3

SNV

Missense_Mutation

rs774307682

c.163N>A

p.Glu55Lys

p.E55K

P14138

protein_coding

tolerated(0.27)

benign(0.015)

TCGA-CA-6717-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Chemotherapy

oxaliplatin

EDN3

SNV

Missense_Mutation

c.95N>T

p.Gly32Val

p.G32V

P14138

protein_coding

deleterious(0.04)

possibly_damaging(0.601)

TCGA-D5-6928-01

Colorectum

colon adenocarcinoma

Male

>=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
1908	EDN3	DRUGGABLE GENOME, HORMONE ACTIVITY		HUMAN CHORIONIC GONADOTROPIN		9870082

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