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: EPHA3

Gene summary for EPHA3

Gene summary.

Gene information	Species	Human
	Gene symbol	EPHA3
	Gene ID	2042
	Gene name	EPH receptor A3
	Gene Alias	EK4
	Cytomap	3p11.1
	Gene Type	protein-coding
	GO ID	GO:0000226
	UniProtAcc	A0A140VJJ0

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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
2042	EPHA3	ATC13	Human	Thyroid	ATC	1.03e-79	1.56e+00	0.34
2042	EPHA3	ATC5	Human	Thyroid	ATC	6.33e-73	1.66e+00	0.34

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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:1903829210	Thyroid	ATC	positive regulation of cellular protein localization	167/6293	276/18723	3.32e-20	5.38e-18	167
GO:007265928	Thyroid	ATC	protein localization to plasma membrane	161/6293	284/18723	8.45e-16	6.52e-14	161
GO:003158928	Thyroid	ATC	cell-substrate adhesion	195/6293	363/18723	1.58e-15	1.17e-13	195
GO:199077826	Thyroid	ATC	protein localization to cell periphery	181/6293	333/18723	3.72e-15	2.56e-13	181
GO:0032970210	Thyroid	ATC	regulation of actin filament-based process	208/6293	397/18723	5.82e-15	3.80e-13	208
GO:0032956210	Thyroid	ATC	regulation of actin cytoskeleton organization	190/6293	358/18723	1.73e-14	1.01e-12	190
GO:003134623	Thyroid	ATC	positive regulation of cell projection organization	186/6293	353/18723	7.99e-14	4.23e-12	186
GO:001081029	Thyroid	ATC	regulation of cell-substrate adhesion	128/6293	221/18723	8.74e-14	4.57e-12	128
GO:015011527	Thyroid	ATC	cell-substrate junction organization	70/6293	101/18723	2.29e-13	1.09e-11	70
GO:0007044111	Thyroid	ATC	cell-substrate junction assembly	65/6293	95/18723	4.11e-12	1.62e-10	65
GO:0007160111	Thyroid	ATC	cell-matrix adhesion	128/6293	233/18723	1.49e-11	5.41e-10	128
GO:015011627	Thyroid	ATC	regulation of cell-substrate junction organization	51/6293	71/18723	5.01e-11	1.63e-09	51
GO:0048041110	Thyroid	ATC	focal adhesion assembly	59/6293	87/18723	7.05e-11	2.23e-09	59
GO:0001952110	Thyroid	ATC	regulation of cell-matrix adhesion	78/6293	128/18723	2.09e-10	6.15e-09	78
GO:001097523	Thyroid	ATC	regulation of neuron projection development	212/6293	445/18723	4.16e-10	1.14e-08	212
GO:005189325	Thyroid	ATC	regulation of focal adhesion assembly	47/6293	66/18723	4.64e-10	1.25e-08	47
GO:009010925	Thyroid	ATC	regulation of cell-substrate junction assembly	47/6293	66/18723	4.64e-10	1.25e-08	47
GO:006156423	Thyroid	ATC	axon development	220/6293	467/18723	6.85e-10	1.80e-08	220
GO:0030100111	Thyroid	ATC	regulation of endocytosis	113/6293	211/18723	1.71e-09	4.22e-08	113
GO:007050723	Thyroid	ATC	regulation of microtubule cytoskeleton organization	85/6293	148/18723	2.17e-09	5.21e-08	85

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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
EFNA1	EPHA3	EFNA1_EPHA3	EPHA	CRC	ADJ
EFNA5	EPHA3	EFNA5_EPHA3	EPHA	CRC	ADJ
EFNA1	EPHA3	EFNA1_EPHA3	EPHA	CRC	FAP
EFNA5	EPHA3	EFNA5_EPHA3	EPHA	CRC	FAP
EFNA1	EPHA3	EFNA1_EPHA3	EPHA	Endometrium	ADJ
EFNA5	EPHA3	EFNA5_EPHA3	EPHA	Endometrium	ADJ
EFNA1	EPHA3	EFNA1_EPHA3	EPHA	Endometrium	AEH
EFNA5	EPHA3	EFNA5_EPHA3	EPHA	Endometrium	AEH
EFNA1	EPHA3	EFNA1_EPHA3	EPHA	Esophagus	ESCC
EFNA3	EPHA3	EFNA3_EPHA3	EPHA	Esophagus	ESCC
EFNA4	EPHA3	EFNA4_EPHA3	EPHA	Esophagus	ESCC
EFNA5	EPHA3	EFNA5_EPHA3	EPHA	Esophagus	ESCC
EFNA1	EPHA3	EFNA1_EPHA3	EPHA	GC	ADJ
EFNA5	EPHA3	EFNA5_EPHA3	EPHA	GC	ADJ
EFNA1	EPHA3	EFNA1_EPHA3	EPHA	GC	GC
EFNA5	EPHA3	EFNA5_EPHA3	EPHA	GC	GC
EFNA1	EPHA3	EFNA1_EPHA3	EPHA	Liver	Healthy
EFNA5	EPHA3	EFNA5_EPHA3	EPHA	Liver	Healthy
EFNA1	EPHA3	EFNA1_EPHA3	EPHA	Liver	Precancer
EFNA5	EPHA3	EFNA5_EPHA3	EPHA	Liver	Precancer

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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

EPHA3

SNV

Missense_Mutation

c.960N>T

p.Met320Ile

p.M320I

P29320

protein_coding

tolerated(0.13)

benign(0.014)

TCGA-A2-A25A-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Cytoxan

EPHA3

SNV

Missense_Mutation

novel

c.1535N>A

p.Arg512Gln

p.R512Q

P29320

protein_coding

deleterious(0.01)

probably_damaging(0.994)

TCGA-A8-A07B-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

EPHA3

SNV

Missense_Mutation

novel

c.649N>A

p.Pro217Thr

p.P217T

P29320

protein_coding

tolerated(1)

probably_damaging(0.991)

TCGA-A8-A095-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

EPHA3

SNV

Missense_Mutation

c.285N>G

p.Ile95Met

p.I95M

P29320

protein_coding

deleterious(0)

probably_damaging(0.991)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

EPHA3

SNV

Missense_Mutation

c.2147N>T

p.Ala716Val

p.A716V

P29320

protein_coding

deleterious(0.01)

probably_damaging(0.985)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

EPHA3

SNV

Missense_Mutation

c.947A>T

p.Asp316Val

p.D316V

P29320

protein_coding

deleterious(0)

possibly_damaging(0.598)

TCGA-AR-A24Q-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

EPHA3

SNV

Missense_Mutation

c.1457N>C

p.Ile486Thr

p.I486T

P29320

protein_coding

tolerated(1)

probably_damaging(0.994)

TCGA-BH-A18G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

EPHA3

SNV

Missense_Mutation

c.2712N>G

p.Asp904Glu

p.D904E

P29320

protein_coding

tolerated(0.44)

possibly_damaging(0.857)

TCGA-E9-A1R2-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

taxotere

EPHA3

insertion

Frame_Shift_Ins

novel

c.1227_1228insTTTTTACATTTCTATTCCCTCTTGCTGTATGTTGGTCATAG

p.Asp410PhefsTer23

p.D410Ffs*23

P29320

protein_coding

TCGA-A7-A0CJ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

EPHA3

deletion

Frame_Shift_Del

c.2115_2122delTTCCTTGG

p.Ser706Ter

p.S706*

P29320

protein_coding

TCGA-BH-A18Q-01

Breast

breast invasive 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
2042	EPHA3	ENZYME, KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, DRUGGABLE GENOME	inhibitor	249565850
2042	EPHA3	ENZYME, KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, DRUGGABLE GENOME	inhibitor	HESPERADIN	HESPERADIN	19035792
2042	EPHA3	ENZYME, KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, DRUGGABLE GENOME	antibody	310264706
2042	EPHA3	ENZYME, KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, DRUGGABLE GENOME		Ifabotuzumab
2042	EPHA3	ENZYME, KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, DRUGGABLE GENOME		KB004
2042	EPHA3	ENZYME, KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, DRUGGABLE GENOME		KB-004	KB-004
2042	EPHA3	ENZYME, KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, DRUGGABLE GENOME	inhibitor	249565821
2042	EPHA3	ENZYME, KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, DRUGGABLE GENOME	inhibitor	363894214	SITRAVATINIB
2042	EPHA3	ENZYME, KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, DRUGGABLE GENOME	inhibitor	CHEMBL24828	VANDETANIB

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