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: EFNA5

Gene summary for EFNA5

Gene summary.

Gene information	Species	Human
	Gene symbol	EFNA5
	Gene ID	1946
	Gene name	ephrin A5
	Gene Alias	AF1
	Cytomap	5q21.3
	Gene Type	protein-coding
	GO ID	GO:0000226
	UniProtAcc	P52803

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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
1946	EFNA5	CA_HPV_1	Human	Cervix	CC	1.72e-03	-1.51e-01	0.0264
1946	EFNA5	CCI_2	Human	Cervix	CC	1.58e-03	7.92e-01	0.5249
1946	EFNA5	CCI_3	Human	Cervix	CC	4.11e-15	1.09e+00	0.516
1946	EFNA5	HTA11_3410_2000001011	Human	Colorectum	AD	3.10e-50	-1.22e+00	0.0155
1946	EFNA5	HTA11_2487_2000001011	Human	Colorectum	SER	5.75e-08	-7.54e-01	-0.1808
1946	EFNA5	HTA11_2951_2000001011	Human	Colorectum	AD	3.21e-09	-1.18e+00	0.0216
1946	EFNA5	HTA11_1938_2000001011	Human	Colorectum	AD	1.13e-04	-6.94e-01	-0.0811
1946	EFNA5	HTA11_3361_2000001011	Human	Colorectum	AD	2.99e-21	-9.79e-01	-0.1207
1946	EFNA5	HTA11_696_2000001011	Human	Colorectum	AD	1.26e-31	-7.70e-01	-0.1464
1946	EFNA5	HTA11_866_2000001011	Human	Colorectum	AD	1.47e-11	-6.04e-01	-0.1001
1946	EFNA5	HTA11_1391_2000001011	Human	Colorectum	AD	1.30e-15	-8.20e-01	-0.059
1946	EFNA5	HTA11_2992_2000001011	Human	Colorectum	SER	6.02e-03	-6.91e-01	-0.1706
1946	EFNA5	HTA11_5212_2000001011	Human	Colorectum	AD	1.53e-09	-7.67e-01	-0.2061
1946	EFNA5	HTA11_5216_2000001011	Human	Colorectum	SER	7.15e-04	-6.95e-01	-0.1462
1946	EFNA5	HTA11_7862_2000001011	Human	Colorectum	AD	3.18e-03	-4.56e-01	-0.0179
1946	EFNA5	HTA11_866_3004761011	Human	Colorectum	AD	2.15e-41	-1.18e+00	0.096
1946	EFNA5	HTA11_9408_2000001011	Human	Colorectum	AD	9.12e-06	-1.10e+00	0.0451
1946	EFNA5	HTA11_8622_2000001021	Human	Colorectum	SER	2.88e-13	-1.27e+00	0.0528
1946	EFNA5	HTA11_6801_2000001011	Human	Colorectum	SER	1.21e-04	-6.10e-01	0.0171
1946	EFNA5	HTA11_10711_2000001011	Human	Colorectum	AD	3.60e-19	-9.00e-01	0.0338

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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
GC		CAG: Chronic atrophic gastritis
		CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
		CSG: Chronic superficial gastritis
		GC: Gastric cancer
		SIM: Severe intestinal metaplasia
		WIM: Wild intestinal metaplasia
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:000195224	Skin	cSCC	regulation of cell-matrix adhesion	57/4864	128/18723	4.07e-06	6.07e-05	57
GO:001081027	Skin	cSCC	regulation of cell-substrate adhesion	88/4864	221/18723	4.26e-06	6.32e-05	88
GO:005189324	Skin	cSCC	regulation of focal adhesion assembly	34/4864	66/18723	8.09e-06	1.09e-04	34
GO:009010924	Skin	cSCC	regulation of cell-substrate junction assembly	34/4864	66/18723	8.09e-06	1.09e-04	34
GO:003297029	Skin	cSCC	regulation of actin filament-based process	142/4864	397/18723	8.50e-06	1.13e-04	142
GO:002260427	Skin	cSCC	regulation of cell morphogenesis	114/4864	309/18723	1.34e-05	1.68e-04	114
GO:004804124	Skin	cSCC	focal adhesion assembly	41/4864	87/18723	1.71e-05	2.07e-04	41
GO:003158926	Skin	cSCC	cell-substrate adhesion	130/4864	363/18723	1.87e-05	2.23e-04	130
GO:007050716	Skin	cSCC	regulation of microtubule cytoskeleton organization	61/4864	148/18723	3.61e-05	3.90e-04	61
GO:003295629	Skin	cSCC	regulation of actin cytoskeleton organization	127/4864	358/18723	3.83e-05	4.13e-04	127
GO:001076925	Skin	cSCC	regulation of cell morphogenesis involved in differentiation	43/4864	96/18723	5.00e-05	5.18e-04	43
GO:1900024110	Skin	cSCC	regulation of substrate adhesion-dependent cell spreading	28/4864	57/18723	1.47e-04	1.32e-03	28
GO:000716024	Skin	cSCC	cell-matrix adhesion	85/4864	233/18723	2.43e-04	1.98e-03	85
GO:000974328	Skin	cSCC	response to carbohydrate	88/4864	253/18723	1.11e-03	7.31e-03	88
GO:0034446110	Skin	cSCC	substrate adhesion-dependent cell spreading	43/4864	108/18723	1.12e-03	7.36e-03	43
GO:003428427	Skin	cSCC	response to monosaccharide	79/4864	225/18723	1.43e-03	9.02e-03	79
GO:004801321	Skin	cSCC	ephrin receptor signaling pathway	23/4864	51/18723	2.41e-03	1.38e-02	23
GO:003288612	Skin	cSCC	regulation of microtubule-based process	82/4864	240/18723	2.82e-03	1.58e-02	82
GO:001077121	Skin	cSCC	negative regulation of cell morphogenesis involved in differentiation	9/4864	14/18723	2.87e-03	1.60e-02	9
GO:190002521	Skin	cSCC	negative regulation of substrate adhesion-dependent cell spreading	9/4864	14/18723	2.87e-03	1.60e-02	9

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0401512	Cervix	CC	Rap1 signaling pathway	56/1267	210/8465	6.23e-06	5.61e-05	3.32e-05	56
hsa043609	Cervix	CC	Axon guidance	47/1267	182/8465	8.13e-05	5.38e-04	3.18e-04	47
hsa040142	Cervix	CC	Ras signaling pathway	51/1267	236/8465	3.55e-03	1.34e-02	7.91e-03	51
hsa040109	Cervix	CC	MAPK signaling pathway	62/1267	302/8465	4.89e-03	1.67e-02	9.86e-03	62
hsa0401513	Cervix	CC	Rap1 signaling pathway	56/1267	210/8465	6.23e-06	5.61e-05	3.32e-05	56
hsa0436012	Cervix	CC	Axon guidance	47/1267	182/8465	8.13e-05	5.38e-04	3.18e-04	47
hsa0401411	Cervix	CC	Ras signaling pathway	51/1267	236/8465	3.55e-03	1.34e-02	7.91e-03	51
hsa0401012	Cervix	CC	MAPK signaling pathway	62/1267	302/8465	4.89e-03	1.67e-02	9.86e-03	62
hsa04015	Colorectum	AD	Rap1 signaling pathway	71/2092	210/8465	1.72e-03	9.68e-03	6.18e-03	71
hsa04360	Colorectum	AD	Axon guidance	61/2092	182/8465	4.36e-03	2.17e-02	1.38e-02	61
hsa040151	Colorectum	AD	Rap1 signaling pathway	71/2092	210/8465	1.72e-03	9.68e-03	6.18e-03	71
hsa043601	Colorectum	AD	Axon guidance	61/2092	182/8465	4.36e-03	2.17e-02	1.38e-02	61
hsa040152	Colorectum	SER	Rap1 signaling pathway	54/1580	210/8465	6.55e-03	3.68e-02	2.67e-02	54
hsa040153	Colorectum	SER	Rap1 signaling pathway	54/1580	210/8465	6.55e-03	3.68e-02	2.67e-02	54
hsa040154	Colorectum	MSS	Rap1 signaling pathway	66/1875	210/8465	1.03e-03	5.94e-03	3.64e-03	66
hsa043602	Colorectum	MSS	Axon guidance	54/1875	182/8465	1.03e-02	3.69e-02	2.26e-02	54
hsa040155	Colorectum	MSS	Rap1 signaling pathway	66/1875	210/8465	1.03e-03	5.94e-03	3.64e-03	66
hsa043603	Colorectum	MSS	Axon guidance	54/1875	182/8465	1.03e-02	3.69e-02	2.26e-02	54
hsa040156	Colorectum	FAP	Rap1 signaling pathway	53/1404	210/8465	7.93e-04	5.14e-03	3.13e-03	53
hsa043604	Colorectum	FAP	Axon guidance	47/1404	182/8465	9.09e-04	5.20e-03	3.16e-03	47

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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
EFNA5	EPHA2	EFNA5_EPHA2	EPHA	Breast	DCIS
EFNA5	EPHA2	EFNA5_EPHA2	EPHA	Cervix	CC
EFNA5	EPHA4	EFNA5_EPHA4	EPHA	Cervix	CC
EFNA5	EPHB2	EFNA5_EPHB2	EPHA	Cervix	CC
EFNA5	EPHA4	EFNA5_EPHA4	EPHA	CRC	AD
EFNA5	EPHB2	EFNA5_EPHB2	EPHA	CRC	AD
EFNA5	EPHA3	EFNA5_EPHA3	EPHA	CRC	ADJ
EFNA5	EPHA4	EFNA5_EPHA4	EPHA	CRC	ADJ
EFNA5	EPHB2	EFNA5_EPHB2	EPHA	CRC	ADJ
EFNA5	EPHB2	EFNA5_EPHB2	EPHA	CRC	CRC
EFNA5	EPHA2	EFNA5_EPHA2	EPHA	CRC	FAP
EFNA5	EPHA3	EFNA5_EPHA3	EPHA	CRC	FAP
EFNA5	EPHA4	EFNA5_EPHA4	EPHA	CRC	FAP
EFNA5	EPHB2	EFNA5_EPHB2	EPHA	CRC	FAP
EFNA5	EPHA4	EFNA5_EPHA4	EPHA	CRC	Healthy
EFNA5	EPHB2	EFNA5_EPHB2	EPHA	CRC	Healthy
EFNA5	EPHA2	EFNA5_EPHA2	EPHA	CRC	MSI-H
EFNA5	EPHA4	EFNA5_EPHA4	EPHA	CRC	MSI-H
EFNA5	EPHA5	EFNA5_EPHA5	EPHA	CRC	MSI-H
EFNA5	EPHB2	EFNA5_EPHB2	EPHA	CRC	MSI-H

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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

EFNA5

SNV

Missense_Mutation

novel

c.560N>A

p.Pro187Gln

p.P187Q

P52803

protein_coding

tolerated(0.08)

possibly_damaging(0.641)

TCGA-A2-A25A-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Cytoxan

EFNA5

SNV

Missense_Mutation

novel

c.533A>G

p.Asn178Ser

p.N178S

P52803

protein_coding

tolerated(0.21)

benign(0.038)

TCGA-EW-A423-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

anastrozole

EFNA5

SNV

Missense_Mutation

c.644N>C

p.Leu215Ser

p.L215S

P52803

protein_coding

deleterious_low_confidence(0)

possibly_damaging(0.766)

TCGA-A6-6780-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

EFNA5

SNV

Missense_Mutation

rs767938203

c.680N>T

p.Thr227Ile

p.T227I

P52803

protein_coding

tolerated_low_confidence(0.2)

benign(0)

TCGA-AA-3975-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

EFNA5

SNV

Missense_Mutation

c.517C>T

p.Arg173Cys

p.R173C

P52803

protein_coding

deleterious(0)

possibly_damaging(0.759)

TCGA-AG-A002-01

Colorectum

rectum adenocarcinoma

Male

<65

I/II

Unknown

EFNA5

SNV

Missense_Mutation

novel

c.374C>T

p.Ser125Phe

p.S125F

P52803

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-AG-A002-01

Colorectum

rectum adenocarcinoma

Male

<65

I/II

Unknown

EFNA5

SNV

Missense_Mutation

rs780608946

c.271G>A

p.Asp91Asn

p.D91N

P52803

protein_coding

tolerated(0.23)

benign(0.083)

TCGA-AG-A002-01

Colorectum

rectum adenocarcinoma

Male

<65

I/II

Unknown

EFNA5

SNV

Missense_Mutation

novel

c.15N>T

p.Glu5Asp

p.E5D

P52803

protein_coding

tolerated(0.25)

benign(0.001)

TCGA-F5-6814-01

Colorectum

rectum adenocarcinoma

Male

<65

I/II

Unknown

EFNA5

SNV

Missense_Mutation

novel

c.618N>T

p.Gln206His

p.Q206H

P52803

protein_coding

tolerated_low_confidence(0.14)

benign(0)

TCGA-AJ-A23O-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

EFNA5

SNV

Missense_Mutation

novel

c.446G>T

p.Arg149Met

p.R149M

P52803

protein_coding

deleterious(0)

possibly_damaging(0.774)

TCGA-AP-A056-01

Endometrium

uterine corpus endometrioid 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

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