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: ACVR1

Gene summary for ACVR1

Gene summary.

Gene information	Species	Human
	Gene symbol	ACVR1
	Gene ID	90
	Gene name	activin A receptor type 1
	Gene Alias	ACTRI
	Cytomap	2q24.1
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	D3DPA4

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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
90	ACVR1	LZE4T	Human	Esophagus	ESCC	6.78e-03	2.20e-01	0.0811
90	ACVR1	P2T-E	Human	Esophagus	ESCC	2.02e-13	9.83e-02	0.1177
90	ACVR1	P4T-E	Human	Esophagus	ESCC	1.41e-05	1.01e-01	0.1323
90	ACVR1	P5T-E	Human	Esophagus	ESCC	3.59e-06	-1.87e-02	0.1327
90	ACVR1	P8T-E	Human	Esophagus	ESCC	1.02e-14	1.29e-01	0.0889
90	ACVR1	P9T-E	Human	Esophagus	ESCC	1.13e-08	1.07e-01	0.1131
90	ACVR1	P10T-E	Human	Esophagus	ESCC	3.26e-22	2.80e-01	0.116
90	ACVR1	P11T-E	Human	Esophagus	ESCC	3.92e-03	1.92e-01	0.1426
90	ACVR1	P12T-E	Human	Esophagus	ESCC	2.04e-19	2.95e-01	0.1122
90	ACVR1	P15T-E	Human	Esophagus	ESCC	9.29e-15	3.26e-01	0.1149
90	ACVR1	P16T-E	Human	Esophagus	ESCC	2.10e-07	4.62e-02	0.1153
90	ACVR1	P20T-E	Human	Esophagus	ESCC	1.20e-04	7.04e-02	0.1124
90	ACVR1	P21T-E	Human	Esophagus	ESCC	5.00e-12	7.49e-02	0.1617
90	ACVR1	P22T-E	Human	Esophagus	ESCC	4.25e-10	1.21e-01	0.1236
90	ACVR1	P23T-E	Human	Esophagus	ESCC	4.02e-13	2.42e-01	0.108
90	ACVR1	P24T-E	Human	Esophagus	ESCC	3.58e-05	5.75e-02	0.1287
90	ACVR1	P26T-E	Human	Esophagus	ESCC	9.97e-08	7.79e-02	0.1276
90	ACVR1	P27T-E	Human	Esophagus	ESCC	9.24e-04	-1.80e-02	0.1055
90	ACVR1	P28T-E	Human	Esophagus	ESCC	2.22e-11	1.42e-01	0.1149
90	ACVR1	P30T-E	Human	Esophagus	ESCC	1.23e-11	3.03e-01	0.137

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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
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:001821015	Oral cavity	EOLP	peptidyl-threonine modification	35/2218	125/18723	7.33e-07	1.85e-05	35
GO:001810715	Oral cavity	EOLP	peptidyl-threonine phosphorylation	33/2218	116/18723	1.02e-06	2.51e-05	33
GO:004269214	Oral cavity	EOLP	muscle cell differentiation	77/2218	384/18723	2.18e-06	4.91e-05	77
GO:007155916	Oral cavity	EOLP	response to transforming growth factor beta	56/2218	256/18723	3.54e-06	7.58e-05	56
GO:007156016	Oral cavity	EOLP	cellular response to transforming growth factor beta stimulus	54/2218	250/18723	7.76e-06	1.49e-04	54
GO:004477222	Oral cavity	EOLP	mitotic cell cycle phase transition	81/2218	424/18723	8.32e-06	1.59e-04	81
GO:000170123	Oral cavity	EOLP	in utero embryonic development	72/2218	367/18723	1.02e-05	1.83e-04	72
GO:006053715	Oral cavity	EOLP	muscle tissue development	77/2218	403/18723	1.37e-05	2.31e-04	77
GO:00511467	Oral cavity	EOLP	striated muscle cell differentiation	57/2218	283/18723	3.82e-05	5.25e-04	57
GO:000008221	Oral cavity	EOLP	G1/S transition of mitotic cell cycle	46/2218	214/18723	4.02e-05	5.51e-04	46
GO:200123724	Oral cavity	EOLP	negative regulation of extrinsic apoptotic signaling pathway	26/2218	97/18723	4.30e-05	5.82e-04	26
GO:001470614	Oral cavity	EOLP	striated muscle tissue development	72/2218	384/18723	4.87e-05	6.43e-04	72
GO:000717916	Oral cavity	EOLP	transforming growth factor beta receptor signaling pathway	43/2218	198/18723	5.48e-05	7.03e-04	43
GO:000736913	Oral cavity	EOLP	gastrulation	39/2218	185/18723	2.29e-04	2.25e-03	39
GO:004484321	Oral cavity	EOLP	cell cycle G1/S phase transition	47/2218	241/18723	3.79e-04	3.41e-03	47
GO:000717816	Oral cavity	EOLP	transmembrane receptor protein serine/threonine kinase signaling pathway	64/2218	355/18723	3.85e-04	3.46e-03	64
GO:00031702	Oral cavity	EOLP	heart valve development	18/2218	65/18723	4.03e-04	3.58e-03	18
GO:000150322	Oral cavity	EOLP	ossification	70/2218	408/18723	8.89e-04	6.81e-03	70
GO:00182121	Oral cavity	EOLP	peptidyl-tyrosine modification	65/2218	378/18723	1.25e-03	9.02e-03	65
GO:00031792	Oral cavity	EOLP	heart valve morphogenesis	15/2218	55/18723	1.42e-03	9.62e-03	15

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa05418211	Esophagus	ESCC	Fluid shear stress and atherosclerosis	109/4205	139/8465	2.00e-12	3.72e-11	1.90e-11	109
hsa043507	Esophagus	ESCC	TGF-beta signaling pathway	69/4205	108/8465	1.92e-03	5.54e-03	2.84e-03	69
hsa05418310	Esophagus	ESCC	Fluid shear stress and atherosclerosis	109/4205	139/8465	2.00e-12	3.72e-11	1.90e-11	109
hsa0435014	Esophagus	ESCC	TGF-beta signaling pathway	69/4205	108/8465	1.92e-03	5.54e-03	2.84e-03	69
hsa0541830	Oral cavity	OSCC	Fluid shear stress and atherosclerosis	92/3704	139/8465	6.51e-08	4.84e-07	2.47e-07	92
hsa043506	Oral cavity	OSCC	TGF-beta signaling pathway	60/3704	108/8465	8.66e-03	1.97e-02	1.00e-02	60
hsa05418114	Oral cavity	OSCC	Fluid shear stress and atherosclerosis	92/3704	139/8465	6.51e-08	4.84e-07	2.47e-07	92
hsa0435013	Oral cavity	OSCC	TGF-beta signaling pathway	60/3704	108/8465	8.66e-03	1.97e-02	1.00e-02	60
hsa0541846	Oral cavity	EOLP	Fluid shear stress and atherosclerosis	41/1218	139/8465	2.95e-06	2.16e-05	1.28e-05	41
hsa0541856	Oral cavity	EOLP	Fluid shear stress and atherosclerosis	41/1218	139/8465	2.95e-06	2.16e-05	1.28e-05	41
hsa0541863	Oral cavity	NEOLP	Fluid shear stress and atherosclerosis	40/1112	139/8465	7.44e-07	9.10e-06	5.72e-06	40
hsa0541873	Oral cavity	NEOLP	Fluid shear stress and atherosclerosis	40/1112	139/8465	7.44e-07	9.10e-06	5.72e-06	40

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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
TGFB1	ACVR1_TGFbR	TGFB1_ACVR1_TGFBR1	TGFb	Breast	DCIS
TGFB3	ACVR1_TGFbR	TGFB3_ACVR1_TGFBR1	TGFb	Breast	DCIS
BMP7	ACVR1_ACVR2A	BMP7_ACVR1_ACVR2A	BMP	Cervix	CC
BMP7	ACVR1_BMPR2	BMP7_ACVR1_BMPR2	BMP	Cervix	CC
TGFB1	ACVR1_TGFbR	TGFB1_ACVR1_TGFBR1	TGFb	Cervix	CC
INHBA	ACVR1B_ACVR2A	INHBA_ACVR1B_ACVR2A	ACTIVIN	Cervix	CC
INHBB	ACVR1B_ACVR2A	INHBB_ACVR1B_ACVR2A	ACTIVIN	Cervix	CC
TGFB1	ACVR1B_TGFbR2	TGFB1_ACVR1B_TGFBR2	TGFb	CRC	AD
TGFB1	ACVR1B_TGFbR2	TGFB1_ACVR1B_TGFBR2	TGFb	CRC	CRC
TGFB1	ACVR1C_TGFbR2	TGFB1_ACVR1C_TGFBR2	TGFb	CRC	CRC
BMP6	ACVR1_ACVR2A	BMP6_ACVR1_ACVR2A	BMP	CRC	MSI-H
BMP6	ACVR1_ACVR2B	BMP6_ACVR1_ACVR2B	BMP	CRC	MSI-H
BMP6	ACVR1_BMPR2	BMP6_ACVR1_BMPR2	BMP	CRC	MSI-H
TGFB1	ACVR1B_TGFbR2	TGFB1_ACVR1B_TGFBR2	TGFb	CRC	MSI-H
TGFB1	ACVR1_TGFbR	TGFB1_ACVR1_TGFBR1	TGFb	CRC	MSI-H
INHBB	ACVR1B_ACVR2A	INHBB_ACVR1B_ACVR2A	ACTIVIN	CRC	MSI-H
INHBB	ACVR1B_ACVR2B	INHBB_ACVR1B_ACVR2B	ACTIVIN	CRC	MSI-H
BMP8A	ACVR1_BMPR2	BMP8A_ACVR1_BMPR2	BMP	Endometrium	ADJ
TGFB1	ACVR1B_TGFbR2	TGFB1_ACVR1B_TGFBR2	TGFb	Endometrium	AEH
BMP7	ACVR1_BMPR2	BMP7_ACVR1_BMPR2	BMP	Endometrium	AEH

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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

ACVR1

SNV

Missense_Mutation

rs370028017

c.193N>A

p.Val65Ile

p.V65I

Q04771

protein_coding

tolerated(0.21)

benign(0.005)

TCGA-A2-A0D0-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

ACVR1

SNV

Missense_Mutation

novel

c.1270G>A

p.Val424Met

p.V424M

Q04771

protein_coding

tolerated(0.07)

probably_damaging(0.973)

TCGA-LL-A441-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

ACVR1

insertion

In_Frame_Ins

novel

c.260_261insGGATTGCTGCCCTTCATGTGAGTTACAATGTCATGCATG

p.Pro87_Gly88insAspCysCysProSerCysGluLeuGlnCysHisAlaCys

p.P87_G88insDCCPSCELQCHAC

Q04771

protein_coding

TCGA-A8-A07J-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

ACVR1

insertion

Nonsense_Mutation

novel

c.355_356insTAAGGACATTTCATTTCAAAAAGTAGAGAAATACAATTTTTT

p.Asn119delinsIleArgThrPheHisPheLysLysTerArgAsnThrIlePheTyr

p.N119delinsIRTFHFKK*RNTIFY

Q04771

protein_coding

TCGA-AR-A0TY-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Paclitaxel

ACVR1

SNV

Missense_Mutation

novel

c.987N>C

p.Lys329Asn

p.K329N

Q04771

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-A6-3808-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

ACVR1

SNV

Missense_Mutation

c.895N>G

p.Thr299Ala

p.T299A

Q04771

protein_coding

tolerated(0.22)

benign(0.006)

TCGA-AA-3492-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

ACVR1

SNV

Missense_Mutation

c.433N>A

p.Ala145Thr

p.A145T

Q04771

protein_coding

tolerated(0.4)

benign(0.039)

TCGA-AA-3852-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

ACVR1

SNV

Missense_Mutation

novel

c.1411G>T

p.Ala471Ser

p.A471S

Q04771

protein_coding

tolerated(0.42)

benign(0.289)

TCGA-AA-3949-01

Colorectum

colon adenocarcinoma

Female

>=65

III/IV

Unknown

ACVR1

SNV

Missense_Mutation

novel

c.548N>C

p.Leu183Ser

p.L183S

Q04771

protein_coding

deleterious(0.01)

benign(0.307)

TCGA-CA-6717-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Chemotherapy

oxaliplatin

ACVR1

SNV

Missense_Mutation

c.869C>T

p.Ser290Leu

p.S290L

Q04771

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-D5-6530-01

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
90	ACVR1	DRUGGABLE GENOME, ENZYME, KINASE, SERINE THREONINE KINASE		OSI-632	OSI-632
90	ACVR1	DRUGGABLE GENOME, ENZYME, KINASE, SERINE THREONINE KINASE		MEK-1/MEKK-1 INHIBITOR E6201		32142668
90	ACVR1	DRUGGABLE GENOME, ENZYME, KINASE, SERINE THREONINE KINASE	inhibitor	249565824
90	ACVR1	DRUGGABLE GENOME, ENZYME, KINASE, SERINE THREONINE KINASE		681640	CHEMBL379975
90	ACVR1	DRUGGABLE GENOME, ENZYME, KINASE, SERINE THREONINE KINASE		AG-1879	CHEMBL406845
90	ACVR1	DRUGGABLE GENOME, ENZYME, KINASE, SERINE THREONINE KINASE		TANDUTINIB	TANDUTINIB
90	ACVR1	DRUGGABLE GENOME, ENZYME, KINASE, SERINE THREONINE KINASE		VANDETANIB	VANDETANIB
90	ACVR1	DRUGGABLE GENOME, ENZYME, KINASE, SERINE THREONINE KINASE	inhibitor	404859109
90	ACVR1	DRUGGABLE GENOME, ENZYME, KINASE, SERINE THREONINE KINASE		ALK2 INHIBITOR LDN-193189		24705252
90	ACVR1	DRUGGABLE GENOME, ENZYME, KINASE, SERINE THREONINE KINASE	inhibitor	252166689

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