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: COL4A1

Gene summary for COL4A1

Gene summary.

Gene information	Species	Human
	Gene symbol	COL4A1
	Gene ID	1282
	Gene name	collagen type IV alpha 1 chain
	Gene Alias	BSVD
	Cytomap	13q34
	Gene Type	protein-coding
	GO ID	GO:0001101
	UniProtAcc	A5PKV2

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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
1282	COL4A1	AEH-subject1	Human	Endometrium	AEH	2.99e-02	-5.15e-02	-0.3059
1282	COL4A1	AEH-subject2	Human	Endometrium	AEH	5.00e-03	-1.53e-01	-0.2525
1282	COL4A1	AEH-subject3	Human	Endometrium	AEH	4.98e-04	-1.43e-01	-0.2576
1282	COL4A1	AEH-subject4	Human	Endometrium	AEH	3.30e-07	3.57e-01	-0.2657
1282	COL4A1	AEH-subject5	Human	Endometrium	AEH	2.43e-02	1.91e-02	-0.2953
1282	COL4A1	EEC-subject2	Human	Endometrium	EEC	3.85e-04	-1.13e-01	-0.2607
1282	COL4A1	EEC-subject3	Human	Endometrium	EEC	1.80e-20	-3.86e-02	-0.2525
1282	COL4A1	EEC-subject4	Human	Endometrium	EEC	1.66e-03	-2.43e-02	-0.2571
1282	COL4A1	EEC-subject5	Human	Endometrium	EEC	1.46e-03	-1.46e-01	-0.249
1282	COL4A1	GSM5276937	Human	Endometrium	EEC	4.14e-14	5.73e-01	-0.0897
1282	COL4A1	GSM6177620_NYU_UCEC1_lib1_lib1	Human	Endometrium	EEC	4.41e-12	-1.95e-01	-0.1869
1282	COL4A1	GSM6177620_NYU_UCEC1_lib2_lib2	Human	Endometrium	EEC	2.21e-15	-2.08e-01	-0.1875
1282	COL4A1	GSM6177620_NYU_UCEC1_lib3_lib3	Human	Endometrium	EEC	9.39e-14	-2.07e-01	-0.1883
1282	COL4A1	GSM6177621_NYU_UCEC2_lib1_lib1	Human	Endometrium	EEC	9.80e-08	-7.29e-02	-0.1934
1282	COL4A1	GSM6177622_NYU_UCEC3_lib1_lib1	Human	Endometrium	EEC	1.03e-16	-2.84e-01	-0.1917
1282	COL4A1	GSM6177622_NYU_UCEC3_lib2_lib2	Human	Endometrium	EEC	1.50e-17	-3.09e-01	-0.1916
1282	COL4A1	GSM6177623_NYU_UCEC3_Vis	Human	Endometrium	EEC	3.28e-02	1.91e-01	-0.1269
1282	COL4A1	LZE2T	Human	Esophagus	ESCC	4.73e-03	4.95e-01	0.082
1282	COL4A1	LZE4T	Human	Esophagus	ESCC	2.37e-02	1.01e-01	0.0811
1282	COL4A1	LZE7T	Human	Esophagus	ESCC	6.13e-07	4.11e-01	0.0667

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
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
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:00016556	Endometrium	AEH	urogenital system development	67/2100	338/18723	2.30e-06	6.76e-05	67
GO:00720015	Endometrium	AEH	renal system development	61/2100	302/18723	3.43e-06	9.24e-05	61
GO:00605627	Endometrium	AEH	epithelial tube morphogenesis	63/2100	325/18723	9.63e-06	2.23e-04	63
GO:00611384	Endometrium	AEH	morphogenesis of a branching epithelium	40/2100	182/18723	2.16e-05	4.20e-04	40
GO:00017637	Endometrium	AEH	morphogenesis of a branching structure	42/2100	196/18723	2.58e-05	4.86e-04	42
GO:00487542	Endometrium	AEH	branching morphogenesis of an epithelial tube	33/2100	151/18723	1.22e-04	1.68e-03	33
GO:00613263	Endometrium	AEH	renal tubule development	22/2100	94/18723	5.89e-04	5.82e-03	22
GO:00011017	Endometrium	AEH	response to acid chemical	28/2100	135/18723	9.24e-04	8.43e-03	28
GO:0061333	Endometrium	AEH	renal tubule morphogenesis	18/2100	75/18723	1.32e-03	1.12e-02	18
GO:00432005	Endometrium	AEH	response to amino acid	24/2100	116/18723	2.14e-03	1.65e-02	24
GO:00508086	Endometrium	AEH	synapse organization	67/2100	426/18723	2.67e-03	1.94e-02	67
GO:00712302	Endometrium	AEH	cellular response to amino acid stimulus	16/2100	71/18723	4.68e-03	2.99e-02	16
GO:00712293	Endometrium	AEH	cellular response to acid chemical	17/2100	80/18723	6.76e-03	3.94e-02	17
GO:000165512	Endometrium	EEC	urogenital system development	69/2168	338/18723	1.70e-06	5.18e-05	69
GO:007200112	Endometrium	EEC	renal system development	63/2168	302/18723	2.24e-06	6.59e-05	63
GO:006056213	Endometrium	EEC	epithelial tube morphogenesis	64/2168	325/18723	1.35e-05	2.70e-04	64
GO:006113812	Endometrium	EEC	morphogenesis of a branching epithelium	41/2168	182/18723	1.96e-05	3.57e-04	41
GO:000176313	Endometrium	EEC	morphogenesis of a branching structure	43/2168	196/18723	2.47e-05	4.37e-04	43
GO:00487541	Endometrium	EEC	branching morphogenesis of an epithelial tube	33/2168	151/18723	2.23e-04	2.67e-03	33
GO:000110113	Endometrium	EEC	response to acid chemical	29/2168	135/18723	6.98e-04	6.68e-03	29

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0451015	Endometrium	AEH	Focal adhesion	58/1197	203/8465	4.99e-08	7.37e-07	5.39e-07	58
hsa051466	Endometrium	AEH	Amoebiasis	29/1197	102/8465	1.22e-04	1.10e-03	8.06e-04	29
hsa049337	Endometrium	AEH	AGE-RAGE signaling pathway in diabetic complications	28/1197	100/8465	2.11e-04	1.80e-03	1.32e-03	28
hsa0451016	Endometrium	AEH	Focal adhesion	58/1197	203/8465	4.99e-08	7.37e-07	5.39e-07	58
hsa0514613	Endometrium	AEH	Amoebiasis	29/1197	102/8465	1.22e-04	1.10e-03	8.06e-04	29
hsa0493314	Endometrium	AEH	AGE-RAGE signaling pathway in diabetic complications	28/1197	100/8465	2.11e-04	1.80e-03	1.32e-03	28
hsa0451024	Endometrium	EEC	Focal adhesion	58/1237	203/8465	1.61e-07	2.30e-06	1.71e-06	58
hsa0493321	Endometrium	EEC	AGE-RAGE signaling pathway in diabetic complications	28/1237	100/8465	3.68e-04	3.03e-03	2.26e-03	28
hsa0514622	Endometrium	EEC	Amoebiasis	28/1237	102/8465	5.23e-04	3.83e-03	2.85e-03	28
hsa0451034	Endometrium	EEC	Focal adhesion	58/1237	203/8465	1.61e-07	2.30e-06	1.71e-06	58
hsa0493331	Endometrium	EEC	AGE-RAGE signaling pathway in diabetic complications	28/1237	100/8465	3.68e-04	3.03e-03	2.26e-03	28
hsa0514632	Endometrium	EEC	Amoebiasis	28/1237	102/8465	5.23e-04	3.83e-03	2.85e-03	28
hsa0516510	Esophagus	ESCC	Human papillomavirus infection	215/4205	331/8465	7.86e-09	7.12e-08	3.65e-08	215
hsa052229	Esophagus	ESCC	Small cell lung cancer	69/4205	92/8465	5.40e-07	3.85e-06	1.97e-06	69
hsa0493310	Esophagus	ESCC	AGE-RAGE signaling pathway in diabetic complications	72/4205	100/8465	4.15e-06	2.28e-05	1.17e-05	72
hsa0451020	Esophagus	ESCC	Focal adhesion	127/4205	203/8465	1.25e-04	4.99e-04	2.56e-04	127
hsa049268	Esophagus	ESCC	Relaxin signaling pathway	81/4205	129/8465	1.72e-03	5.09e-03	2.61e-03	81
hsa041517	Esophagus	ESCC	PI3K-Akt signaling pathway	197/4205	354/8465	1.24e-02	2.83e-02	1.45e-02	197
hsa0516515	Esophagus	ESCC	Human papillomavirus infection	215/4205	331/8465	7.86e-09	7.12e-08	3.65e-08	215
hsa0522216	Esophagus	ESCC	Small cell lung cancer	69/4205	92/8465	5.40e-07	3.85e-06	1.97e-06	69

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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
COL4A1	ITGA1_ITGB1	COL4A1_ITGA1_ITGB1	COLLAGEN	Breast	ADJ
COL4A1	ITGA2_ITGB1	COL4A1_ITGA2_ITGB1	COLLAGEN	Breast	ADJ
COL4A1	CD44	COL4A1_CD44	COLLAGEN	Breast	ADJ
COL4A1	SDC4	COL4A1_SDC4	COLLAGEN	Breast	ADJ
COL4A1	ITGA1_ITGB1	COL4A1_ITGA1_ITGB1	COLLAGEN	Breast	DCIS
COL4A1	ITGA2_ITGB1	COL4A1_ITGA2_ITGB1	COLLAGEN	Breast	DCIS
COL4A1	CD44	COL4A1_CD44	COLLAGEN	Breast	DCIS
COL4A1	SDC1	COL4A1_SDC1	COLLAGEN	Breast	DCIS
COL4A1	SDC4	COL4A1_SDC4	COLLAGEN	Breast	DCIS
COL4A1	ITGA1_ITGB1	COL4A1_ITGA1_ITGB1	COLLAGEN	Breast	Healthy
COL4A1	ITGA2_ITGB1	COL4A1_ITGA2_ITGB1	COLLAGEN	Breast	Healthy
COL4A1	ITGAV_ITGB8	COL4A1_ITGAV_ITGB8	COLLAGEN	Breast	Healthy
COL4A1	CD44	COL4A1_CD44	COLLAGEN	Breast	Healthy
COL4A1	SDC1	COL4A1_SDC1	COLLAGEN	Breast	Healthy
COL4A1	SDC4	COL4A1_SDC4	COLLAGEN	Breast	Healthy
COL4A1	ITGA1_ITGB1	COL4A1_ITGA1_ITGB1	COLLAGEN	Breast	IDC
COL4A1	CD44	COL4A1_CD44	COLLAGEN	Breast	IDC
COL4A1	SDC1	COL4A1_SDC1	COLLAGEN	Breast	IDC
COL4A1	SDC4	COL4A1_SDC4	COLLAGEN	Breast	IDC
COL4A1	ITGA1_ITGB1	COL4A1_ITGA1_ITGB1	COLLAGEN	Breast	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

COL4A1

SNV

Missense_Mutation

c.667N>C

p.Ser223Arg

p.S223R

P02462

protein_coding

tolerated(0.09)

possibly_damaging(0.571)

TCGA-A8-A08G-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

COL4A1

SNV

Missense_Mutation

novel

c.3467N>T

p.Asp1156Val

p.D1156V

P02462

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-A8-A09E-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

anastrozole

COL4A1

SNV

Missense_Mutation

rs367914388

c.2559A>G

p.Ile853Met

p.I853M

P02462

protein_coding

tolerated(0.21)

possibly_damaging(0.629)

TCGA-AC-A23C-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

chemo

COL4A1

SNV

Missense_Mutation

c.3220N>A

p.Phe1074Ile

p.F1074I

P02462

protein_coding

tolerated(0.13)

probably_damaging(0.991)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL4A1

SNV

Missense_Mutation

rs753989899

c.343N>A

p.Gly115Ser

p.G115S

P02462

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AN-A03Y-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL4A1

SNV

Missense_Mutation

novel

c.4395N>C

p.Lys1465Asn

p.K1465N

P02462

protein_coding

tolerated(0.34)

benign(0.268)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL4A1

SNV

Missense_Mutation

novel

c.2863N>A

p.Glu955Lys

p.E955K

P02462

protein_coding

tolerated(0.32)

probably_damaging(0.979)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL4A1

SNV

Missense_Mutation

novel

c.781N>A

p.Gly261Ser

p.G261S

P02462

protein_coding

deleterious(0)

possibly_damaging(0.49)

TCGA-AO-A0JB-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cyclophosphamide

COL4A1

SNV

Missense_Mutation

novel

c.3716G>A

p.Gly1239Glu

p.G1239E

P02462

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AO-A0JD-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cyclophosphamide

COL4A1

SNV

Missense_Mutation

c.3307N>A

p.Gly1103Arg

p.G1103R

P02462

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AR-A1AP-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

anastrozole

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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
1282	COL4A1	DRUGGABLE GENOME		CHEMBL2095222	OCRIPLASMIN
1282	COL4A1	DRUGGABLE GENOME		CHEMBL2108709	COLLAGENASE CLOSTRIDIUM HISTOLYTICUM

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