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: COL4A2

Gene summary for COL4A2

Gene summary.

Gene information	Species	Human
	Gene symbol	COL4A2
	Gene ID	1284
	Gene name	collagen type IV alpha 2 chain
	Gene Alias	BSVD2
	Cytomap	13q34
	Gene Type	protein-coding
	GO ID	GO:0001525
	UniProtAcc	A0A024RDW8

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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
1284	COL4A2	LZE2T	Human	Esophagus	ESCC	6.05e-08	8.38e-01	0.082
1284	COL4A2	LZE7T	Human	Esophagus	ESCC	5.86e-13	7.32e-01	0.0667
1284	COL4A2	LZE22T	Human	Esophagus	ESCC	1.17e-03	4.73e-01	0.068
1284	COL4A2	LZE21T	Human	Esophagus	ESCC	1.38e-03	2.82e-01	0.0655
1284	COL4A2	P2T-E	Human	Esophagus	ESCC	1.26e-79	1.45e+00	0.1177
1284	COL4A2	P4T-E	Human	Esophagus	ESCC	2.79e-24	8.24e-01	0.1323
1284	COL4A2	P5T-E	Human	Esophagus	ESCC	1.37e-04	4.87e-01	0.1327
1284	COL4A2	P8T-E	Human	Esophagus	ESCC	6.52e-08	2.33e-01	0.0889
1284	COL4A2	P9T-E	Human	Esophagus	ESCC	9.01e-27	1.02e+00	0.1131
1284	COL4A2	P10T-E	Human	Esophagus	ESCC	4.13e-53	1.20e+00	0.116
1284	COL4A2	P11T-E	Human	Esophagus	ESCC	2.19e-50	2.09e+00	0.1426
1284	COL4A2	P12T-E	Human	Esophagus	ESCC	6.18e-32	7.20e-01	0.1122
1284	COL4A2	P15T-E	Human	Esophagus	ESCC	1.20e-23	7.83e-01	0.1149
1284	COL4A2	P16T-E	Human	Esophagus	ESCC	1.42e-106	2.88e+00	0.1153
1284	COL4A2	P17T-E	Human	Esophagus	ESCC	1.46e-03	1.11e+00	0.1278
1284	COL4A2	P19T-E	Human	Esophagus	ESCC	1.54e-16	1.98e+00	0.1662
1284	COL4A2	P21T-E	Human	Esophagus	ESCC	2.29e-21	8.71e-01	0.1617
1284	COL4A2	P22T-E	Human	Esophagus	ESCC	5.90e-14	3.54e-01	0.1236
1284	COL4A2	P23T-E	Human	Esophagus	ESCC	6.44e-04	9.90e-01	0.108
1284	COL4A2	P24T-E	Human	Esophagus	ESCC	7.37e-28	1.47e+00	0.1287

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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
Liver		HCC: Hepatocellular carcinoma
		NAFLD: Non-alcoholic fatty liver disease
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:000756820	Esophagus	ESCC	aging	201/8552	339/18723	2.64e-07	3.94e-06	201
GO:00715599	Esophagus	ESCC	response to transforming growth factor beta	157/8552	256/18723	2.95e-07	4.23e-06	157
GO:00715609	Esophagus	ESCC	cellular response to transforming growth factor beta stimulus	151/8552	250/18723	1.78e-06	2.10e-05	151
GO:00073698	Esophagus	ESCC	gastrulation	115/8552	185/18723	4.35e-06	4.64e-05	115
GO:00074926	Esophagus	ESCC	endoderm development	54/8552	77/18723	1.20e-05	1.12e-04	54
GO:00301984	Esophagus	ESCC	extracellular matrix organization	171/8552	301/18723	6.08e-05	4.67e-04	171
GO:00430624	Esophagus	ESCC	extracellular structure organization	171/8552	302/18723	7.73e-05	5.76e-04	171
GO:00452294	Esophagus	ESCC	external encapsulating structure organization	172/8552	304/18723	7.80e-05	5.80e-04	172
GO:00017064	Esophagus	ESCC	endoderm formation	38/8552	54/18723	2.08e-04	1.31e-03	38
GO:00017044	Esophagus	ESCC	formation of primary germ layer	75/8552	121/18723	2.17e-04	1.36e-03	75
GO:00359873	Esophagus	ESCC	endodermal cell differentiation	32/8552	45/18723	4.87e-04	2.70e-03	32
GO:007155911	Liver	Cirrhotic	response to transforming growth factor beta	96/4634	256/18723	3.55e-06	6.09e-05	96
GO:007156011	Liver	Cirrhotic	cellular response to transforming growth factor beta stimulus	93/4634	250/18723	7.34e-06	1.13e-04	93
GO:000756812	Liver	Cirrhotic	aging	117/4634	339/18723	3.13e-05	3.91e-04	117
GO:0014823	Liver	Cirrhotic	response to activity	30/4634	76/18723	3.19e-03	1.80e-02	30
GO:0007492	Liver	Cirrhotic	endoderm development	29/4634	77/18723	8.02e-03	3.76e-02	29
GO:000756822	Liver	HCC	aging	185/7958	339/18723	4.28e-06	5.50e-05	185
GO:007155921	Liver	HCC	response to transforming growth factor beta	141/7958	256/18723	3.08e-05	3.16e-04	141
GO:007156021	Liver	HCC	cellular response to transforming growth factor beta stimulus	137/7958	250/18723	5.47e-05	5.14e-04	137
GO:00148231	Liver	HCC	response to activity	45/7958	76/18723	2.42e-03	1.18e-02	45

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
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
hsa0493317	Esophagus	ESCC	AGE-RAGE signaling pathway in diabetic complications	72/4205	100/8465	4.15e-06	2.28e-05	1.17e-05	72
hsa04510111	Esophagus	ESCC	Focal adhesion	127/4205	203/8465	1.25e-04	4.99e-04	2.56e-04	127
hsa0492616	Esophagus	ESCC	Relaxin signaling pathway	81/4205	129/8465	1.72e-03	5.09e-03	2.61e-03	81
hsa0415114	Esophagus	ESCC	PI3K-Akt signaling pathway	197/4205	354/8465	1.24e-02	2.83e-02	1.45e-02	197
hsa0451021	Liver	Cirrhotic	Focal adhesion	93/2530	203/8465	9.27e-07	1.10e-05	6.80e-06	93
hsa05165	Liver	Cirrhotic	Human papillomavirus infection	124/2530	331/8465	1.55e-03	7.83e-03	4.83e-03	124
hsa0451031	Liver	Cirrhotic	Focal adhesion	93/2530	203/8465	9.27e-07	1.10e-05	6.80e-06	93
hsa051651	Liver	Cirrhotic	Human papillomavirus infection	124/2530	331/8465	1.55e-03	7.83e-03	4.83e-03	124
hsa0451041	Liver	HCC	Focal adhesion	125/4020	203/8465	3.12e-05	1.88e-04	1.04e-04	125
hsa051652	Liver	HCC	Human papillomavirus infection	188/4020	331/8465	3.34e-04	1.49e-03	8.29e-04	188
hsa049334	Liver	HCC	AGE-RAGE signaling pathway in diabetic complications	62/4020	100/8465	2.35e-03	7.95e-03	4.42e-03	62
hsa052224	Liver	HCC	Small cell lung cancer	57/4020	92/8465	3.54e-03	1.12e-02	6.22e-03	57

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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
COL4A2	ITGA1_ITGB1	COL4A2_ITGA1_ITGB1	COLLAGEN	Breast	ADJ
COL4A2	ITGA2_ITGB1	COL4A2_ITGA2_ITGB1	COLLAGEN	Breast	ADJ
COL4A2	CD44	COL4A2_CD44	COLLAGEN	Breast	ADJ
COL4A2	SDC4	COL4A2_SDC4	COLLAGEN	Breast	ADJ
COL4A2	ITGA1_ITGB1	COL4A2_ITGA1_ITGB1	COLLAGEN	Breast	DCIS
COL4A2	ITGA2_ITGB1	COL4A2_ITGA2_ITGB1	COLLAGEN	Breast	DCIS
COL4A2	CD44	COL4A2_CD44	COLLAGEN	Breast	DCIS
COL4A2	SDC1	COL4A2_SDC1	COLLAGEN	Breast	DCIS
COL4A2	SDC4	COL4A2_SDC4	COLLAGEN	Breast	DCIS
COL4A2	ITGA1_ITGB1	COL4A2_ITGA1_ITGB1	COLLAGEN	Breast	Healthy
COL4A2	ITGA2_ITGB1	COL4A2_ITGA2_ITGB1	COLLAGEN	Breast	Healthy
COL4A2	ITGAV_ITGB8	COL4A2_ITGAV_ITGB8	COLLAGEN	Breast	Healthy
COL4A2	CD44	COL4A2_CD44	COLLAGEN	Breast	Healthy
COL4A2	SDC1	COL4A2_SDC1	COLLAGEN	Breast	Healthy
COL4A2	SDC4	COL4A2_SDC4	COLLAGEN	Breast	Healthy
COL4A2	ITGA1_ITGB1	COL4A2_ITGA1_ITGB1	COLLAGEN	Breast	IDC
COL4A2	CD44	COL4A2_CD44	COLLAGEN	Breast	IDC
COL4A2	SDC1	COL4A2_SDC1	COLLAGEN	Breast	IDC
COL4A2	SDC4	COL4A2_SDC4	COLLAGEN	Breast	IDC
COL4A2	ITGA1_ITGB1	COL4A2_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

COL4A2

SNV

Missense_Mutation

rs531542947

c.289G>A

p.Gly97Arg

p.G97R

P08572

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-A7-A2KD-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cytoxan

COL4A2

SNV

Missense_Mutation

c.730N>A

p.Asp244Asn

p.D244N

P08572

protein_coding

deleterious(0.03)

possibly_damaging(0.651)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL4A2

SNV

Missense_Mutation

c.3910N>A

p.Ala1304Thr

p.A1304T

P08572

protein_coding

tolerated(0.1)

benign(0.262)

TCGA-AN-A04D-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

COL4A2

SNV

Missense_Mutation

novel

c.2884G>A

p.Gly962Ser

p.G962S

P08572

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AR-A1AO-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

COL4A2

SNV

Missense_Mutation

c.2728N>C

p.Asp910His

p.D910H

P08572

protein_coding

tolerated(0.13)

probably_damaging(0.976)

TCGA-B6-A0RT-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

COL4A2

SNV

Missense_Mutation

c.3088N>T

p.Gly1030Cys

p.G1030C

P08572

protein_coding

deleterious(0.02)

probably_damaging(0.994)

TCGA-BH-A18G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL4A2

SNV

Missense_Mutation

c.2323N>A

p.Glu775Lys

p.E775K

P08572

protein_coding

deleterious(0.01)

possibly_damaging(0.824)

TCGA-D8-A27G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL4A2

SNV

Missense_Mutation

c.1865N>T

p.Gly622Val

p.G622V

P08572

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-E2-A1LG-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

COL4A2

SNV

Missense_Mutation

c.4229N>A

p.Arg1410Gln

p.R1410Q

P08572

protein_coding

tolerated(0.61)

benign(0.19)

TCGA-E2-A1LG-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

COL4A2

SNV

Missense_Mutation

rs373521529

c.1832N>T

p.Thr611Met

p.T611M

P08572

protein_coding

tolerated(0.1)

benign(0.015)

TCGA-LL-A73Y-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

taxotere

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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
1284	COL4A2	DRUGGABLE GENOME		NLG919	NAVOXIMOD
1284	COL4A2	DRUGGABLE GENOME		CHEMBL2095222	OCRIPLASMIN
1284	COL4A2	DRUGGABLE GENOME		CHEMBL2108709	COLLAGENASE CLOSTRIDIUM HISTOLYTICUM
1284	COL4A2	DRUGGABLE GENOME		AK107

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