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: COL4A5

Gene summary for COL4A5

Gene summary.

Gene information	Species	Human
	Gene symbol	COL4A5
	Gene ID	1287
	Gene name	collagen type IV alpha 5 chain
	Gene Alias	ASLN
	Cytomap	Xq22.3
	Gene Type	protein-coding
	GO ID	GO:0007154
	UniProtAcc	A7MBN3

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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
1287	COL4A5	LZE4T	Human	Esophagus	ESCC	1.05e-11	4.32e-01	0.0811
1287	COL4A5	LZE7T	Human	Esophagus	ESCC	1.26e-08	5.22e-01	0.0667
1287	COL4A5	LZE8T	Human	Esophagus	ESCC	5.82e-03	1.25e-01	0.067
1287	COL4A5	LZE22T	Human	Esophagus	ESCC	2.43e-03	4.23e-01	0.068
1287	COL4A5	LZE24T	Human	Esophagus	ESCC	5.37e-09	4.64e-01	0.0596
1287	COL4A5	LZE6T	Human	Esophagus	ESCC	5.81e-04	3.54e-01	0.0845
1287	COL4A5	P1T-E	Human	Esophagus	ESCC	2.12e-04	3.73e-01	0.0875
1287	COL4A5	P2T-E	Human	Esophagus	ESCC	1.02e-14	3.51e-01	0.1177
1287	COL4A5	P4T-E	Human	Esophagus	ESCC	1.12e-05	1.74e-01	0.1323
1287	COL4A5	P5T-E	Human	Esophagus	ESCC	7.29e-11	1.42e-01	0.1327
1287	COL4A5	P8T-E	Human	Esophagus	ESCC	6.83e-31	7.10e-01	0.0889
1287	COL4A5	P9T-E	Human	Esophagus	ESCC	5.74e-04	1.40e-01	0.1131
1287	COL4A5	P10T-E	Human	Esophagus	ESCC	1.97e-32	7.26e-01	0.116
1287	COL4A5	P11T-E	Human	Esophagus	ESCC	8.02e-09	4.11e-01	0.1426
1287	COL4A5	P12T-E	Human	Esophagus	ESCC	1.95e-23	4.62e-01	0.1122
1287	COL4A5	P15T-E	Human	Esophagus	ESCC	1.77e-16	3.78e-01	0.1149
1287	COL4A5	P16T-E	Human	Esophagus	ESCC	5.60e-11	1.25e-01	0.1153
1287	COL4A5	P20T-E	Human	Esophagus	ESCC	4.50e-29	6.89e-01	0.1124
1287	COL4A5	P21T-E	Human	Esophagus	ESCC	1.71e-13	1.93e-01	0.1617
1287	COL4A5	P22T-E	Human	Esophagus	ESCC	2.78e-11	2.82e-01	0.1236

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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
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

∗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: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:005080811	Lung	AIS	synapse organization	63/1849	426/18723	7.39e-04	1.07e-02	63
GO:00301983	Oral cavity	OSCC	extracellular matrix organization	146/7305	301/18723	4.67e-04	2.77e-03	146
GO:00452293	Oral cavity	OSCC	external encapsulating structure organization	147/7305	304/18723	5.30e-04	3.08e-03	147
GO:00430623	Oral cavity	OSCC	extracellular structure organization	146/7305	302/18723	5.59e-04	3.23e-03	146
GO:00301982	Oral cavity	NEOLP	extracellular matrix organization	64/2005	301/18723	5.66e-08	2.24e-06	64
GO:00430622	Oral cavity	NEOLP	extracellular structure organization	64/2005	302/18723	6.44e-08	2.50e-06	64
GO:00452292	Oral cavity	NEOLP	external encapsulating structure organization	64/2005	304/18723	8.33e-08	3.17e-06	64
GO:00508087	Prostate	BPH	synapse organization	103/3107	426/18723	3.19e-05	3.61e-04	103
GO:00430621	Prostate	BPH	extracellular structure organization	67/3107	302/18723	6.67e-03	3.00e-02	67
GO:0038063	Prostate	BPH	collagen-activated tyrosine kinase receptor signaling pathway	6/3107	12/18723	7.73e-03	3.39e-02	6
GO:00301981	Prostate	BPH	extracellular matrix organization	66/3107	301/18723	9.20e-03	3.92e-02	66
GO:00452291	Prostate	BPH	external encapsulating structure organization	66/3107	304/18723	1.15e-02	4.66e-02	66
GO:005080813	Prostate	Tumor	synapse organization	105/3246	426/18723	7.20e-05	7.62e-04	105
GO:00508088	Skin	AK	synapse organization	71/1910	426/18723	2.21e-05	4.07e-04	71
GO:005080814	Skin	SCCIS	synapse organization	42/919	426/18723	1.43e-05	4.70e-04	42
GO:00301985	Skin	SCCIS	extracellular matrix organization	32/919	301/18723	3.46e-05	9.17e-04	32
GO:00430625	Skin	SCCIS	extracellular structure organization	32/919	302/18723	3.69e-05	9.65e-04	32

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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
hsa0451022	Lung	AIS	Focal adhesion	57/961	203/8465	3.17e-11	3.43e-09	2.19e-09	57
hsa0516521	Lung	AIS	Human papillomavirus infection	64/961	331/8465	1.03e-05	3.04e-04	1.95e-04	64
hsa0522221	Lung	AIS	Small cell lung cancer	21/961	92/8465	1.23e-03	9.02e-03	5.77e-03	21
hsa045122	Lung	AIS	ECM-receptor interaction	20/961	89/8465	1.95e-03	1.26e-02	8.09e-03	20
hsa0415121	Lung	AIS	PI3K-Akt signaling pathway	57/961	354/8465	3.72e-03	2.00e-02	1.28e-02	57
hsa0492621	Lung	AIS	Relaxin signaling pathway	25/961	129/8465	4.95e-03	2.47e-02	1.58e-02	25
hsa0514621	Lung	AIS	Amoebiasis	20/961	102/8465	9.86e-03	4.20e-02	2.69e-02	20
hsa0451032	Lung	AIS	Focal adhesion	57/961	203/8465	3.17e-11	3.43e-09	2.19e-09	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
COL4A5	ITGA1_ITGB1	COL4A5_ITGA1_ITGB1	COLLAGEN	Cervix	CC
COL4A5	ITGA2_ITGB1	COL4A5_ITGA2_ITGB1	COLLAGEN	Cervix	CC
COL4A5	ITGA3_ITGB1	COL4A5_ITGA3_ITGB1	COLLAGEN	Cervix	CC
COL4A5	ITGA9_ITGB1	COL4A5_ITGA9_ITGB1	COLLAGEN	Cervix	CC
COL4A5	ITGA11_ITGB1	COL4A5_ITGA11_ITGB1	COLLAGEN	Cervix	CC
COL4A5	ITGAV_ITGB8	COL4A5_ITGAV_ITGB8	COLLAGEN	Cervix	CC
COL4A5	CD44	COL4A5_CD44	COLLAGEN	Cervix	CC
COL4A5	SDC1	COL4A5_SDC1	COLLAGEN	Cervix	CC
COL4A5	SDC4	COL4A5_SDC4	COLLAGEN	Cervix	CC
COL4A5	ITGA1_ITGB1	COL4A5_ITGA1_ITGB1	COLLAGEN	CRC	AD
COL4A5	ITGA2_ITGB1	COL4A5_ITGA2_ITGB1	COLLAGEN	CRC	AD
COL4A5	ITGA3_ITGB1	COL4A5_ITGA3_ITGB1	COLLAGEN	CRC	AD
COL4A5	ITGA11_ITGB1	COL4A5_ITGA11_ITGB1	COLLAGEN	CRC	AD
COL4A5	CD44	COL4A5_CD44	COLLAGEN	CRC	AD
COL4A5	SDC1	COL4A5_SDC1	COLLAGEN	CRC	AD
COL4A5	SDC4	COL4A5_SDC4	COLLAGEN	CRC	AD
COL4A5	ITGA1_ITGB1	COL4A5_ITGA1_ITGB1	COLLAGEN	CRC	ADJ
COL4A5	ITGA2_ITGB1	COL4A5_ITGA2_ITGB1	COLLAGEN	CRC	ADJ
COL4A5	ITGA3_ITGB1	COL4A5_ITGA3_ITGB1	COLLAGEN	CRC	ADJ
COL4A5	CD44	COL4A5_CD44	COLLAGEN	CRC	ADJ

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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

COL4A5

SNV

Missense_Mutation

c.1843N>A

p.Gly615Arg

p.G615R

P29400

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-A8-A0A1-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

COL4A5

SNV

Missense_Mutation

rs757706609

c.3932N>T

p.Pro1311Leu

p.P1311L

P29400

protein_coding

deleterious(0.02)

possibly_damaging(0.463)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL4A5

SNV

Missense_Mutation

rs750941179

c.4847N>T

p.Ser1616Leu

p.S1616L

P29400

protein_coding

deleterious(0)

probably_damaging(0.996)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL4A5

SNV

Missense_Mutation

novel

c.2129N>A

p.Gly710Glu

p.G710E

P29400

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AC-A8OP-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL4A5

SNV

Missense_Mutation

rs866974052

c.746G>A

p.Arg249Lys

p.R249K

P29400

protein_coding

tolerated(0.93)

benign(0.085)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL4A5

SNV

Missense_Mutation

novel

c.4237G>A

p.Asp1413Asn

p.D1413N

P29400

protein_coding

tolerated(0.46)

benign(0.189)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL4A5

SNV

Missense_Mutation

novel

c.4575N>A

p.Met1525Ile

p.M1525I

P29400

protein_coding

deleterious(0.03)

probably_damaging(0.91)

TCGA-AN-A04D-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

COL4A5

SNV

Missense_Mutation

c.4093N>T

p.Pro1365Ser

p.P1365S

P29400

protein_coding

tolerated(0.06)

probably_damaging(0.998)

TCGA-AN-A0XN-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

COL4A5

SNV

Missense_Mutation

c.4052G>T

p.Gly1351Val

p.G1351V

P29400

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-BH-A0DK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

COL4A5

SNV

Missense_Mutation

novel

c.4219C>T

p.Pro1407Ser

p.P1407S

P29400

protein_coding

tolerated(0.33)

benign(0.005)

TCGA-BH-A0HF-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

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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
1287	COL4A5	DRUGGABLE GENOME		CHEMBL2108709	COLLAGENASE CLOSTRIDIUM HISTOLYTICUM
1287	COL4A5	DRUGGABLE GENOME		CHEMBL2095222	OCRIPLASMIN

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