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: COL6A3

Gene summary for COL6A3

Gene summary.

Gene information	Species	Human
	Gene symbol	COL6A3
	Gene ID	1293
	Gene name	collagen type VI alpha 3 chain
	Gene Alias	BTHLM1
	Cytomap	2q37.3
	Gene Type	protein-coding
	GO ID	GO:0006508
	UniProtAcc	D9ZGF2

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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
1293	COL6A3	AEH-subject1	Human	Endometrium	AEH	3.00e-24	-5.62e-01	-0.3059
1293	COL6A3	AEH-subject2	Human	Endometrium	AEH	1.43e-27	-5.88e-01	-0.2525
1293	COL6A3	AEH-subject3	Human	Endometrium	AEH	2.14e-16	-5.00e-01	-0.2576
1293	COL6A3	AEH-subject4	Human	Endometrium	AEH	1.66e-03	-2.89e-01	-0.2657
1293	COL6A3	AEH-subject5	Human	Endometrium	AEH	5.26e-23	-5.65e-01	-0.2953
1293	COL6A3	EEC-subject1	Human	Endometrium	EEC	9.90e-26	-5.86e-01	-0.2682
1293	COL6A3	EEC-subject2	Human	Endometrium	EEC	1.26e-32	-6.03e-01	-0.2607
1293	COL6A3	EEC-subject3	Human	Endometrium	EEC	1.22e-25	-5.23e-01	-0.2525
1293	COL6A3	EEC-subject4	Human	Endometrium	EEC	9.17e-19	-5.57e-01	-0.2571
1293	COL6A3	EEC-subject5	Human	Endometrium	EEC	2.06e-26	-5.83e-01	-0.249
1293	COL6A3	GSM5276935	Human	Endometrium	EEC	2.25e-23	-5.85e-01	-0.123
1293	COL6A3	GSM6177620_NYU_UCEC1_lib1_lib1	Human	Endometrium	EEC	1.68e-26	-6.03e-01	-0.1869
1293	COL6A3	GSM6177620_NYU_UCEC1_lib2_lib2	Human	Endometrium	EEC	6.11e-21	-5.84e-01	-0.1875
1293	COL6A3	GSM6177620_NYU_UCEC1_lib3_lib3	Human	Endometrium	EEC	2.23e-24	-5.90e-01	-0.1883
1293	COL6A3	GSM6177621_NYU_UCEC2_lib1_lib1	Human	Endometrium	EEC	3.44e-28	-5.61e-01	-0.1934
1293	COL6A3	GSM6177622_NYU_UCEC3_lib1_lib1	Human	Endometrium	EEC	8.01e-32	-6.03e-01	-0.1917
1293	COL6A3	GSM6177622_NYU_UCEC3_lib2_lib2	Human	Endometrium	EEC	2.73e-35	-6.03e-01	-0.1916
1293	COL6A3	LZE2T	Human	Esophagus	ESCC	6.17e-05	5.97e-01	0.082
1293	COL6A3	P4T-E	Human	Esophagus	ESCC	2.18e-07	1.67e+00	0.1323
1293	COL6A3	P9T-E	Human	Esophagus	ESCC	5.11e-06	1.52e+00	0.1131

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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
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
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:005254716	Endometrium	AEH	regulation of peptidase activity	85/2100	461/18723	2.47e-06	7.11e-05	85
GO:005254816	Endometrium	AEH	regulation of endopeptidase activity	76/2100	432/18723	4.42e-05	7.43e-04	76
GO:00075174	Endometrium	AEH	muscle organ development	60/2100	327/18723	8.19e-05	1.22e-03	60
GO:004586116	Endometrium	AEH	negative regulation of proteolysis	63/2100	351/18723	1.07e-04	1.53e-03	63
GO:005134610	Endometrium	AEH	negative regulation of hydrolase activity	65/2100	379/18723	3.18e-04	3.57e-03	65
GO:001046610	Endometrium	AEH	negative regulation of peptidase activity	43/2100	262/18723	6.78e-03	3.95e-02	43
GO:005254717	Endometrium	EEC	regulation of peptidase activity	91/2168	461/18723	2.00e-07	8.93e-06	91
GO:004586117	Endometrium	EEC	negative regulation of proteolysis	72/2168	351/18723	8.46e-07	2.98e-05	72
GO:005254817	Endometrium	EEC	regulation of endopeptidase activity	82/2168	432/18723	3.96e-06	1.04e-04	82
GO:005134615	Endometrium	EEC	negative regulation of hydrolase activity	72/2168	379/18723	1.46e-05	2.87e-04	72
GO:000751712	Endometrium	EEC	muscle organ development	59/2168	327/18723	3.49e-04	3.85e-03	59
GO:001046615	Endometrium	EEC	negative regulation of peptidase activity	49/2168	262/18723	4.64e-04	4.79e-03	49
GO:001095114	Endometrium	EEC	negative regulation of endopeptidase activity	47/2168	252/18723	6.37e-04	6.25e-03	47
GO:0052547111	Esophagus	ESCC	regulation of peptidase activity	275/8552	461/18723	7.54e-10	1.88e-08	275
GO:0052548111	Esophagus	ESCC	regulation of endopeptidase activity	253/8552	432/18723	3.68e-08	6.78e-07	253
GO:0045861111	Esophagus	ESCC	negative regulation of proteolysis	195/8552	351/18723	1.13e-04	7.85e-04	195
GO:0051346110	Esophagus	ESCC	negative regulation of hydrolase activity	208/8552	379/18723	1.76e-04	1.14e-03	208
GO:001046620	Esophagus	ESCC	negative regulation of peptidase activity	140/8552	262/18723	6.73e-03	2.46e-02	140
GO:001095119	Esophagus	ESCC	negative regulation of endopeptidase activity	135/8552	252/18723	6.86e-03	2.51e-02	135
GO:005254720	Oral cavity	OSCC	regulation of peptidase activity	255/7305	461/18723	5.78e-13	2.75e-11	255

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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
hsa0451016	Endometrium	AEH	Focal adhesion	58/1197	203/8465	4.99e-08	7.37e-07	5.39e-07	58
hsa0451024	Endometrium	EEC	Focal adhesion	58/1237	203/8465	1.61e-07	2.30e-06	1.71e-06	58
hsa0451034	Endometrium	EEC	Focal adhesion	58/1237	203/8465	1.61e-07	2.30e-06	1.71e-06	58
hsa0516510	Esophagus	ESCC	Human papillomavirus infection	215/4205	331/8465	7.86e-09	7.12e-08	3.65e-08	215
hsa0451020	Esophagus	ESCC	Focal adhesion	127/4205	203/8465	1.25e-04	4.99e-04	2.56e-04	127
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
hsa04510111	Esophagus	ESCC	Focal adhesion	127/4205	203/8465	1.25e-04	4.99e-04	2.56e-04	127
hsa0415114	Esophagus	ESCC	PI3K-Akt signaling pathway	197/4205	354/8465	1.24e-02	2.83e-02	1.45e-02	197
hsa051659	Oral cavity	OSCC	Human papillomavirus infection	200/3704	331/8465	3.83e-10	4.93e-09	2.51e-09	200
hsa0451019	Oral cavity	OSCC	Focal adhesion	128/3704	203/8465	1.71e-08	1.63e-07	8.31e-08	128
hsa041516	Oral cavity	OSCC	PI3K-Akt signaling pathway	185/3704	354/8465	6.26e-04	1.86e-03	9.49e-04	185
hsa0516514	Oral cavity	OSCC	Human papillomavirus infection	200/3704	331/8465	3.83e-10	4.93e-09	2.51e-09	200
hsa04510110	Oral cavity	OSCC	Focal adhesion	128/3704	203/8465	1.71e-08	1.63e-07	8.31e-08	128
hsa0415113	Oral cavity	OSCC	PI3K-Akt signaling pathway	185/3704	354/8465	6.26e-04	1.86e-03	9.49e-04	185
hsa0451043	Oral cavity	NEOLP	Focal adhesion	71/1112	203/8465	7.25e-16	7.68e-14	4.83e-14	71
hsa0516561	Oral cavity	NEOLP	Human papillomavirus infection	90/1112	331/8465	2.75e-12	1.75e-10	1.10e-10	90
hsa0415141	Oral cavity	NEOLP	PI3K-Akt signaling pathway	79/1112	354/8465	8.42e-07	9.92e-06	6.24e-06	79
hsa045126	Oral cavity	NEOLP	ECM-receptor interaction	24/1112	89/8465	3.56e-04	2.18e-03	1.37e-03	24

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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
COL6A3	ITGA1_ITGB1	COL6A3_ITGA1_ITGB1	COLLAGEN	Breast	ADJ
COL6A3	ITGA2_ITGB1	COL6A3_ITGA2_ITGB1	COLLAGEN	Breast	ADJ
COL6A3	CD44	COL6A3_CD44	COLLAGEN	Breast	ADJ
COL6A3	SDC4	COL6A3_SDC4	COLLAGEN	Breast	ADJ
COL6A3	ITGA1_ITGB1	COL6A3_ITGA1_ITGB1	COLLAGEN	Breast	DCIS
COL6A3	ITGA2_ITGB1	COL6A3_ITGA2_ITGB1	COLLAGEN	Breast	DCIS
COL6A3	CD44	COL6A3_CD44	COLLAGEN	Breast	DCIS
COL6A3	SDC1	COL6A3_SDC1	COLLAGEN	Breast	DCIS
COL6A3	SDC4	COL6A3_SDC4	COLLAGEN	Breast	DCIS
COL6A3	ITGA1_ITGB1	COL6A3_ITGA1_ITGB1	COLLAGEN	Breast	Healthy
COL6A3	ITGA2_ITGB1	COL6A3_ITGA2_ITGB1	COLLAGEN	Breast	Healthy
COL6A3	ITGAV_ITGB8	COL6A3_ITGAV_ITGB8	COLLAGEN	Breast	Healthy
COL6A3	CD44	COL6A3_CD44	COLLAGEN	Breast	Healthy
COL6A3	SDC1	COL6A3_SDC1	COLLAGEN	Breast	Healthy
COL6A3	SDC4	COL6A3_SDC4	COLLAGEN	Breast	Healthy
COL6A3	ITGA1_ITGB1	COL6A3_ITGA1_ITGB1	COLLAGEN	Breast	IDC
COL6A3	CD44	COL6A3_CD44	COLLAGEN	Breast	IDC
COL6A3	SDC1	COL6A3_SDC1	COLLAGEN	Breast	IDC
COL6A3	SDC4	COL6A3_SDC4	COLLAGEN	Breast	IDC
COL6A3	ITGA1_ITGB1	COL6A3_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

COL6A3

SNV

Missense_Mutation

novel

c.1195G>C

p.Val399Leu

p.V399L

P12111

protein_coding

tolerated(0.07)

benign(0.285)

TCGA-5L-AAT1-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

letrozol

COL6A3

SNV

Missense_Mutation

rs770436761

c.8639C>T

p.Thr2880Met

p.T2880M

P12111

protein_coding

deleterious(0.03)

benign(0.255)

TCGA-A2-A0YM-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL6A3

SNV

Missense_Mutation

c.4490C>T

p.Ala1497Val

p.A1497V

P12111

protein_coding

tolerated(0.28)

benign(0.09)

TCGA-A2-A25D-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

tamoxiphen

COL6A3

SNV

Missense_Mutation

c.7274N>C

p.Val2425Ala

p.V2425A

P12111

protein_coding

tolerated(0.07)

probably_damaging(0.93)

TCGA-A8-A07R-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Ancillary

zoledronic

COL6A3

SNV

Missense_Mutation

novel

c.2173N>C

p.Tyr725His

p.Y725H

P12111

protein_coding

tolerated(0.24)

possibly_damaging(0.757)

TCGA-A8-A08G-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

COL6A3

SNV

Missense_Mutation

c.3938N>T

p.Gly1313Val

p.G1313V

P12111

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-A8-A09G-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

COL6A3

SNV

Missense_Mutation

c.175N>G

p.Arg59Gly

p.R59G

P12111

protein_coding

deleterious(0)

possibly_damaging(0.905)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL6A3

SNV

Missense_Mutation

novel

c.8020N>G

p.Ser2674Ala

p.S2674A

P12111

protein_coding

tolerated(0.51)

benign(0.339)

TCGA-AC-A3QQ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

COL6A3

SNV

Missense_Mutation

novel

c.3736C>T

p.Pro1246Ser

p.P1246S

P12111

protein_coding

tolerated(0.62)

benign(0.038)

TCGA-AC-A7VB-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

COL6A3

SNV

Missense_Mutation

c.3758N>A

p.Thr1253Asn

p.T1253N

P12111

protein_coding

tolerated(0.47)

benign(0.009)

TCGA-AN-A0AJ-01

Breast

breast invasive 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
1293	COL6A3	DRUGGABLE GENOME, PROTEASE INHIBITOR		CHEMBL2108709	COLLAGENASE CLOSTRIDIUM HISTOLYTICUM
1293	COL6A3	DRUGGABLE GENOME, PROTEASE INHIBITOR		CHEMBL2095222	OCRIPLASMIN

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