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: COL6A1

Gene summary for COL6A1

Gene summary.

Gene information	Species	Human
	Gene symbol	COL6A1
	Gene ID	1291
	Gene name	collagen type VI alpha 1 chain
	Gene Alias	BTHLM1
	Cytomap	21q22.3
	Gene Type	protein-coding
	GO ID	GO:0001101
	UniProtAcc	P12109

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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
1291	COL6A1	AEH-subject1	Human	Endometrium	AEH	1.31e-23	-7.49e-01	-0.3059
1291	COL6A1	AEH-subject2	Human	Endometrium	AEH	1.41e-15	-6.54e-01	-0.2525
1291	COL6A1	AEH-subject3	Human	Endometrium	AEH	1.08e-06	-5.37e-01	-0.2576
1291	COL6A1	AEH-subject4	Human	Endometrium	AEH	1.09e-09	-6.12e-01	-0.2657
1291	COL6A1	AEH-subject5	Human	Endometrium	AEH	3.27e-26	-8.20e-01	-0.2953
1291	COL6A1	EEC-subject1	Human	Endometrium	EEC	1.57e-28	-8.53e-01	-0.2682
1291	COL6A1	EEC-subject2	Human	Endometrium	EEC	1.59e-16	-6.40e-01	-0.2607
1291	COL6A1	EEC-subject3	Human	Endometrium	EEC	1.12e-42	-8.26e-01	-0.2525
1291	COL6A1	EEC-subject4	Human	Endometrium	EEC	1.87e-20	-7.20e-01	-0.2571
1291	COL6A1	EEC-subject5	Human	Endometrium	EEC	1.75e-13	-6.34e-01	-0.249
1291	COL6A1	GSM5276935	Human	Endometrium	EEC	1.45e-33	-8.21e-01	-0.123
1291	COL6A1	GSM6177620_NYU_UCEC1_lib1_lib1	Human	Endometrium	EEC	3.84e-34	-8.21e-01	-0.1869
1291	COL6A1	GSM6177620_NYU_UCEC1_lib2_lib2	Human	Endometrium	EEC	3.62e-24	-7.51e-01	-0.1875
1291	COL6A1	GSM6177620_NYU_UCEC1_lib3_lib3	Human	Endometrium	EEC	3.39e-26	-7.59e-01	-0.1883
1291	COL6A1	GSM6177621_NYU_UCEC2_lib1_lib1	Human	Endometrium	EEC	2.47e-24	-7.67e-01	-0.1934
1291	COL6A1	GSM6177622_NYU_UCEC3_lib1_lib1	Human	Endometrium	EEC	1.88e-25	-7.21e-01	-0.1917
1291	COL6A1	GSM6177622_NYU_UCEC3_lib2_lib2	Human	Endometrium	EEC	3.57e-29	-6.71e-01	-0.1916
1291	COL6A1	GSM6177623_NYU_UCEC3_Vis	Human	Endometrium	EEC	1.15e-05	2.87e-01	-0.1269
1291	COL6A1	LZE2T	Human	Esophagus	ESCC	1.48e-09	5.23e-01	0.082
1291	COL6A1	LZE8T	Human	Esophagus	ESCC	1.22e-07	-2.47e-02	0.067

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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
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:00016498	Endometrium	AEH	osteoblast differentiation	52/2100	229/18723	4.74e-07	1.92e-05	52
GO:00015038	Endometrium	AEH	ossification	78/2100	408/18723	1.54e-06	4.85e-05	78
GO:00011017	Endometrium	AEH	response to acid chemical	28/2100	135/18723	9.24e-04	8.43e-03	28
GO:00432005	Endometrium	AEH	response to amino acid	24/2100	116/18723	2.14e-03	1.65e-02	24
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:000164914	Endometrium	EEC	osteoblast differentiation	53/2168	229/18723	5.32e-07	2.02e-05	53
GO:000150313	Endometrium	EEC	ossification	79/2168	408/18723	2.72e-06	7.67e-05	79
GO:000110113	Endometrium	EEC	response to acid chemical	29/2168	135/18723	6.98e-04	6.68e-03	29
GO:004320012	Endometrium	EEC	response to amino acid	25/2168	116/18723	1.50e-03	1.21e-02	25
GO:007123011	Endometrium	EEC	cellular response to amino acid stimulus	17/2168	71/18723	2.57e-03	1.86e-02	17
GO:007122911	Endometrium	EEC	cellular response to acid chemical	18/2168	80/18723	4.02e-03	2.66e-02	18
GO:000164918	Esophagus	ESCC	osteoblast differentiation	140/8552	229/18723	1.63e-06	1.95e-05	140
GO:000150317	Esophagus	ESCC	ossification	232/8552	408/18723	3.00e-06	3.40e-05	232
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:00432007	Esophagus	ESCC	response to amino acid	74/8552	116/18723	6.23e-05	4.76e-04	74
GO:000110110	Esophagus	ESCC	response to acid chemical	84/8552	135/18723	7.70e-05	5.74e-04	84
GO:00712305	Esophagus	ESCC	cellular response to amino acid stimulus	48/8552	71/18723	1.55e-04	1.03e-03	48
GO:00017064	Esophagus	ESCC	endoderm formation	38/8552	54/18723	2.08e-04	1.31e-03	38

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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
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
hsa0451051	Liver	HCC	Focal adhesion	125/4020	203/8465	3.12e-05	1.88e-04	1.04e-04	125
hsa051653	Liver	HCC	Human papillomavirus infection	188/4020	331/8465	3.34e-04	1.49e-03	8.29e-04	188
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

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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
COL6A1	ITGA1_ITGB1	COL6A1_ITGA1_ITGB1	COLLAGEN	Breast	ADJ
COL6A1	ITGA2_ITGB1	COL6A1_ITGA2_ITGB1	COLLAGEN	Breast	ADJ
COL6A1	CD44	COL6A1_CD44	COLLAGEN	Breast	ADJ
COL6A1	SDC4	COL6A1_SDC4	COLLAGEN	Breast	ADJ
COL6A1	ITGA1_ITGB1	COL6A1_ITGA1_ITGB1	COLLAGEN	Breast	DCIS
COL6A1	ITGA2_ITGB1	COL6A1_ITGA2_ITGB1	COLLAGEN	Breast	DCIS
COL6A1	CD44	COL6A1_CD44	COLLAGEN	Breast	DCIS
COL6A1	SDC1	COL6A1_SDC1	COLLAGEN	Breast	DCIS
COL6A1	SDC4	COL6A1_SDC4	COLLAGEN	Breast	DCIS
COL6A1	ITGA1_ITGB1	COL6A1_ITGA1_ITGB1	COLLAGEN	Breast	Healthy
COL6A1	ITGA2_ITGB1	COL6A1_ITGA2_ITGB1	COLLAGEN	Breast	Healthy
COL6A1	ITGAV_ITGB8	COL6A1_ITGAV_ITGB8	COLLAGEN	Breast	Healthy
COL6A1	CD44	COL6A1_CD44	COLLAGEN	Breast	Healthy
COL6A1	SDC1	COL6A1_SDC1	COLLAGEN	Breast	Healthy
COL6A1	SDC4	COL6A1_SDC4	COLLAGEN	Breast	Healthy
COL6A1	ITGA1_ITGB1	COL6A1_ITGA1_ITGB1	COLLAGEN	Breast	IDC
COL6A1	CD44	COL6A1_CD44	COLLAGEN	Breast	IDC
COL6A1	SDC1	COL6A1_SDC1	COLLAGEN	Breast	IDC
COL6A1	SDC4	COL6A1_SDC4	COLLAGEN	Breast	IDC
COL6A1	ITGA1_ITGB1	COL6A1_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

COL6A1

SNV

Missense_Mutation

novel

c.142N>T

p.Val48Leu

p.V48L

P12109

protein_coding

deleterious(0)

probably_damaging(0.996)

TCGA-A7-A26H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

anastrozole

COL6A1

SNV

Missense_Mutation

rs780891158

c.2782C>T

p.Arg928Cys

p.R928C

P12109

protein_coding

deleterious(0)

probably_damaging(0.949)

TCGA-A7-A426-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

COL6A1

SNV

Missense_Mutation

c.1933C>A

p.Leu645Met

p.L645M

P12109

protein_coding

deleterious(0.01)

probably_damaging(0.993)

TCGA-A8-A06X-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL6A1

SNV

Missense_Mutation

rs752259110

c.784N>T

p.Arg262Trp

p.R262W

P12109

protein_coding

deleterious(0.02)

probably_damaging(0.969)

TCGA-E9-A1R2-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

taxotere

COL6A1

SNV

Missense_Mutation

rs368239109

c.1315N>T

p.Arg439Trp

p.R439W

P12109

protein_coding

deleterious(0.01)

probably_damaging(0.986)

TCGA-E9-A1RE-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

tamoxiphen

COL6A1

deletion

Frame_Shift_Del

novel

c.1242delN

p.Pro415GlnfsTer90

p.P415Qfs*90

P12109

protein_coding

TCGA-D8-A27V-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

COL6A1

deletion

Frame_Shift_Del

novel

c.1821delN

p.Cys607TrpfsTer39

p.C607Wfs*39

P12109

protein_coding

TCGA-D8-A27V-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

COL6A1

deletion

Frame_Shift_Del

novel

c.2339delN

p.Gln781ArgfsTer22

p.Q781Rfs*22

P12109

protein_coding

TCGA-EW-A2FV-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

docetaxel

COL6A1

SNV

Missense_Mutation

rs201456885

c.2998N>A

p.Glu1000Lys

p.E1000K

P12109

protein_coding

deleterious(0.02)

benign(0.251)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

COL6A1

SNV

Missense_Mutation

c.1870N>C

p.Glu624Gln

p.E624Q

P12109

protein_coding

deleterious(0.02)

probably_damaging(0.999)

TCGA-C5-A1BQ-01

Cervix

cervical & endocervical cancer

Female

>=65

III/IV

Chemotherapy

cisplatin

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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
1291	COL6A1	DRUGGABLE GENOME		CHEMBL2108709	COLLAGENASE CLOSTRIDIUM HISTOLYTICUM
1291	COL6A1	DRUGGABLE GENOME		CHEMBL2095222	OCRIPLASMIN

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