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

Home

Download

Statistics

Help

Contact

	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: COL4A6

Gene summary for COL4A6

Gene summary.

Gene information	Species	Human
	Gene symbol	COL4A6
	Gene ID	1288
	Gene name	collagen type IV alpha 6 chain
	Gene Alias	CXDELq22.3
	Cytomap	Xq22.3
	Gene Type	protein-coding
	GO ID	GO:0001101
	UniProtAcc	A8MXH5

Top

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
1288	COL4A6	LZE4T	Human	Esophagus	ESCC	1.38e-13	4.27e-01	0.0811
1288	COL4A6	LZE24T	Human	Esophagus	ESCC	8.21e-08	3.75e-01	0.0596
1288	COL4A6	LZE6T	Human	Esophagus	ESCC	2.77e-06	3.88e-01	0.0845
1288	COL4A6	P2T-E	Human	Esophagus	ESCC	2.73e-08	3.04e-01	0.1177
1288	COL4A6	P4T-E	Human	Esophagus	ESCC	1.36e-08	3.00e-01	0.1323
1288	COL4A6	P5T-E	Human	Esophagus	ESCC	1.04e-07	2.15e-01	0.1327
1288	COL4A6	P8T-E	Human	Esophagus	ESCC	3.67e-12	2.99e-01	0.0889
1288	COL4A6	P10T-E	Human	Esophagus	ESCC	1.14e-14	3.11e-01	0.116
1288	COL4A6	P11T-E	Human	Esophagus	ESCC	1.35e-03	2.15e-01	0.1426
1288	COL4A6	P12T-E	Human	Esophagus	ESCC	5.93e-13	3.65e-01	0.1122
1288	COL4A6	P15T-E	Human	Esophagus	ESCC	1.86e-07	1.70e-01	0.1149
1288	COL4A6	P16T-E	Human	Esophagus	ESCC	2.46e-02	1.30e-01	0.1153
1288	COL4A6	P17T-E	Human	Esophagus	ESCC	1.39e-04	1.68e-01	0.1278
1288	COL4A6	P20T-E	Human	Esophagus	ESCC	1.91e-32	8.95e-01	0.1124
1288	COL4A6	P21T-E	Human	Esophagus	ESCC	7.55e-12	2.75e-01	0.1617
1288	COL4A6	P22T-E	Human	Esophagus	ESCC	1.82e-04	1.47e-01	0.1236
1288	COL4A6	P26T-E	Human	Esophagus	ESCC	5.65e-52	9.44e-01	0.1276
1288	COL4A6	P27T-E	Human	Esophagus	ESCC	7.09e-10	2.46e-01	0.1055
1288	COL4A6	P37T-E	Human	Esophagus	ESCC	1.43e-24	5.57e-01	0.1371
1288	COL4A6	P40T-E	Human	Esophagus	ESCC	2.45e-07	3.14e-01	0.109

Page: 1 2 3 4

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
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.

Top

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).

Page: 1 2 3 4 5 6 7 8 9

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: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: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:00712305	Esophagus	ESCC	cellular response to amino acid stimulus	48/8552	71/18723	1.55e-04	1.03e-03	48
GO:00712296	Esophagus	ESCC	cellular response to acid chemical	52/8552	80/18723	3.79e-04	2.20e-03	52
GO:00011019	Oral cavity	OSCC	response to acid chemical	74/7305	135/18723	1.38e-04	9.76e-04	74
GO:00432006	Oral cavity	OSCC	response to amino acid	64/7305	116/18723	2.96e-04	1.86e-03	64
GO:00712304	Oral cavity	OSCC	cellular response to amino acid stimulus	42/7305	71/18723	4.59e-04	2.76e-03	42
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:00712295	Oral cavity	OSCC	cellular response to acid chemical	46/7305	80/18723	6.08e-04	3.44e-03	46
GO:00011018	Prostate	BPH	response to acid chemical	37/3107	135/18723	1.03e-03	6.46e-03	37
GO:00712294	Prostate	BPH	cellular response to acid chemical	23/3107	80/18723	4.53e-03	2.19e-02	23
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:00712303	Prostate	BPH	cellular response to amino acid stimulus	20/3107	71/18723	9.89e-03	4.16e-02	20

Page: 1 2

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
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
hsa052228	Oral cavity	OSCC	Small cell lung cancer	66/3704	92/8465	4.43e-08	3.38e-07	1.72e-07	66
hsa049339	Oral cavity	OSCC	AGE-RAGE signaling pathway in diabetic complications	69/3704	100/8465	2.61e-07	1.65e-06	8.41e-07	69
hsa041516	Oral cavity	OSCC	PI3K-Akt signaling pathway	185/3704	354/8465	6.26e-04	1.86e-03	9.49e-04	185
hsa049267	Oral cavity	OSCC	Relaxin signaling pathway	74/3704	129/8465	1.20e-03	3.37e-03	1.72e-03	74
hsa051468	Oral cavity	OSCC	Amoebiasis	59/3704	102/8465	2.78e-03	7.17e-03	3.65e-03	59
hsa0516514	Oral cavity	OSCC	Human papillomavirus infection	200/3704	331/8465	3.83e-10	4.93e-09	2.51e-09	200

Page: 1 2 3

Top

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
COL4A6	ITGA1_ITGB1	COL4A6_ITGA1_ITGB1	COLLAGEN	CRC	AD
COL4A6	ITGA2_ITGB1	COL4A6_ITGA2_ITGB1	COLLAGEN	CRC	AD
COL4A6	ITGA3_ITGB1	COL4A6_ITGA3_ITGB1	COLLAGEN	CRC	AD
COL4A6	ITGA11_ITGB1	COL4A6_ITGA11_ITGB1	COLLAGEN	CRC	AD
COL4A6	CD44	COL4A6_CD44	COLLAGEN	CRC	AD
COL4A6	SDC1	COL4A6_SDC1	COLLAGEN	CRC	AD
COL4A6	SDC4	COL4A6_SDC4	COLLAGEN	CRC	AD
COL4A6	ITGA1_ITGB1	COL4A6_ITGA1_ITGB1	COLLAGEN	CRC	ADJ
COL4A6	ITGA2_ITGB1	COL4A6_ITGA2_ITGB1	COLLAGEN	CRC	ADJ
COL4A6	ITGA3_ITGB1	COL4A6_ITGA3_ITGB1	COLLAGEN	CRC	ADJ
COL4A6	CD44	COL4A6_CD44	COLLAGEN	CRC	ADJ
COL4A6	SDC1	COL4A6_SDC1	COLLAGEN	CRC	ADJ
COL4A6	SDC4	COL4A6_SDC4	COLLAGEN	CRC	ADJ
COL4A6	ITGA1_ITGB1	COL4A6_ITGA1_ITGB1	COLLAGEN	Endometrium	ADJ
COL4A6	ITGA3_ITGB1	COL4A6_ITGA3_ITGB1	COLLAGEN	Endometrium	ADJ
COL4A6	ITGA9_ITGB1	COL4A6_ITGA9_ITGB1	COLLAGEN	Endometrium	ADJ
COL4A6	ITGAV_ITGB8	COL4A6_ITGAV_ITGB8	COLLAGEN	Endometrium	ADJ
COL4A6	CD44	COL4A6_CD44	COLLAGEN	Endometrium	ADJ
COL4A6	ITGA1_ITGB1	COL4A6_ITGA1_ITGB1	COLLAGEN	Endometrium	AEH
COL4A6	ITGA2_ITGB1	COL4A6_ITGA2_ITGB1	COLLAGEN	Endometrium	AEH

Page: 1 2

Top

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.

Page: 1

Top

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

COL4A6

SNV

Missense_Mutation

novel

c.2647N>C

p.Gly883Arg

p.G883R

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-A2-A3Y0-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

COL4A6

SNV

Missense_Mutation

novel

c.3239N>C

p.Leu1080Pro

p.L1080P

protein_coding

tolerated(0.35)

benign(0.332)

TCGA-A7-A6VX-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

docetaxel

COL4A6

SNV

Missense_Mutation

c.1876N>A

p.Pro626Thr

p.P626T

protein_coding

tolerated(0.19)

benign(0.033)

TCGA-A8-A08H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL4A6

SNV

Missense_Mutation

c.1076N>G

p.Asn359Ser

p.N359S

protein_coding

tolerated(0.41)

benign(0.001)

TCGA-A8-A09G-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

COL4A6

SNV

Missense_Mutation

novel

c.4554G>T

p.Glu1518Asp

p.E1518D

protein_coding

deleterious(0.02)

probably_damaging(0.998)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL4A6

SNV

Missense_Mutation

c.1099N>T

p.Gly367Cys

p.G367C

protein_coding

deleterious(0)

probably_damaging(0.986)

TCGA-BH-A1F2-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

COL4A6

SNV

Missense_Mutation

c.3721N>G

p.Arg1241Gly

p.R1241G

protein_coding

deleterious(0.03)

possibly_damaging(0.852)

TCGA-C8-A1HN-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

COL4A6

SNV

Missense_Mutation

c.4832G>T

p.Arg1611Leu

p.R1611L

protein_coding

deleterious(0)

probably_damaging(0.96)

TCGA-D8-A27K-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin+cyclophosphamid

COL4A6

SNV

Missense_Mutation

c.4261N>G

p.Leu1421Val

p.L1421V

protein_coding

tolerated(0.25)

possibly_damaging(0.852)

TCGA-E2-A1LH-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

COL4A6

SNV

Missense_Mutation

rs768504005

c.4440N>A

p.Met1480Ile

p.M1480I

protein_coding

tolerated(0.14)

benign(0.039)

TCGA-E2-A2P6-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

anastrozole

Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

Top

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
1288	COL4A6	DRUGGABLE GENOME		CHEMBL2095222	OCRIPLASMIN
1288	COL4A6	DRUGGABLE GENOME		CHEMBL2108709	COLLAGENASE CLOSTRIDIUM HISTOLYTICUM

Page: 1