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: EXT1

Gene summary for EXT1

Gene summary.

Gene information	Species	Human
	Gene symbol	EXT1
	Gene ID	2131
	Gene name	exostosin glycosyltransferase 1
	Gene Alias	EXT
	Cytomap	8q24.11
	Gene Type	protein-coding
	GO ID	GO:0000271
	UniProtAcc	Q16394

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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
2131	EXT1	CA_HPV_1	Human	Cervix	CC	5.11e-04	-1.08e-01	0.0264
2131	EXT1	N_HPV_1	Human	Cervix	N_HPV	2.26e-05	-1.08e-01	0.0079
2131	EXT1	CCI_1	Human	Cervix	CC	1.40e-25	2.19e+00	0.528
2131	EXT1	CCI_2	Human	Cervix	CC	1.54e-21	3.95e+00	0.5249
2131	EXT1	CCI_3	Human	Cervix	CC	1.51e-34	2.17e+00	0.516
2131	EXT1	CCII_1	Human	Cervix	CC	2.23e-08	5.83e-01	0.3249
2131	EXT1	HTA11_3410_2000001011	Human	Colorectum	AD	2.01e-21	-6.82e-01	0.0155
2131	EXT1	HTA11_2951_2000001011	Human	Colorectum	AD	3.40e-16	-1.02e+00	0.0216
2131	EXT1	HTA11_78_2000001011	Human	Colorectum	AD	8.65e-09	6.64e-01	-0.1088
2131	EXT1	HTA11_347_2000001011	Human	Colorectum	AD	2.04e-40	1.31e+00	-0.1954
2131	EXT1	HTA11_411_2000001011	Human	Colorectum	SER	6.95e-07	7.34e-01	-0.2602
2131	EXT1	HTA11_83_2000001011	Human	Colorectum	SER	2.28e-16	8.93e-01	-0.1526
2131	EXT1	HTA11_696_2000001011	Human	Colorectum	AD	3.75e-06	4.89e-01	-0.1464
2131	EXT1	HTA11_866_2000001011	Human	Colorectum	AD	4.16e-05	5.42e-01	-0.1001
2131	EXT1	HTA11_1391_2000001011	Human	Colorectum	AD	1.05e-06	7.67e-01	-0.059
2131	EXT1	HTA11_2992_2000001011	Human	Colorectum	SER	1.07e-05	6.20e-01	-0.1706
2131	EXT1	HTA11_546_2000001011	Human	Colorectum	AD	3.71e-03	4.10e-01	-0.0842
2131	EXT1	HTA11_866_3004761011	Human	Colorectum	AD	2.69e-21	-7.72e-01	0.096
2131	EXT1	HTA11_9408_2000001011	Human	Colorectum	AD	1.53e-07	-8.80e-01	0.0451
2131	EXT1	HTA11_10711_2000001011	Human	Colorectum	AD	9.98e-04	-4.90e-01	0.0338

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Cervix		CC: Cervix cancer
		HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
		N_HPV: HPV-infected normal cervix
Colorectum (GSE201348)		FAP: Familial adenomatous polyposis
		CRC: Colorectal cancer
Colorectum (HTA11)		AD: Adenomas
		SER: Sessile serrated lesions
		MSI-H: Microsatellite-high colorectal cancer
		MSS: Microsatellite stable colorectal cancer
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
GC		CAG: Chronic atrophic gastritis
		CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
		CSG: Chronic superficial gastritis
		GC: Gastric cancer
		SIM: Severe intestinal metaplasia
		WIM: Wild intestinal metaplasia
Liver		HCC: Hepatocellular carcinoma
		NAFLD: Non-alcoholic fatty liver disease
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
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:00071787	Endometrium	AEH	transmembrane receptor protein serine/threonine kinase signaling pathway	67/2100	355/18723	1.28e-05	2.80e-04	67
GO:00611384	Endometrium	AEH	morphogenesis of a branching epithelium	40/2100	182/18723	2.16e-05	4.20e-04	40
GO:00018224	Endometrium	AEH	kidney development	57/2100	293/18723	2.25e-05	4.35e-04	57
GO:00485887	Endometrium	AEH	developmental cell growth	48/2100	234/18723	2.39e-05	4.53e-04	48
GO:00017637	Endometrium	AEH	morphogenesis of a branching structure	42/2100	196/18723	2.58e-05	4.86e-04	42
GO:00600708	Endometrium	AEH	canonical Wnt signaling pathway	58/2100	303/18723	3.12e-05	5.66e-04	58
GO:004887216	Endometrium	AEH	homeostasis of number of cells	53/2100	272/18723	4.10e-05	6.99e-04	53
GO:004521610	Endometrium	AEH	cell-cell junction organization	42/2100	200/18723	4.26e-05	7.20e-04	42
GO:00487542	Endometrium	AEH	branching morphogenesis of an epithelial tube	33/2100	151/18723	1.22e-04	1.68e-03	33
GO:00487625	Endometrium	AEH	mesenchymal cell differentiation	46/2100	236/18723	1.27e-04	1.74e-03	46
GO:00604853	Endometrium	AEH	mesenchyme development	54/2100	291/18723	1.34e-04	1.83e-03	54
GO:000189410	Endometrium	AEH	tissue homeostasis	50/2100	268/18723	2.04e-04	2.54e-03	50
GO:00509008	Endometrium	AEH	leukocyte migration	64/2100	369/18723	2.57e-04	3.04e-03	64
GO:19908235	Endometrium	AEH	response to leukemia inhibitory factor	23/2100	95/18723	2.65e-04	3.09e-03	23
GO:00305092	Endometrium	AEH	BMP signaling pathway	32/2100	152/18723	3.15e-04	3.54e-03	32
GO:00488635	Endometrium	AEH	stem cell differentiation	40/2100	206/18723	3.67e-04	3.99e-03	40
GO:00096159	Endometrium	AEH	response to virus	63/2100	367/18723	3.81e-04	4.10e-03	63
GO:00720736	Endometrium	AEH	kidney epithelium development	29/2100	136/18723	4.71e-04	4.91e-03	29
GO:00071599	Endometrium	AEH	leukocyte cell-cell adhesion	63/2100	371/18723	5.11e-04	5.21e-03	63
GO:00602499	Endometrium	AEH	anatomical structure homeostasis	55/2100	314/18723	5.27e-04	5.32e-03	55

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Enriched KEGG pathways.

Pathway ID

Tissue

Disease Stage

Description

Gene Ratio

Bg Ratio

pvalue

p.adjust

qvalue

Count

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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

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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

EXT1

SNV

Missense_Mutation

c.781N>G

p.Lys261Glu

p.K261E

Q16394

protein_coding

tolerated(0.14)

possibly_damaging(0.627)

TCGA-A2-A0CT-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

cytoxan

EXT1

SNV

Missense_Mutation

novel

c.119N>C

p.His40Pro

p.H40P

Q16394

protein_coding

tolerated(0.29)

benign(0.007)

TCGA-A8-A08R-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

EXT1

SNV

Missense_Mutation

c.1024N>A

p.Leu342Ile

p.L342I

Q16394

protein_coding

deleterious(0.02)

possibly_damaging(0.883)

TCGA-C8-A12V-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

EXT1

insertion

In_Frame_Ins

novel

c.807_808insTCTCACTGTCTAAAC

p.Lys269_Arg270insSerHisCysLeuAsn

p.K269_R270insSHCLN

Q16394

protein_coding

TCGA-AN-A04A-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

EXT1

insertion

Nonsense_Mutation

novel

c.805_806insTAAACTTTTTTTTTTTTTTTTAAATGTGGGCCTC

p.Lys269IlefsTer8

p.K269Ifs*8

Q16394

protein_coding

TCGA-AN-A04A-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

EXT1

SNV

Missense_Mutation

novel

c.1651N>G

p.Leu551Val

p.L551V

Q16394

protein_coding

tolerated(0.1)

benign(0.099)

TCGA-VS-A8EB-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Unknown

EXT1

SNV

Missense_Mutation

c.793G>A

p.Val265Ile

p.V265I

Q16394

protein_coding

tolerated(0.1)

benign(0.223)

TCGA-A6-2686-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

EXT1

SNV

Missense_Mutation

rs767492816

c.1612N>A

p.Val538Ile

p.V538I

Q16394

protein_coding

tolerated(0.23)

benign(0.386)

TCGA-A6-5656-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

EXT1

SNV

Missense_Mutation

c.542N>C

p.Leu181Pro

p.L181P

Q16394

protein_coding

deleterious(0.02)

probably_damaging(0.992)

TCGA-AA-3666-01

Colorectum

colon adenocarcinoma

Male

>=65

III/IV

Unknown

EXT1

SNV

Missense_Mutation

c.452N>T

p.Ala151Val

p.A151V

Q16394

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-AA-3715-01

Colorectum

colon adenocarcinoma

Male

>=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

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