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: MGMT

Gene summary for MGMT

Gene summary.

Gene information	Species	Human
	Gene symbol	MGMT
	Gene ID	4255
	Gene name	O-6-methylguanine-DNA methyltransferase
	Gene Alias	MGMT
	Cytomap	10q26.3
	Gene Type	protein-coding
	GO ID	GO:0006139
	UniProtAcc	B4DEE8

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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
4255	MGMT	LZE4T	Human	Esophagus	ESCC	3.55e-14	2.08e-01	0.0811
4255	MGMT	LZE7T	Human	Esophagus	ESCC	2.38e-06	3.45e-01	0.0667
4255	MGMT	LZE8T	Human	Esophagus	ESCC	2.92e-08	3.69e-01	0.067
4255	MGMT	LZE20T	Human	Esophagus	ESCC	1.11e-11	5.09e-01	0.0662
4255	MGMT	LZE22T	Human	Esophagus	ESCC	7.32e-12	4.63e-01	0.068
4255	MGMT	LZE24T	Human	Esophagus	ESCC	1.98e-23	8.52e-01	0.0596
4255	MGMT	LZE6T	Human	Esophagus	ESCC	2.49e-08	3.22e-01	0.0845
4255	MGMT	P1T-E	Human	Esophagus	ESCC	1.00e-15	9.13e-01	0.0875
4255	MGMT	P2T-E	Human	Esophagus	ESCC	6.37e-53	9.83e-01	0.1177
4255	MGMT	P4T-E	Human	Esophagus	ESCC	2.07e-45	1.12e+00	0.1323
4255	MGMT	P5T-E	Human	Esophagus	ESCC	4.71e-76	1.54e+00	0.1327
4255	MGMT	P8T-E	Human	Esophagus	ESCC	4.83e-12	3.29e-01	0.0889
4255	MGMT	P9T-E	Human	Esophagus	ESCC	6.07e-18	4.28e-01	0.1131
4255	MGMT	P10T-E	Human	Esophagus	ESCC	1.00e-16	3.24e-01	0.116
4255	MGMT	P11T-E	Human	Esophagus	ESCC	1.30e-20	1.05e+00	0.1426
4255	MGMT	P12T-E	Human	Esophagus	ESCC	2.55e-47	9.19e-01	0.1122
4255	MGMT	P15T-E	Human	Esophagus	ESCC	1.87e-30	5.42e-01	0.1149
4255	MGMT	P16T-E	Human	Esophagus	ESCC	5.95e-41	8.09e-01	0.1153
4255	MGMT	P17T-E	Human	Esophagus	ESCC	2.78e-15	6.82e-01	0.1278
4255	MGMT	P19T-E	Human	Esophagus	ESCC	2.75e-09	1.23e+00	0.1662

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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
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
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:0006979111	Esophagus	ESCC	response to oxidative stress	303/8552	446/18723	7.15e-22	1.30e-19	303
GO:0062197111	Esophagus	ESCC	cellular response to chemical stress	234/8552	337/18723	5.37e-19	5.97e-17	234
GO:0034599111	Esophagus	ESCC	cellular response to oxidative stress	197/8552	288/18723	3.76e-15	2.15e-13	197
GO:005105215	Esophagus	ESCC	regulation of DNA metabolic process	232/8552	359/18723	2.40e-13	1.13e-11	232
GO:001021217	Esophagus	ESCC	response to ionizing radiation	110/8552	148/18723	1.11e-12	4.78e-11	110
GO:0048732111	Esophagus	ESCC	gland development	269/8552	436/18723	7.81e-12	2.95e-10	269
GO:0031667111	Esophagus	ESCC	response to nutrient levels	289/8552	474/18723	9.25e-12	3.47e-10	289
GO:005105417	Esophagus	ESCC	positive regulation of DNA metabolic process	139/8552	201/18723	1.20e-11	4.33e-10	139
GO:2000116111	Esophagus	ESCC	regulation of cysteine-type endopeptidase activity	158/8552	235/18723	1.67e-11	5.90e-10	158
GO:0043281111	Esophagus	ESCC	regulation of cysteine-type endopeptidase activity involved in apoptotic process	143/8552	209/18723	2.12e-11	7.31e-10	143
GO:000931419	Esophagus	ESCC	response to radiation	277/8552	456/18723	4.42e-11	1.43e-09	277
GO:00434143	Esophagus	ESCC	macromolecule methylation	199/8552	316/18723	3.44e-10	9.57e-09	199
GO:2001020110	Esophagus	ESCC	regulation of response to DNA damage stimulus	145/8552	219/18723	5.97e-10	1.50e-08	145
GO:007121419	Esophagus	ESCC	cellular response to abiotic stimulus	206/8552	331/18723	7.52e-10	1.88e-08	206
GO:010400419	Esophagus	ESCC	cellular response to environmental stimulus	206/8552	331/18723	7.52e-10	1.88e-08	206
GO:0052547111	Esophagus	ESCC	regulation of peptidase activity	275/8552	461/18723	7.54e-10	1.88e-08	275
GO:00322592	Esophagus	ESCC	methylation	222/8552	364/18723	2.26e-09	5.09e-08	222
GO:007147816	Esophagus	ESCC	cellular response to radiation	122/8552	186/18723	3.07e-08	5.73e-07	122
GO:0052548111	Esophagus	ESCC	regulation of endopeptidase activity	253/8552	432/18723	3.68e-08	6.78e-07	253
GO:000758410	Esophagus	ESCC	response to nutrient	114/8552	174/18723	9.43e-08	1.56e-06	114

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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

MGMT

SNV

Missense_Mutation

rs768667991

c.380G>A

p.Arg127Lys

p.R127K

P16455

protein_coding

tolerated(0.31)

benign(0.059)

TCGA-BH-A0HK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

MGMT

SNV

Missense_Mutation

rs374717890

c.446N>T

p.Ala149Val

p.A149V

P16455

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-S3-AA0Z-01

Breast

breast invasive carcinoma

Female

<65

I/II

Ancillary

neulasta

MGMT

SNV

Missense_Mutation

c.610G>C

p.Gly204Arg

p.G204R

P16455

protein_coding

deleterious(0.02)

possibly_damaging(0.719)

TCGA-EA-A43B-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

MGMT

SNV

Missense_Mutation

rs544050191

c.119G>A

p.Arg40His

p.R40H

P16455

protein_coding

tolerated(0.55)

benign(0.013)

TCGA-AZ-4315-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

MGMT

SNV

Missense_Mutation

c.80N>C

p.Leu27Ser

p.L27S

P16455

protein_coding

tolerated_low_confidence(0.77)

benign(0.039)

TCGA-AZ-6601-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

MGMT

SNV

Missense_Mutation

rs544050191

c.119N>A

p.Arg40His

p.R40H

P16455

protein_coding

tolerated(0.55)

benign(0.013)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

MGMT

SNV

Missense_Mutation

rs748040489

c.473C>T

p.Ala158Val

p.A158V

P16455

protein_coding

tolerated(0.17)

benign(0.208)

TCGA-AP-A1DV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

MGMT

SNV

Missense_Mutation

rs373120552

c.583N>A

p.Val195Met

p.V195M

P16455

protein_coding

tolerated(0.23)

benign(0.318)

TCGA-AX-A2HA-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

MGMT

SNV

Missense_Mutation

rs748040489

c.473N>T

p.Ala158Val

p.A158V

P16455

protein_coding

tolerated(0.17)

benign(0.208)

TCGA-B5-A11E-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

MGMT

SNV

Missense_Mutation

novel

c.298T>C

p.Tyr100His

p.Y100H

P16455

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-DI-A1BU-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Chemotherapy

paclitaxel

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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
4255	MGMT	CLINICALLY ACTIONABLE, DRUGGABLE GENOME, DNA REPAIR, ENZYME		CHLORAMBUCIL	CHLORAMBUCIL	8621235
4255	MGMT	CLINICALLY ACTIONABLE, DRUGGABLE GENOME, DNA REPAIR, ENZYME		CPT-11	IRINOTECAN HYDROCHLORIDE	11802813
4255	MGMT	CLINICALLY ACTIONABLE, DRUGGABLE GENOME, DNA REPAIR, ENZYME		GENISTEIN	GENISTEIN	16203797
4255	MGMT	CLINICALLY ACTIONABLE, DRUGGABLE GENOME, DNA REPAIR, ENZYME		NITROSOUREAS		9393761
4255	MGMT	CLINICALLY ACTIONABLE, DRUGGABLE GENOME, DNA REPAIR, ENZYME		CDDP	CISPLATIN	16043385
4255	MGMT	CLINICALLY ACTIONABLE, DRUGGABLE GENOME, DNA REPAIR, ENZYME		TGFBETA1		11262404
4255	MGMT	CLINICALLY ACTIONABLE, DRUGGABLE GENOME, DNA REPAIR, ENZYME		DOX		1387586
4255	MGMT	CLINICALLY ACTIONABLE, DRUGGABLE GENOME, DNA REPAIR, ENZYME		ANTIOXIDANT		17016661
4255	MGMT	CLINICALLY ACTIONABLE, DRUGGABLE GENOME, DNA REPAIR, ENZYME		temozolomide	TEMOZOLOMIDE	24444404
4255	MGMT	CLINICALLY ACTIONABLE, DRUGGABLE GENOME, DNA REPAIR, ENZYME		CARMUSTINE	CARMUSTINE	11070098

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