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: MAGT1

Gene summary for MAGT1

Gene summary.

Gene information	Species	Human
	Gene symbol	MAGT1
	Gene ID	84061
	Gene name	magnesium transporter 1
	Gene Alias	CDG1CC
	Cytomap	Xq21.1
	Gene Type	protein-coding
	GO ID	GO:0003008
	UniProtAcc	A0A087WU53

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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
84061	MAGT1	LZE4T	Human	Esophagus	ESCC	3.77e-11	3.33e-01	0.0811
84061	MAGT1	LZE7T	Human	Esophagus	ESCC	1.41e-04	5.17e-01	0.0667
84061	MAGT1	LZE8T	Human	Esophagus	ESCC	2.98e-12	1.55e-01	0.067
84061	MAGT1	LZE20T	Human	Esophagus	ESCC	3.41e-07	2.18e-01	0.0662
84061	MAGT1	LZE22D1	Human	Esophagus	HGIN	1.41e-02	9.19e-02	0.0595
84061	MAGT1	LZE22T	Human	Esophagus	ESCC	2.62e-04	3.08e-01	0.068
84061	MAGT1	LZE24T	Human	Esophagus	ESCC	4.45e-25	7.16e-01	0.0596
84061	MAGT1	P2T-E	Human	Esophagus	ESCC	1.87e-30	6.54e-01	0.1177
84061	MAGT1	P4T-E	Human	Esophagus	ESCC	2.47e-20	5.99e-01	0.1323
84061	MAGT1	P5T-E	Human	Esophagus	ESCC	3.47e-12	2.11e-01	0.1327
84061	MAGT1	P8T-E	Human	Esophagus	ESCC	3.70e-29	6.43e-01	0.0889
84061	MAGT1	P9T-E	Human	Esophagus	ESCC	3.50e-18	3.65e-01	0.1131
84061	MAGT1	P10T-E	Human	Esophagus	ESCC	5.46e-24	3.47e-01	0.116
84061	MAGT1	P11T-E	Human	Esophagus	ESCC	1.84e-10	4.92e-01	0.1426
84061	MAGT1	P12T-E	Human	Esophagus	ESCC	3.14e-28	7.32e-01	0.1122
84061	MAGT1	P15T-E	Human	Esophagus	ESCC	4.65e-19	4.05e-01	0.1149
84061	MAGT1	P16T-E	Human	Esophagus	ESCC	9.85e-20	2.84e-01	0.1153
84061	MAGT1	P17T-E	Human	Esophagus	ESCC	3.43e-08	2.47e-01	0.1278
84061	MAGT1	P20T-E	Human	Esophagus	ESCC	1.50e-18	5.02e-01	0.1124
84061	MAGT1	P21T-E	Human	Esophagus	ESCC	1.25e-20	3.69e-01	0.1617

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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
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
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:00064876	Esophagus	HGIN	protein N-linked glycosylation	17/2587	65/18723	6.04e-03	4.87e-02	17
GO:000648714	Esophagus	ESCC	protein N-linked glycosylation	51/8552	65/18723	6.41e-08	1.13e-06	51
GO:00091002	Esophagus	ESCC	glycoprotein metabolic process	226/8552	387/18723	2.64e-07	3.94e-06	226
GO:00181969	Esophagus	ESCC	peptidyl-asparagine modification	22/8552	24/18723	2.82e-06	3.21e-05	22
GO:00700854	Esophagus	ESCC	glycosylation	144/8552	240/18723	5.12e-06	5.38e-05	144
GO:00182799	Esophagus	ESCC	protein N-linked glycosylation via asparagine	21/8552	23/18723	5.69e-06	5.90e-05	21
GO:00064865	Esophagus	ESCC	protein glycosylation	135/8552	226/18723	1.36e-05	1.24e-04	135
GO:00434135	Esophagus	ESCC	macromolecule glycosylation	135/8552	226/18723	1.36e-05	1.24e-04	135
GO:00091012	Esophagus	ESCC	glycoprotein biosynthetic process	181/8552	317/18723	2.54e-05	2.15e-04	181
GO:00182795	Liver	Cirrhotic	protein N-linked glycosylation via asparagine	16/4634	23/18723	7.54e-06	1.15e-04	16
GO:00181965	Liver	Cirrhotic	peptidyl-asparagine modification	16/4634	24/18723	1.74e-05	2.37e-04	16
GO:00064873	Liver	Cirrhotic	protein N-linked glycosylation	30/4634	65/18723	1.40e-04	1.36e-03	30
GO:000648711	Liver	HCC	protein N-linked glycosylation	48/7958	65/18723	2.85e-07	5.00e-06	48
GO:001819611	Liver	HCC	peptidyl-asparagine modification	21/7958	24/18723	6.62e-06	7.97e-05	21
GO:001827911	Liver	HCC	protein N-linked glycosylation via asparagine	20/7958	23/18723	1.37e-05	1.51e-04	20
GO:00064862	Liver	HCC	protein glycosylation	122/7958	226/18723	3.11e-04	2.21e-03	122
GO:00434132	Liver	HCC	macromolecule glycosylation	122/7958	226/18723	3.11e-04	2.21e-03	122
GO:00700852	Liver	HCC	glycosylation	128/7958	240/18723	4.35e-04	2.92e-03	128
GO:0009100	Liver	HCC	glycoprotein metabolic process	193/7958	387/18723	1.89e-03	9.62e-03	193
GO:00064875	Oral cavity	OSCC	protein N-linked glycosylation	44/7305	65/18723	2.63e-06	3.26e-05	44

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0414139	Esophagus	HGIN	Protein processing in endoplasmic reticulum	67/1383	174/8465	1.06e-12	2.16e-11	1.72e-11	67
hsa005106	Esophagus	HGIN	N-Glycan biosynthesis	17/1383	53/8465	3.43e-03	2.54e-02	2.02e-02	17
hsa04141114	Esophagus	HGIN	Protein processing in endoplasmic reticulum	67/1383	174/8465	1.06e-12	2.16e-11	1.72e-11	67
hsa0051013	Esophagus	HGIN	N-Glycan biosynthesis	17/1383	53/8465	3.43e-03	2.54e-02	2.02e-02	17
hsa04141211	Esophagus	ESCC	Protein processing in endoplasmic reticulum	147/4205	174/8465	3.29e-22	1.10e-19	5.64e-20	147
hsa0051023	Esophagus	ESCC	N-Glycan biosynthesis	39/4205	53/8465	3.26e-04	1.15e-03	5.89e-04	39
hsa005136	Esophagus	ESCC	Various types of N-glycan biosynthesis	31/4205	42/8465	1.23e-03	3.78e-03	1.93e-03	31
hsa04141310	Esophagus	ESCC	Protein processing in endoplasmic reticulum	147/4205	174/8465	3.29e-22	1.10e-19	5.64e-20	147
hsa0051033	Esophagus	ESCC	N-Glycan biosynthesis	39/4205	53/8465	3.26e-04	1.15e-03	5.89e-04	39
hsa0051313	Esophagus	ESCC	Various types of N-glycan biosynthesis	31/4205	42/8465	1.23e-03	3.78e-03	1.93e-03	31
hsa0414114	Liver	Cirrhotic	Protein processing in endoplasmic reticulum	114/2530	174/8465	1.16e-22	9.67e-21	5.96e-21	114
hsa005104	Liver	Cirrhotic	N-Glycan biosynthesis	32/2530	53/8465	3.82e-06	4.10e-05	2.53e-05	32
hsa005134	Liver	Cirrhotic	Various types of N-glycan biosynthesis	26/2530	42/8465	1.65e-05	1.41e-04	8.69e-05	26
hsa0414115	Liver	Cirrhotic	Protein processing in endoplasmic reticulum	114/2530	174/8465	1.16e-22	9.67e-21	5.96e-21	114
hsa0051011	Liver	Cirrhotic	N-Glycan biosynthesis	32/2530	53/8465	3.82e-06	4.10e-05	2.53e-05	32
hsa0051311	Liver	Cirrhotic	Various types of N-glycan biosynthesis	26/2530	42/8465	1.65e-05	1.41e-04	8.69e-05	26
hsa0414122	Liver	HCC	Protein processing in endoplasmic reticulum	146/4020	174/8465	7.34e-24	2.46e-21	1.37e-21	146
hsa0051021	Liver	HCC	N-Glycan biosynthesis	40/4020	53/8465	2.95e-05	1.87e-04	1.04e-04	40
hsa005132	Liver	HCC	Various types of N-glycan biosynthesis	30/4020	42/8465	1.41e-03	5.07e-03	2.82e-03	30
hsa0414132	Liver	HCC	Protein processing in endoplasmic reticulum	146/4020	174/8465	7.34e-24	2.46e-21	1.37e-21	146

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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

MAGT1

SNV

Missense_Mutation

novel

c.749G>T

p.Gly250Val

p.G250V

protein_coding

tolerated(0.51)

benign(0.108)

TCGA-A1-A0SI-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

MAGT1

SNV

Missense_Mutation

novel

c.420T>G

p.Ser140Arg

p.S140R

protein_coding

tolerated(0.14)

benign(0.091)

TCGA-BH-A18T-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MAGT1

SNV

Missense_Mutation

rs782076867

c.410N>A

p.Arg137Gln

p.R137Q

protein_coding

tolerated(0.18)

possibly_damaging(0.852)

TCGA-D8-A4Z1-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

MAGT1

SNV

Missense_Mutation

novel

c.1088N>T

p.Ser363Ile

p.S363I

protein_coding

deleterious(0)

probably_damaging(0.921)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

MAGT1

SNV

Missense_Mutation

c.188N>T

p.Arg63Ile

p.R63I

protein_coding

tolerated(0.06)

possibly_damaging(0.481)

TCGA-C5-A1BE-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

MAGT1

SNV

Missense_Mutation

c.35N>T

p.Ser12Leu

p.S12L

protein_coding

deleterious_low_confidence(0)

benign(0.001)

TCGA-C5-A7UH-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Chemotherapy

cisplatin

MAGT1

SNV

Missense_Mutation

novel

c.672G>T

p.Leu224Phe

p.L224F

protein_coding

tolerated(0.07)

possibly_damaging(0.618)

TCGA-C5-A8XI-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Chemotherapy

cisplatin

MAGT1

SNV

Missense_Mutation

novel

c.1019G>C

p.Gly340Ala

p.G340A

protein_coding

tolerated(0.56)

benign(0.007)

TCGA-EK-A2PG-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Unknown

MAGT1

SNV

Missense_Mutation

c.716G>T

p.Arg239Ile

p.R239I

protein_coding

deleterious(0)

probably_damaging(0.979)

TCGA-FU-A23L-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

MAGT1

SNV

Missense_Mutation

novel

c.733N>T

p.Leu245Phe

p.L245F

protein_coding

tolerated(0.09)

benign(0.401)

TCGA-HM-A4S6-01

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

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