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: NMT1

Gene summary for NMT1

Gene summary.

Gene information	Species	Human
	Gene symbol	NMT1
	Gene ID	4836
	Gene name	N-myristoyltransferase 1
	Gene Alias	NMT
	Cytomap	17q21.31
	Gene Type	protein-coding
	GO ID	GO:0001701
	UniProtAcc	P30419

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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
4836	NMT1	LZE2T	Human	Esophagus	ESCC	2.46e-03	3.67e-01	0.082
4836	NMT1	LZE4T	Human	Esophagus	ESCC	2.79e-04	1.88e-01	0.0811
4836	NMT1	LZE7T	Human	Esophagus	ESCC	5.87e-06	3.14e-01	0.0667
4836	NMT1	LZE21D1	Human	Esophagus	HGIN	1.03e-02	1.49e-01	0.0632
4836	NMT1	LZE22D1	Human	Esophagus	HGIN	1.06e-03	1.61e-01	0.0595
4836	NMT1	LZE22T	Human	Esophagus	ESCC	2.58e-04	2.67e-01	0.068
4836	NMT1	LZE24T	Human	Esophagus	ESCC	5.95e-08	2.97e-01	0.0596
4836	NMT1	P1T-E	Human	Esophagus	ESCC	3.04e-07	4.23e-01	0.0875
4836	NMT1	P2T-E	Human	Esophagus	ESCC	7.90e-17	2.84e-01	0.1177
4836	NMT1	P4T-E	Human	Esophagus	ESCC	2.27e-16	3.60e-01	0.1323
4836	NMT1	P5T-E	Human	Esophagus	ESCC	6.14e-37	5.92e-01	0.1327
4836	NMT1	P8T-E	Human	Esophagus	ESCC	1.88e-27	4.74e-01	0.0889
4836	NMT1	P9T-E	Human	Esophagus	ESCC	1.26e-10	2.82e-01	0.1131
4836	NMT1	P10T-E	Human	Esophagus	ESCC	1.05e-27	1.41e-01	0.116
4836	NMT1	P11T-E	Human	Esophagus	ESCC	3.51e-18	6.10e-01	0.1426
4836	NMT1	P12T-E	Human	Esophagus	ESCC	8.83e-20	3.37e-01	0.1122
4836	NMT1	P15T-E	Human	Esophagus	ESCC	1.32e-16	4.56e-01	0.1149
4836	NMT1	P16T-E	Human	Esophagus	ESCC	8.04e-22	2.03e-01	0.1153
4836	NMT1	P17T-E	Human	Esophagus	ESCC	6.69e-16	5.44e-01	0.1278
4836	NMT1	P19T-E	Human	Esophagus	ESCC	7.33e-05	6.20e-01	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
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:00905599	Esophagus	ESCC	regulation of membrane permeability	58/8552	78/18723	2.38e-07	3.61e-06	58
GO:00357948	Esophagus	ESCC	positive regulation of mitochondrial membrane permeability	36/8552	43/18723	2.90e-07	4.20e-06	36
GO:000647914	Esophagus	ESCC	protein methylation	115/8552	181/18723	9.07e-07	1.16e-05	115
GO:000821314	Esophagus	ESCC	protein alkylation	115/8552	181/18723	9.07e-07	1.16e-05	115
GO:009734510	Esophagus	ESCC	mitochondrial outer membrane permeabilization	28/8552	32/18723	1.02e-06	1.29e-05	28
GO:00310583	Esophagus	ESCC	positive regulation of histone modification	65/8552	92/18723	1.04e-06	1.31e-05	65
GO:190547719	Esophagus	ESCC	positive regulation of protein localization to membrane	73/8552	106/18723	1.13e-06	1.40e-05	73
GO:190268614	Esophagus	ESCC	mitochondrial outer membrane permeabilization involved in programmed cell death	33/8552	40/18723	1.80e-06	2.11e-05	33
GO:009015118	Esophagus	ESCC	establishment of protein localization to mitochondrial membrane	26/8552	30/18723	3.79e-06	4.12e-05	26
GO:19021108	Esophagus	ESCC	positive regulation of mitochondrial membrane permeability involved in apoptotic process	31/8552	38/18723	5.93e-06	6.10e-05	31
GO:00015101	Esophagus	ESCC	RNA methylation	58/8552	83/18723	6.87e-06	6.94e-05	58
GO:19057108	Esophagus	ESCC	positive regulation of membrane permeability	37/8552	48/18723	8.99e-06	8.65e-05	37
GO:00421573	Esophagus	ESCC	lipoprotein metabolic process	86/8552	135/18723	1.78e-05	1.57e-04	86
GO:000941611	Esophagus	ESCC	response to light stimulus	183/8552	320/18723	2.03e-05	1.76e-04	183
GO:00064973	Esophagus	ESCC	protein lipidation	62/8552	92/18723	2.08e-05	1.80e-04	62
GO:00165718	Esophagus	ESCC	histone methylation	89/8552	141/18723	2.17e-05	1.87e-04	89
GO:19010289	Esophagus	ESCC	regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway	19/8552	21/18723	2.28e-05	1.96e-04	19
GO:00421583	Esophagus	ESCC	lipoprotein biosynthetic process	64/8552	96/18723	2.61e-05	2.20e-04	64
GO:19021086	Esophagus	ESCC	regulation of mitochondrial membrane permeability involved in apoptotic process	34/8552	45/18723	4.37e-05	3.49e-04	34
GO:190374715	Esophagus	ESCC	regulation of establishment of protein localization to mitochondrion	37/8552	50/18723	4.42e-05	3.51e-04	37

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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

NMT1

SNV

Missense_Mutation

c.344N>A

p.Arg115Gln

p.R115Q

P30419

protein_coding

tolerated(0.08)

benign(0.138)

TCGA-A8-A08H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NMT1

SNV

Missense_Mutation

novel

c.763N>T

p.Arg255Cys

p.R255C

P30419

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AC-A3W6-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

NMT1

SNV

Missense_Mutation

novel

c.177N>T

p.Lys59Asn

p.K59N

P30419

protein_coding

tolerated(0.12)

benign(0.264)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NMT1

SNV

Missense_Mutation

c.732N>T

p.Glu244Asp

p.E244D

P30419

protein_coding

deleterious(0.02)

benign(0.232)

TCGA-BH-A18G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NMT1

insertion

Frame_Shift_Ins

novel

c.965_966insAGGTATTCATTGTCTGGTGACTTTATATAAGAAAGGAA

p.Thr323GlyfsTer15

p.T323Gfs*15

P30419

protein_coding

TCGA-A8-A07Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unspecific

Exemestane

NMT1

insertion

Frame_Shift_Ins

novel

c.792_793insAGTT

p.Arg265SerfsTer45

p.R265Sfs*45

P30419

protein_coding

TCGA-B6-A0IA-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

NMT1

insertion

Frame_Shift_Ins

novel

c.793_794insCTACCATGCCAGGGGGCAGAAGGATTTGT

p.Arg265ProfsTer47

p.R265Pfs*47

P30419

protein_coding

TCGA-B6-A0IA-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

NMT1

SNV

Missense_Mutation

novel

c.532G>C

p.Glu178Gln

p.E178Q

P30419

protein_coding

tolerated(0.1)

probably_damaging(0.996)

TCGA-C5-A1MH-01

Cervix

cervical & endocervical cancer

Female

>=65

III/IV

Chemotherapy

cisplatin

NMT1

SNV

Missense_Mutation

novel

c.1368N>T

p.Met456Ile

p.M456I

P30419

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-C5-A901-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

NMT1

SNV

Missense_Mutation

c.10G>A

p.Glu4Lys

p.E4K

P30419

protein_coding

deleterious_low_confidence(0.04)

benign(0.017)

TCGA-JX-A3Q0-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

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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