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: RNMT

Gene summary for RNMT

Gene summary.

Gene information	Species	Human
	Gene symbol	RNMT
	Gene ID	8731
	Gene name	RNA guanine-7 methyltransferase
	Gene Alias	CMT1
	Cytomap	18p11.21
	Gene Type	protein-coding
	GO ID	GO:0001510
	UniProtAcc	A8K946

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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
8731	RNMT	LZE2D	Human	Esophagus	HGIN	6.71e-05	7.70e-01	0.0642
8731	RNMT	LZE2T	Human	Esophagus	ESCC	3.37e-09	1.31e+00	0.082
8731	RNMT	LZE4T	Human	Esophagus	ESCC	1.55e-13	5.53e-01	0.0811
8731	RNMT	LZE5T	Human	Esophagus	ESCC	9.98e-10	4.06e-01	0.0514
8731	RNMT	LZE7T	Human	Esophagus	ESCC	4.38e-10	7.24e-01	0.0667
8731	RNMT	LZE8T	Human	Esophagus	ESCC	2.78e-10	3.42e-01	0.067
8731	RNMT	LZE20T	Human	Esophagus	ESCC	1.41e-10	2.24e-01	0.0662
8731	RNMT	LZE21D1	Human	Esophagus	HGIN	8.90e-04	4.70e-01	0.0632
8731	RNMT	LZE22D1	Human	Esophagus	HGIN	2.35e-05	1.35e-01	0.0595
8731	RNMT	LZE22T	Human	Esophagus	ESCC	1.97e-02	2.85e-01	0.068
8731	RNMT	LZE24T	Human	Esophagus	ESCC	2.67e-17	4.21e-01	0.0596
8731	RNMT	LZE21T	Human	Esophagus	ESCC	8.21e-10	6.35e-01	0.0655
8731	RNMT	LZE6T	Human	Esophagus	ESCC	1.77e-08	2.41e-01	0.0845
8731	RNMT	P1T-E	Human	Esophagus	ESCC	1.83e-19	8.87e-01	0.0875
8731	RNMT	P2T-E	Human	Esophagus	ESCC	1.08e-41	8.59e-01	0.1177
8731	RNMT	P4T-E	Human	Esophagus	ESCC	6.77e-38	9.03e-01	0.1323
8731	RNMT	P5T-E	Human	Esophagus	ESCC	1.64e-63	1.29e+00	0.1327
8731	RNMT	P8T-E	Human	Esophagus	ESCC	1.33e-38	6.62e-01	0.0889
8731	RNMT	P9T-E	Human	Esophagus	ESCC	1.25e-31	7.98e-01	0.1131
8731	RNMT	P10T-E	Human	Esophagus	ESCC	5.07e-43	7.59e-01	0.116

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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:19908308	Esophagus	HGIN	cellular response to leukemia inhibitory factor	23/2587	94/18723	3.92e-03	3.54e-02	23
GO:19908238	Esophagus	HGIN	response to leukemia inhibitory factor	23/2587	95/18723	4.51e-03	3.93e-02	23
GO:00434143	Esophagus	ESCC	macromolecule methylation	199/8552	316/18723	3.44e-10	9.57e-09	199
GO:00322592	Esophagus	ESCC	methylation	222/8552	364/18723	2.26e-09	5.09e-08	222
GO:00094512	Esophagus	ESCC	RNA modification	114/8552	167/18723	2.76e-09	6.04e-08	114
GO:00015101	Esophagus	ESCC	RNA methylation	58/8552	83/18723	6.87e-06	6.94e-05	58
GO:199082316	Esophagus	ESCC	response to leukemia inhibitory factor	60/8552	95/18723	4.41e-04	2.48e-03	60
GO:199083015	Esophagus	ESCC	cellular response to leukemia inhibitory factor	59/8552	94/18723	6.19e-04	3.32e-03	59
GO:0043414	Liver	NAFLD	macromolecule methylation	47/1882	316/18723	4.08e-03	3.41e-02	47
GO:00434141	Liver	HCC	macromolecule methylation	183/7958	316/18723	2.00e-08	4.72e-07	183
GO:0032259	Liver	HCC	methylation	206/7958	364/18723	3.35e-08	7.53e-07	206
GO:0009451	Liver	HCC	RNA modification	101/7958	167/18723	2.02e-06	2.78e-05	101
GO:0001510	Liver	HCC	RNA methylation	53/7958	83/18723	6.96e-05	6.29e-04	53
GO:00094511	Oral cavity	OSCC	RNA modification	95/7305	167/18723	2.05e-06	2.62e-05	95
GO:19908237	Oral cavity	OSCC	response to leukemia inhibitory factor	58/7305	95/18723	1.10e-05	1.14e-04	58
GO:19908307	Oral cavity	OSCC	cellular response to leukemia inhibitory factor	57/7305	94/18723	1.75e-05	1.71e-04	57
GO:00434142	Oral cavity	OSCC	macromolecule methylation	149/7305	316/18723	1.82e-03	8.60e-03	149
GO:00322591	Oral cavity	OSCC	methylation	168/7305	364/18723	3.03e-03	1.31e-02	168
GO:199082315	Oral cavity	EOLP	response to leukemia inhibitory factor	26/2218	95/18723	2.91e-05	4.20e-04	26
GO:199083014	Oral cavity	EOLP	cellular response to leukemia inhibitory factor	25/2218	94/18723	6.89e-05	8.53e-04	25

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa030159	Esophagus	HGIN	mRNA surveillance pathway	30/1383	97/8465	2.48e-04	2.69e-03	2.14e-03	30
hsa0301514	Esophagus	HGIN	mRNA surveillance pathway	30/1383	97/8465	2.48e-04	2.69e-03	2.14e-03	30
hsa0301524	Esophagus	ESCC	mRNA surveillance pathway	72/4205	97/8465	6.12e-07	4.10e-06	2.10e-06	72
hsa0301534	Esophagus	ESCC	mRNA surveillance pathway	72/4205	97/8465	6.12e-07	4.10e-06	2.10e-06	72
hsa030154	Liver	Cirrhotic	mRNA surveillance pathway	46/2530	97/8465	1.92e-04	1.30e-03	8.03e-04	46
hsa0301511	Liver	Cirrhotic	mRNA surveillance pathway	46/2530	97/8465	1.92e-04	1.30e-03	8.03e-04	46
hsa0301521	Liver	HCC	mRNA surveillance pathway	66/4020	97/8465	3.16e-05	1.88e-04	1.04e-04	66
hsa0301531	Liver	HCC	mRNA surveillance pathway	66/4020	97/8465	3.16e-05	1.88e-04	1.04e-04	66
hsa030158	Oral cavity	OSCC	mRNA surveillance pathway	75/3704	97/8465	1.30e-11	2.01e-10	1.02e-10	75
hsa0301513	Oral cavity	OSCC	mRNA surveillance pathway	75/3704	97/8465	1.30e-11	2.01e-10	1.02e-10	75
hsa0301541	Oral cavity	EOLP	mRNA surveillance pathway	30/1218	97/8465	2.26e-05	1.20e-04	7.07e-05	30
hsa0301551	Oral cavity	EOLP	mRNA surveillance pathway	30/1218	97/8465	2.26e-05	1.20e-04	7.07e-05	30
hsa030156	Oral cavity	NEOLP	mRNA surveillance pathway	25/1112	97/8465	5.70e-04	3.18e-03	2.00e-03	25
hsa030157	Oral cavity	NEOLP	mRNA surveillance pathway	25/1112	97/8465	5.70e-04	3.18e-03	2.00e-03	25
hsa030155	Prostate	BPH	mRNA surveillance pathway	32/1718	97/8465	2.20e-03	8.63e-03	5.34e-03	32
hsa0301512	Prostate	BPH	mRNA surveillance pathway	32/1718	97/8465	2.20e-03	8.63e-03	5.34e-03	32
hsa0301522	Prostate	Tumor	mRNA surveillance pathway	33/1791	97/8465	2.18e-03	8.60e-03	5.33e-03	33
hsa0301532	Prostate	Tumor	mRNA surveillance pathway	33/1791	97/8465	2.18e-03	8.60e-03	5.33e-03	33

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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

RNMT

SNV

Missense_Mutation

c.1138G>A

p.Glu380Lys

p.E380K

O43148

protein_coding

tolerated(0.85)

benign(0.061)

TCGA-D8-A27G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RNMT

deletion

Frame_Shift_Del

novel

c.808delN

p.Lys270AsnfsTer30

p.K270Nfs*30

O43148

protein_coding

TCGA-D8-A27V-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

RNMT

SNV

Missense_Mutation

c.100N>C

p.Glu34Gln

p.E34Q

O43148

protein_coding

deleterious_low_confidence(0.01)

probably_damaging(0.994)

TCGA-DR-A0ZM-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Unspecific

Cisplatin

RNMT

SNV

Missense_Mutation

novel

c.355N>T

p.Thr119Ser

p.T119S

O43148

protein_coding

tolerated(0.37)

benign(0.003)

TCGA-DS-A1OB-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

carboplatin

RNMT

SNV

Missense_Mutation

rs771795058

c.365N>A

p.Gly122Asp

p.G122D

O43148

protein_coding

tolerated(0.19)

benign(0.006)

TCGA-HM-A4S6-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Chemotherapy

cisplatin

RNMT

SNV

Missense_Mutation

c.271N>C

p.Glu91Gln

p.E91Q

O43148

protein_coding

deleterious_low_confidence(0.02)

possibly_damaging(0.836)

TCGA-IR-A3LA-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

RNMT

SNV

Missense_Mutation

rs779338611

c.814N>T

p.Arg272Cys

p.R272C

O43148

protein_coding

tolerated(0.11)

benign(0.01)

TCGA-AA-3510-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

RNMT

SNV

Missense_Mutation

novel

c.161N>G

p.Asp54Gly

p.D54G

O43148

protein_coding

tolerated_low_confidence(0.19)

benign(0.003)

TCGA-AA-3984-01

Colorectum

colon adenocarcinoma

Female

<65

I/II

Unknown

RNMT

SNV

Missense_Mutation

c.1067N>A

p.Cys356Tyr

p.C356Y

O43148

protein_coding

deleterious(0)

probably_damaging(0.991)

TCGA-AZ-4615-01

Colorectum

colon adenocarcinoma

Male

>=65

III/IV

Chemotherapy

xeloda

RNMT

SNV

Missense_Mutation

c.1113C>A

p.Phe371Leu

p.F371L

O43148

protein_coding

deleterious(0)

probably_damaging(0.98)

TCGA-CA-6718-01

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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