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: MTHFD1

Gene summary for MTHFD1

Gene summary.

Gene information	Species	Human
	Gene symbol	MTHFD1
	Gene ID	4522
	Gene name	methylenetetrahydrofolate dehydrogenase, cyclohydrolase and formyltetrahydrofolate synthetase 1
	Gene Alias	CIMAH
	Cytomap	14q23.3
	Gene Type	protein-coding
	GO ID	GO:0000096
	UniProtAcc	P11586

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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
4522	MTHFD1	LZE4T	Human	Esophagus	ESCC	7.94e-08	2.44e-01	0.0811
4522	MTHFD1	LZE7T	Human	Esophagus	ESCC	8.17e-05	2.94e-01	0.0667
4522	MTHFD1	LZE22D1	Human	Esophagus	HGIN	1.28e-02	8.92e-02	0.0595
4522	MTHFD1	LZE24T	Human	Esophagus	ESCC	1.24e-06	1.72e-01	0.0596
4522	MTHFD1	LZE6T	Human	Esophagus	ESCC	3.55e-04	1.30e-01	0.0845
4522	MTHFD1	P2T-E	Human	Esophagus	ESCC	5.69e-21	4.34e-01	0.1177
4522	MTHFD1	P4T-E	Human	Esophagus	ESCC	6.99e-12	3.86e-01	0.1323
4522	MTHFD1	P5T-E	Human	Esophagus	ESCC	2.11e-11	2.55e-01	0.1327
4522	MTHFD1	P8T-E	Human	Esophagus	ESCC	2.65e-10	3.40e-01	0.0889
4522	MTHFD1	P9T-E	Human	Esophagus	ESCC	5.87e-13	1.35e-01	0.1131
4522	MTHFD1	P10T-E	Human	Esophagus	ESCC	3.91e-19	3.97e-01	0.116
4522	MTHFD1	P11T-E	Human	Esophagus	ESCC	5.82e-07	1.92e-01	0.1426
4522	MTHFD1	P12T-E	Human	Esophagus	ESCC	2.51e-20	4.55e-01	0.1122
4522	MTHFD1	P15T-E	Human	Esophagus	ESCC	1.02e-20	6.32e-01	0.1149
4522	MTHFD1	P16T-E	Human	Esophagus	ESCC	3.26e-19	4.84e-01	0.1153
4522	MTHFD1	P17T-E	Human	Esophagus	ESCC	5.38e-06	5.48e-01	0.1278
4522	MTHFD1	P19T-E	Human	Esophagus	ESCC	7.91e-06	6.00e-01	0.1662
4522	MTHFD1	P20T-E	Human	Esophagus	ESCC	1.21e-15	3.43e-01	0.1124
4522	MTHFD1	P21T-E	Human	Esophagus	ESCC	1.12e-20	4.98e-01	0.1617
4522	MTHFD1	P22T-E	Human	Esophagus	ESCC	1.11e-18	2.77e-01	0.1236

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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:000184311	Lung	AIS	neural tube closure	20/1849	88/18723	2.99e-04	5.54e-03	20
GO:006060611	Lung	AIS	tube closure	20/1849	89/18723	3.50e-04	6.28e-03	20
GO:000183811	Lung	AIS	embryonic epithelial tube formation	24/1849	121/18723	6.82e-04	1.02e-02	24
GO:002191511	Lung	AIS	neural tube development	28/1849	152/18723	8.81e-04	1.19e-02	28
GO:00163311	Lung	AIS	morphogenesis of embryonic epithelium	27/1849	147/18723	1.13e-03	1.45e-02	27
GO:003514811	Lung	AIS	tube formation	27/1849	148/18723	1.25e-03	1.58e-02	27
GO:007217511	Lung	AIS	epithelial tube formation	24/1849	132/18723	2.37e-03	2.48e-02	24
GO:000675318	Oral cavity	OSCC	nucleoside phosphate metabolic process	247/7305	497/18723	6.28e-07	8.96e-06	247
GO:000911719	Oral cavity	OSCC	nucleotide metabolic process	243/7305	489/18723	7.80e-07	1.09e-05	243
GO:00442724	Oral cavity	OSCC	sulfur compound biosynthetic process	82/7305	148/18723	3.71e-05	3.31e-04	82
GO:000184110	Oral cavity	OSCC	neural tube formation	60/7305	102/18723	3.90e-05	3.43e-04	60
GO:00067905	Oral cavity	OSCC	sulfur compound metabolic process	168/7305	339/18723	4.50e-05	3.84e-04	168
GO:00423985	Oral cavity	OSCC	cellular modified amino acid biosynthetic process	31/7305	46/18723	9.03e-05	6.88e-04	31
GO:00140208	Oral cavity	OSCC	primary neural tube formation	55/7305	94/18723	9.87e-05	7.43e-04	55
GO:00018437	Oral cavity	OSCC	neural tube closure	52/7305	88/18723	1.06e-04	7.84e-04	52
GO:007252120	Oral cavity	OSCC	purine-containing compound metabolic process	199/7305	416/18723	1.34e-04	9.53e-04	199
GO:00606066	Oral cavity	OSCC	tube closure	52/7305	89/18723	1.59e-04	1.10e-03	52
GO:00160537	Oral cavity	OSCC	organic acid biosynthetic process	155/7305	316/18723	1.64e-04	1.13e-03	155
GO:00463947	Oral cavity	OSCC	carboxylic acid biosynthetic process	154/7305	314/18723	1.73e-04	1.19e-03	154
GO:00425594	Oral cavity	OSCC	pteridine-containing compound biosynthetic process	13/7305	15/18723	2.07e-04	1.36e-03	13

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa012405	Esophagus	ESCC	Biosynthesis of cofactors	97/4205	153/8465	3.88e-04	1.35e-03	6.94e-04	97
hsa0124012	Esophagus	ESCC	Biosynthesis of cofactors	97/4205	153/8465	3.88e-04	1.35e-03	6.94e-04	97
hsa01240	Liver	Cirrhotic	Biosynthesis of cofactors	66/2530	153/8465	3.11e-04	1.99e-03	1.23e-03	66
hsa012401	Liver	Cirrhotic	Biosynthesis of cofactors	66/2530	153/8465	3.11e-04	1.99e-03	1.23e-03	66
hsa012402	Liver	HCC	Biosynthesis of cofactors	103/4020	153/8465	4.67e-07	5.05e-06	2.81e-06	103
hsa006702	Liver	HCC	One carbon pool by folate	17/4020	20/8465	6.04e-04	2.50e-03	1.39e-03	17
hsa012403	Liver	HCC	Biosynthesis of cofactors	103/4020	153/8465	4.67e-07	5.05e-06	2.81e-06	103
hsa0067011	Liver	HCC	One carbon pool by folate	17/4020	20/8465	6.04e-04	2.50e-03	1.39e-03	17
hsa012404	Oral cavity	OSCC	Biosynthesis of cofactors	88/3704	153/8465	3.84e-04	1.20e-03	6.12e-04	88
hsa0124011	Oral cavity	OSCC	Biosynthesis of cofactors	88/3704	153/8465	3.84e-04	1.20e-03	6.12e-04	88
hsa0124021	Oral cavity	LP	Biosynthesis of cofactors	57/2418	153/8465	1.17e-02	3.91e-02	2.52e-02	57
hsa0124031	Oral cavity	LP	Biosynthesis of cofactors	57/2418	153/8465	1.17e-02	3.91e-02	2.52e-02	57

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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

TF	Cell Type	Tissue	Disease Stage	Target Gene	RSS	Regulon Activity
MTHFD1	LUMP	Breast	IDC	SAMD9,MCM3,TRAP1, etc.	2.02e-01
MTHFD1	STM	Endometrium	EEC	TAB1,ZNF133,STON2, etc.	4.90e-01

∗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

MTHFD1

SNV

Missense_Mutation

c.1691N>G

p.Ser564Cys

p.S564C

P11586

protein_coding

deleterious(0.01)

probably_damaging(0.919)

TCGA-A2-A04P-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

taxol

MTHFD1

SNV

Missense_Mutation

c.808N>G

p.Pro270Ala

p.P270A

P11586

protein_coding

deleterious(0.02)

probably_damaging(0.999)

TCGA-A2-A04T-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

MTHFD1

SNV

Missense_Mutation

novel

c.1850N>T

p.Asp617Val

p.D617V

P11586

protein_coding

deleterious(0)

probably_damaging(0.995)

TCGA-A2-A0CP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

MTHFD1

SNV

Missense_Mutation

c.1466N>A

p.Phe489Tyr

p.F489Y

P11586

protein_coding

deleterious(0)

probably_damaging(0.993)

TCGA-A8-A07L-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

MTHFD1

SNV

Missense_Mutation

c.782C>T

p.Ala261Val

p.A261V

P11586

protein_coding

tolerated(0.14)

benign(0.139)

TCGA-BH-A0HA-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

MTHFD1

SNV

Missense_Mutation

novel

c.560N>T

p.Trp187Leu

p.W187L

P11586

protein_coding

tolerated(0.72)

possibly_damaging(0.547)

TCGA-C8-A26Z-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

MTHFD1

SNV

Missense_Mutation

c.236N>G

p.Ser79Cys

p.S79C

P11586

protein_coding

tolerated(0.07)

benign(0.336)

TCGA-C8-A274-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

MTHFD1

SNV

Missense_Mutation

novel

c.1238N>T

p.Ser413Phe

p.S413F

P11586

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-OL-A5RW-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

MTHFD1

SNV

Missense_Mutation

novel

c.2645N>T

p.Thr882Ile

p.T882I

P11586

protein_coding

deleterious(0.01)

benign(0.436)

TCGA-S3-AA10-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

cytoxan

MTHFD1

insertion

Nonsense_Mutation

novel

c.1852_1853insTGCTCTAAAATAGTCTAGAATGGATTTCTCACAT

p.Ala618ValfsTer3

p.A618Vfs*3

P11586

protein_coding

TCGA-A2-A0CP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

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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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