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: TH

Gene summary for TH

Gene summary.

Gene information	Species	Human
	Gene symbol	TH
	Gene ID	7054
	Gene name	tyrosine hydroxylase
	Gene Alias	DYT14
	Cytomap	11p15.5
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	P07101

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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
7054	TH	C04	Human	Oral cavity	OSCC	2.26e-15	7.94e-01	0.2633
7054	TH	C21	Human	Oral cavity	OSCC	3.65e-07	1.94e-01	0.2678
7054	TH	C30	Human	Oral cavity	OSCC	2.87e-17	6.63e-01	0.3055
7054	TH	C51	Human	Oral cavity	OSCC	4.98e-04	2.56e-01	0.2674
7054	TH	SYSMH5	Human	Oral cavity	OSCC	3.73e-03	1.34e-01	0.0647
7054	TH	P4_cSCC	Human	Skin	cSCC	3.76e-02	9.18e-02	-0.00290000000000005

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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

∗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:00009562	Colorectum	FAP	nuclear-transcribed mRNA catabolic process	33/2622	112/18723	1.69e-05	4.35e-04	33
GO:19023693	Colorectum	FAP	negative regulation of RNA catabolic process	25/2622	75/18723	1.74e-05	4.42e-04	25
GO:00444034	Colorectum	FAP	biological process involved in symbiotic interaction	66/2622	290/18723	3.47e-05	7.64e-04	66
GO:19013614	Colorectum	FAP	organic cyclic compound catabolic process	101/2622	495/18723	4.87e-05	9.93e-04	101
GO:00605622	Colorectum	FAP	epithelial tube morphogenesis	71/2622	325/18723	7.23e-05	1.33e-03	71
GO:00427523	Colorectum	FAP	regulation of circadian rhythm	33/2622	121/18723	9.26e-05	1.59e-03	33
GO:00351482	Colorectum	FAP	tube formation	38/2622	148/18723	1.17e-04	1.91e-03	38
GO:00434893	Colorectum	FAP	RNA stabilization	21/2622	65/18723	1.33e-04	2.13e-03	21
GO:00064034	Colorectum	FAP	RNA localization	47/2622	201/18723	2.27e-04	3.22e-03	47
GO:00514024	Colorectum	FAP	neuron apoptotic process	55/2622	246/18723	2.42e-04	3.37e-03	55
GO:00313453	Colorectum	FAP	negative regulation of cell projection organization	44/2622	186/18723	2.69e-04	3.64e-03	44
GO:00018413	Colorectum	FAP	neural tube formation	28/2622	102/18723	2.71e-04	3.64e-03	28
GO:00517014	Colorectum	FAP	biological process involved in interaction with host	47/2622	203/18723	2.89e-04	3.77e-03	47
GO:00457872	Colorectum	FAP	positive regulation of cell cycle	66/2622	313/18723	3.66e-04	4.63e-03	66
GO:00140202	Colorectum	FAP	primary neural tube formation	26/2622	94/18723	3.87e-04	4.75e-03	26
GO:00511684	Colorectum	FAP	nuclear export	37/2622	154/18723	5.81e-04	6.46e-03	37
GO:00512364	Colorectum	FAP	establishment of RNA localization	39/2622	166/18723	6.71e-04	7.28e-03	39
GO:19023733	Colorectum	FAP	negative regulation of mRNA catabolic process	19/2622	63/18723	7.22e-04	7.72e-03	19
GO:00219152	Colorectum	FAP	neural tube development	36/2622	152/18723	9.05e-04	9.17e-03	36
GO:00506574	Colorectum	FAP	nucleic acid transport	38/2622	163/18723	9.12e-04	9.19e-03	38

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0501230	Oral cavity	OSCC	Parkinson disease	188/3704	266/8465	1.82e-19	1.52e-17	7.75e-18	188
hsa05012113	Oral cavity	OSCC	Parkinson disease	188/3704	266/8465	1.82e-19	1.52e-17	7.75e-18	188

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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

SNV

Missense_Mutation

c.58N>C

p.Glu20Gln

p.E20Q

P07101

protein_coding

deleterious_low_confidence(0.01)

probably_damaging(0.998)

TCGA-E2-A1LS-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Cyclophosphamide

SNV

Missense_Mutation

novel

c.307N>A

p.Ala103Thr

p.A103T

P07101

protein_coding

tolerated(0.31)

benign(0.055)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SNV

Missense_Mutation

rs760640869

c.374N>T

p.Ser125Leu

p.S125L

P07101

protein_coding

deleterious(0.01)

benign(0.058)

TCGA-EA-A3QD-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Chemotherapy

cisplatin

SNV

Missense_Mutation

c.235N>A

p.Glu79Lys

p.E79K

P07101

protein_coding

deleterious(0.04)

probably_damaging(0.957)

TCGA-MY-A5BD-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SNV

Missense_Mutation

rs372409517

c.677N>T

p.Ser226Leu

p.S226L

P07101

protein_coding

deleterious(0.01)

possibly_damaging(0.661)

TCGA-A6-6780-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

SNV

Missense_Mutation

novel

c.1201N>C

p.Tyr401His

p.Y401H

P07101

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AA-3663-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

SNV

Missense_Mutation

novel

c.944N>A

p.Gly315Asp

p.G315D

P07101

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AA-A010-01

Colorectum

colon adenocarcinoma

Female

<65

I/II

Chemotherapy

folinic

SNV

Missense_Mutation

rs757607038

c.806C>T

p.Thr269Met

p.T269M

P07101

protein_coding

deleterious(0.04)

possibly_damaging(0.904)

TCGA-AA-A022-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

SNV

Missense_Mutation

c.721N>A

p.Ala241Thr

p.A241T

P07101

protein_coding

deleterious(0)

probably_damaging(0.992)

TCGA-F4-6703-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

SNV

Missense_Mutation

rs200751977

c.1492G>A

p.Asp498Asn

p.D498N

P07101

protein_coding

deleterious(0.02)

benign(0.077)

TCGA-EI-6917-01

Colorectum

rectum adenocarcinoma

Male

<65

III/IV

Chemotherapy

5fluorouracil+oxaciplatina+l-folinian

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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
7054	TH	ENZYME, DRUGGABLE GENOME		L-Phenylalanine	PHENYLALANINE
7054	TH	ENZYME, DRUGGABLE GENOME		methylphenidate	METHYLPHENIDATE	26810137
7054	TH	ENZYME, DRUGGABLE GENOME		metyrosine	METYROSINE
7054	TH	ENZYME, DRUGGABLE GENOME		EPO	EPOETIN ALFA	16368081
7054	TH	ENZYME, DRUGGABLE GENOME		TETRAHYDROBIOPTERIN	SAPROPTERIN
7054	TH	ENZYME, DRUGGABLE GENOME		SERTRALINE HYDROCHLORIDE		8629887
7054	TH	ENZYME, DRUGGABLE GENOME		DEHYDROEPIANDROSTERONE	PRASTERONE	8704732
7054	TH	ENZYME, DRUGGABLE GENOME	inhibitor	CHEMBL1200862	METYROSINE
7054	TH	ENZYME, DRUGGABLE GENOME		IFN		8724983
7054	TH	ENZYME, DRUGGABLE GENOME		DOXYCYCLINE	DOXYCYCLINE	15585109

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