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:004854518	Prostate	BPH	response to steroid hormone	109/3107	339/18723	9.35e-13	8.15e-11	109
GO:190305018	Prostate	BPH	regulation of proteolysis involved in cellular protein catabolic process	80/3107	221/18723	1.20e-12	1.02e-10	80
GO:200123418	Prostate	BPH	negative regulation of apoptotic signaling pathway	79/3107	224/18723	7.67e-12	5.94e-10	79
GO:00064468	Prostate	BPH	regulation of translational initiation	39/3107	79/18723	1.57e-11	1.13e-09	39
GO:009719118	Prostate	BPH	extrinsic apoptotic signaling pathway	77/3107	219/18723	1.67e-11	1.19e-09	77
GO:004851110	Prostate	BPH	rhythmic process	96/3107	298/18723	1.88e-11	1.31e-09	96
GO:005254718	Prostate	BPH	regulation of peptidase activity	133/3107	461/18723	2.08e-11	1.43e-09	133
GO:003009918	Prostate	BPH	myeloid cell differentiation	115/3107	381/18723	2.22e-11	1.51e-09	115
GO:000640116	Prostate	BPH	RNA catabolic process	91/3107	278/18723	2.37e-11	1.60e-09	91
GO:200123618	Prostate	BPH	regulation of extrinsic apoptotic signaling pathway	59/3107	151/18723	3.07e-11	2.02e-09	59
GO:003158910	Prostate	BPH	cell-substrate adhesion	110/3107	363/18723	4.64e-11	2.96e-09	110
GO:004206018	Prostate	BPH	wound healing	123/3107	422/18723	5.74e-11	3.59e-09	123
GO:000716316	Prostate	BPH	establishment or maintenance of cell polarity	75/3107	218/18723	9.93e-11	5.97e-09	75
GO:000762310	Prostate	BPH	circadian rhythm	73/3107	210/18723	1.02e-10	6.02e-09	73
GO:006113618	Prostate	BPH	regulation of proteasomal protein catabolic process	67/3107	187/18723	1.34e-10	7.74e-09	67
GO:015011615	Prostate	BPH	regulation of cell-substrate junction organization	35/3107	71/18723	1.81e-10	1.02e-08	35
GO:007048217	Prostate	BPH	response to oxygen levels	104/3107	347/18723	3.13e-10	1.67e-08	104
GO:20012359	Prostate	BPH	positive regulation of apoptotic signaling pathway	50/3107	126/18723	5.08e-10	2.56e-08	50
GO:001081017	Prostate	BPH	regulation of cell-substrate adhesion	74/3107	221/18723	5.40e-10	2.70e-08	74
GO:00072658	Prostate	BPH	Ras protein signal transduction	101/3107	337/18723	5.64e-10	2.79e-08	101

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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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