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: PTHLH

Gene summary for PTHLH

Gene summary.

Gene information	Species	Human
	Gene symbol	PTHLH
	Gene ID	5744
	Gene name	parathyroid hormone like hormone
	Gene Alias	BDE2
	Cytomap	12p11.22
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	P12272

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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
5744	PTHLH	LZE4T	Human	Esophagus	ESCC	5.19e-09	1.39e+00	0.0811
5744	PTHLH	LZE8T	Human	Esophagus	ESCC	4.70e-17	1.89e+00	0.067
5744	PTHLH	LZE20T	Human	Esophagus	ESCC	1.33e-02	1.08e+00	0.0662
5744	PTHLH	LZE22D1	Human	Esophagus	HGIN	1.34e-03	-7.21e-01	0.0595
5744	PTHLH	LZE24T	Human	Esophagus	ESCC	6.55e-12	-7.66e-01	0.0596
5744	PTHLH	LZE6T	Human	Esophagus	ESCC	6.86e-03	-2.02e-01	0.0845
5744	PTHLH	P1T-E	Human	Esophagus	ESCC	4.61e-05	-8.05e-01	0.0875
5744	PTHLH	P2T-E	Human	Esophagus	ESCC	4.87e-11	-6.40e-01	0.1177
5744	PTHLH	P4T-E	Human	Esophagus	ESCC	3.25e-31	2.24e+00	0.1323
5744	PTHLH	P5T-E	Human	Esophagus	ESCC	4.58e-32	1.55e+00	0.1327
5744	PTHLH	P8T-E	Human	Esophagus	ESCC	1.03e-13	-6.00e-01	0.0889
5744	PTHLH	P9T-E	Human	Esophagus	ESCC	3.14e-05	7.14e-01	0.1131
5744	PTHLH	P11T-E	Human	Esophagus	ESCC	9.42e-04	1.42e+00	0.1426
5744	PTHLH	P15T-E	Human	Esophagus	ESCC	1.19e-11	9.77e-01	0.1149
5744	PTHLH	P16T-E	Human	Esophagus	ESCC	1.71e-05	-4.85e-01	0.1153
5744	PTHLH	P17T-E	Human	Esophagus	ESCC	1.91e-11	1.83e+00	0.1278
5744	PTHLH	P19T-E	Human	Esophagus	ESCC	7.59e-10	3.22e+00	0.1662
5744	PTHLH	P20T-E	Human	Esophagus	ESCC	2.77e-23	1.90e+00	0.1124
5744	PTHLH	P21T-E	Human	Esophagus	ESCC	4.50e-17	1.75e+00	0.1617
5744	PTHLH	P22T-E	Human	Esophagus	ESCC	2.04e-25	1.48e+00	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

∗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:000164917	Esophagus	HGIN	osteoblast differentiation	50/2587	229/18723	5.88e-04	8.30e-03	50
GO:000911720	Esophagus	HGIN	nucleotide metabolic process	92/2587	489/18723	1.11e-03	1.36e-02	92
GO:000675320	Esophagus	HGIN	nucleoside phosphate metabolic process	93/2587	497/18723	1.25e-03	1.49e-02	93
GO:000915026	Esophagus	HGIN	purine ribonucleotide metabolic process	71/2587	368/18723	2.00e-03	2.11e-02	71
GO:000616325	Esophagus	HGIN	purine nucleotide metabolic process	75/2587	396/18723	2.53e-03	2.51e-02	75
GO:001969320	Esophagus	HGIN	ribose phosphate metabolic process	75/2587	396/18723	2.53e-03	2.51e-02	75
GO:007252125	Esophagus	HGIN	purine-containing compound metabolic process	78/2587	416/18723	2.78e-03	2.73e-02	78
GO:000150316	Esophagus	HGIN	ossification	75/2587	408/18723	5.49e-03	4.49e-02	75
GO:000925920	Esophagus	HGIN	ribonucleotide metabolic process	71/2587	385/18723	6.25e-03	4.97e-02	71
GO:0006753110	Esophagus	ESCC	nucleoside phosphate metabolic process	288/8552	497/18723	1.80e-08	3.50e-07	288
GO:0019693111	Esophagus	ESCC	ribose phosphate metabolic process	234/8552	396/18723	4.24e-08	7.76e-07	234
GO:0009117111	Esophagus	ESCC	nucleotide metabolic process	282/8552	489/18723	4.70e-08	8.50e-07	282
GO:000854410	Esophagus	ESCC	epidermis development	193/8552	324/18723	2.87e-07	4.19e-06	193
GO:0009259111	Esophagus	ESCC	ribonucleotide metabolic process	224/8552	385/18723	4.41e-07	6.00e-06	224
GO:0072521111	Esophagus	ESCC	purine-containing compound metabolic process	238/8552	416/18723	1.20e-06	1.49e-05	238
GO:0009150111	Esophagus	ESCC	purine ribonucleotide metabolic process	213/8552	368/18723	1.40e-06	1.69e-05	213
GO:000164918	Esophagus	ESCC	osteoblast differentiation	140/8552	229/18723	1.63e-06	1.95e-05	140
GO:0006163111	Esophagus	ESCC	purine nucleotide metabolic process	226/8552	396/18723	2.81e-06	3.21e-05	226
GO:000150317	Esophagus	ESCC	ossification	232/8552	408/18723	3.00e-06	3.40e-05	232
GO:00512161	Esophagus	ESCC	cartilage development	103/8552	190/18723	1.08e-02	3.67e-02	103

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0492816	Esophagus	ESCC	Parathyroid hormone synthesis, secretion and action	66/4205	106/8465	5.86e-03	1.47e-02	7.51e-03	66
hsa0492817	Esophagus	ESCC	Parathyroid hormone synthesis, secretion and action	66/4205	106/8465	5.86e-03	1.47e-02	7.51e-03	66

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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

PTHLH

SNV

Missense_Mutation

c.126N>T

p.Gln42His

p.Q42H

P12272

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-AN-A04C-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

PTHLH

SNV

Missense_Mutation

c.221N>T

p.Ala74Val

p.A74V

P12272

protein_coding

tolerated(0.05)

benign(0.393)

TCGA-BH-A1FD-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

PTHLH

SNV

Missense_Mutation

c.521C>T

p.Ser174Leu

p.S174L

P12272

protein_coding

tolerated_low_confidence(0.46)

benign(0)

TCGA-C8-A26V-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

tamoxiphen

PTHLH

SNV

Missense_Mutation

c.430N>T

p.Arg144Cys

p.R144C

P12272

protein_coding

deleterious(0)

probably_damaging(0.993)

TCGA-ZJ-AAXT-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Unknown

PTHLH

SNV

Missense_Mutation

rs778459165

c.506C>T

p.Ser169Leu

p.S169L

P12272

protein_coding

deleterious_low_confidence(0.04)

benign(0.006)

TCGA-AA-3663-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

PTHLH

SNV

Missense_Mutation

rs758972275

c.397N>T

p.Arg133Cys

p.R133C

P12272

protein_coding

deleterious(0)

probably_damaging(0.993)

TCGA-AA-3977-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

PTHLH

SNV

Missense_Mutation

c.503N>T

p.Thr168Met

p.T168M

P12272

protein_coding

deleterious_low_confidence(0)

benign(0.011)

TCGA-AZ-4615-01

Colorectum

colon adenocarcinoma

Male

>=65

III/IV

Chemotherapy

xeloda

PTHLH

SNV

Missense_Mutation

rs778459165

c.506N>T

p.Ser169Leu

p.S169L

P12272

protein_coding

deleterious_low_confidence(0.04)

benign(0.006)

TCGA-CK-5915-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

PTHLH

SNV

Missense_Mutation

c.398N>A

p.Arg133His

p.R133H

P12272

protein_coding

deleterious(0.04)

probably_damaging(0.991)

TCGA-CM-6171-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

PTHLH

SNV

Missense_Mutation

novel

c.485N>C

p.Leu162Pro

p.L162P

P12272

protein_coding

tolerated_low_confidence(0.16)

benign(0)

TCGA-G4-6314-01

Colorectum

colon adenocarcinoma

Female

>=65

III/IV

Ancillary

leucovorin

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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
5744	PTHLH	HORMONE ACTIVITY, DRUGGABLE GENOME		MAGNESIUM SULFATE		11384692
5744	PTHLH	HORMONE ACTIVITY, DRUGGABLE GENOME		DIFFERENTIATION AGENTS		10839458
5744	PTHLH	HORMONE ACTIVITY, DRUGGABLE GENOME		PROTEOLYTIC ENZYMES		7556886
5744	PTHLH	HORMONE ACTIVITY, DRUGGABLE GENOME		VINBLASTINE	VINBLASTINE	9784008
5744	PTHLH	HORMONE ACTIVITY, DRUGGABLE GENOME		DIMETHYL SULFOXIDE		10839458
5744	PTHLH	HORMONE ACTIVITY, DRUGGABLE GENOME	inhibitor	CHEMBL2109562	CAL

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