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: PNPLA4

Gene summary for PNPLA4

Gene summary.

Gene information	Species	Human
	Gene symbol	PNPLA4
	Gene ID	8228
	Gene name	patatin like phospholipase domain containing 4
	Gene Alias	DXS1283E
	Cytomap	Xp22.31
	Gene Type	protein-coding
	GO ID	GO:0001523
	UniProtAcc	A0A024RBU8

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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
8228	PNPLA4	LP15	Human	Oral cavity	LP	4.22e-17	2.10e+00	0.2174
8228	PNPLA4	LP17	Human	Oral cavity	LP	5.85e-03	4.28e-01	0.2349
8228	PNPLA4	SYSMH1	Human	Oral cavity	OSCC	4.81e-05	2.36e-01	0.1127
8228	PNPLA4	SYSMH2	Human	Oral cavity	OSCC	2.42e-21	5.42e-01	0.2326
8228	PNPLA4	SYSMH3	Human	Oral cavity	OSCC	3.55e-23	6.12e-01	0.2442
8228	PNPLA4	SYSMH6	Human	Oral cavity	OSCC	4.01e-08	3.99e-01	0.1275
8228	PNPLA4	P4_S8_cSCC	Human	Skin	cSCC	3.20e-06	1.46e-01	-0.3095
8228	PNPLA4	P1_cSCC	Human	Skin	cSCC	5.12e-20	6.88e-01	0.0292
8228	PNPLA4	P2_cSCC	Human	Skin	cSCC	1.86e-06	2.97e-01	-0.024
8228	PNPLA4	P4_cSCC	Human	Skin	cSCC	5.56e-21	6.00e-01	-0.00290000000000005
8228	PNPLA4	P10_cSCC	Human	Skin	cSCC	9.43e-11	4.62e-01	0.1017

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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:00060668	Esophagus	ESCC	alcohol metabolic process	202/8552	353/18723	7.32e-06	7.26e-05	202
GO:00464864	Esophagus	ESCC	glycerolipid metabolic process	211/8552	392/18723	6.51e-04	3.46e-03	211
GO:00442427	Esophagus	ESCC	cellular lipid catabolic process	121/8552	214/18723	8.63e-04	4.43e-03	121
GO:00160427	Esophagus	ESCC	lipid catabolic process	168/8552	320/18723	7.97e-03	2.84e-02	168
GO:000606621	Liver	HCC	alcohol metabolic process	208/7958	353/18723	2.80e-10	9.50e-09	208
GO:004424222	Liver	HCC	cellular lipid catabolic process	134/7958	214/18723	2.07e-09	5.79e-08	134
GO:00550882	Liver	HCC	lipid homeostasis	103/7958	167/18723	4.27e-07	7.18e-06	103
GO:004648611	Liver	HCC	glycerolipid metabolic process	215/7958	392/18723	4.54e-07	7.49e-06	215
GO:001604221	Liver	HCC	lipid catabolic process	175/7958	320/18723	6.50e-06	7.88e-05	175
GO:00066412	Liver	HCC	triglyceride metabolic process	59/7958	100/18723	6.35e-04	3.93e-03	59
GO:000663911	Liver	HCC	acylglycerol metabolic process	72/7958	128/18723	1.16e-03	6.54e-03	72
GO:000663811	Liver	HCC	neutral lipid metabolic process	72/7958	129/18723	1.54e-03	8.14e-03	72
GO:000672011	Liver	HCC	isoprenoid metabolic process	65/7958	116/18723	2.23e-03	1.11e-02	65
GO:003430812	Liver	HCC	primary alcohol metabolic process	55/7958	102/18723	1.30e-02	4.67e-02	55
GO:00060667	Oral cavity	OSCC	alcohol metabolic process	179/7305	353/18723	4.54e-06	5.21e-05	179
GO:00442426	Oral cavity	OSCC	cellular lipid catabolic process	104/7305	214/18723	2.61e-03	1.15e-02	104
GO:00067203	Oral cavity	OSCC	isoprenoid metabolic process	59/7305	116/18723	6.18e-03	2.33e-02	59
GO:000606613	Oral cavity	LP	alcohol metabolic process	111/4623	353/18723	2.24e-03	1.62e-02	111
GO:004424213	Oral cavity	LP	cellular lipid catabolic process	70/4623	214/18723	4.82e-03	3.05e-02	70

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Enriched KEGG pathways.

Pathway ID

Tissue

Disease Stage

Description

Gene Ratio

Bg Ratio

pvalue

p.adjust

qvalue

Count

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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

PNPLA4

SNV

Missense_Mutation

c.680N>A

p.Ser227Asn

p.S227N

P41247

protein_coding

tolerated(0.43)

benign(0)

TCGA-AR-A0TW-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

doxorubicin

PNPLA4

SNV

Missense_Mutation

c.679N>T

p.Ser227Cys

p.S227C

P41247

protein_coding

deleterious(0.03)

benign(0.379)

TCGA-AR-A0TW-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

doxorubicin

PNPLA4

SNV

Missense_Mutation

rs767773321

c.188N>G

p.Asn63Ser

p.N63S

P41247

protein_coding

tolerated(0.73)

benign(0)

TCGA-GI-A2C9-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

PNPLA4

insertion

Frame_Shift_Ins

novel

c.182_183insTTATCAAACTGTGAAACCTATGCCTGGAATACTC

p.Glu61AspfsTer14

p.E61Dfs*14

P41247

protein_coding

TCGA-A8-A082-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

PNPLA4

insertion

Frame_Shift_Ins

novel

c.300_301insGCCGCAGCCCAGTACC

p.Pro101AlafsTer42

p.P101Afs*42

P41247

protein_coding

TCGA-AN-A0FX-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

PNPLA4

insertion

Frame_Shift_Ins

novel

c.298_299insA

p.Pro100HisfsTer38

p.P100Hfs*38

P41247

protein_coding

TCGA-AN-A0FX-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

PNPLA4

SNV

Missense_Mutation

c.491N>T

p.Gly164Val

p.G164V

P41247

protein_coding

deleterious(0)

probably_damaging(0.995)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

PNPLA4

SNV

Missense_Mutation

novel

c.437N>T

p.Pro146Leu

p.P146L

P41247

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

PNPLA4

SNV

Missense_Mutation

rs775251646

c.329N>A

p.Arg110Gln

p.R110Q

P41247

protein_coding

deleterious(0)

possibly_damaging(0.876)

TCGA-EA-A3HS-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

PNPLA4

SNV

Missense_Mutation

c.203N>T

p.Lys68Met

p.K68M

P41247

protein_coding

deleterious(0.03)

possibly_damaging(0.799)

TCGA-AA-3672-01

Colorectum

colon adenocarcinoma

Female

>=65

III/IV

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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