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: LPCAT1

Gene summary for LPCAT1

Gene summary.

Gene information	Species	Human
	Gene symbol	LPCAT1
	Gene ID	79888
	Gene name	lysophosphatidylcholine acyltransferase 1
	Gene Alias	AGPAT10
	Cytomap	5p15.33
	Gene Type	protein-coding
	GO ID	GO:0001654
	UniProtAcc	Q8NF37

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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
79888	LPCAT1	LZE24T	Human	Esophagus	ESCC	2.12e-05	1.01e-01	0.0596
79888	LPCAT1	P2T-E	Human	Esophagus	ESCC	4.11e-15	2.70e-01	0.1177
79888	LPCAT1	P4T-E	Human	Esophagus	ESCC	2.06e-09	1.93e-01	0.1323
79888	LPCAT1	P5T-E	Human	Esophagus	ESCC	4.54e-14	3.12e-01	0.1327
79888	LPCAT1	P8T-E	Human	Esophagus	ESCC	1.99e-05	1.30e-01	0.0889
79888	LPCAT1	P9T-E	Human	Esophagus	ESCC	5.26e-07	1.85e-01	0.1131
79888	LPCAT1	P10T-E	Human	Esophagus	ESCC	1.29e-33	6.37e-01	0.116
79888	LPCAT1	P11T-E	Human	Esophagus	ESCC	1.57e-12	3.73e-01	0.1426
79888	LPCAT1	P12T-E	Human	Esophagus	ESCC	9.27e-12	2.82e-01	0.1122
79888	LPCAT1	P15T-E	Human	Esophagus	ESCC	4.00e-02	1.08e-01	0.1149
79888	LPCAT1	P16T-E	Human	Esophagus	ESCC	3.41e-07	1.56e-01	0.1153
79888	LPCAT1	P17T-E	Human	Esophagus	ESCC	3.87e-09	4.67e-01	0.1278
79888	LPCAT1	P19T-E	Human	Esophagus	ESCC	3.94e-02	3.20e-01	0.1662
79888	LPCAT1	P20T-E	Human	Esophagus	ESCC	2.85e-11	2.07e-01	0.1124
79888	LPCAT1	P21T-E	Human	Esophagus	ESCC	7.09e-20	4.69e-01	0.1617
79888	LPCAT1	P22T-E	Human	Esophagus	ESCC	5.45e-11	2.24e-01	0.1236
79888	LPCAT1	P24T-E	Human	Esophagus	ESCC	4.47e-04	1.20e-01	0.1287
79888	LPCAT1	P26T-E	Human	Esophagus	ESCC	6.28e-04	1.53e-01	0.1276
79888	LPCAT1	P27T-E	Human	Esophagus	ESCC	1.24e-03	7.83e-02	0.1055
79888	LPCAT1	P28T-E	Human	Esophagus	ESCC	4.94e-09	2.08e-01	0.1149

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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
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
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:0042176111	Esophagus	ESCC	regulation of protein catabolic process	280/8552	391/18723	8.65e-26	2.39e-23	280
GO:0009896111	Esophagus	ESCC	positive regulation of catabolic process	332/8552	492/18723	4.36e-23	9.22e-21	332
GO:0045732111	Esophagus	ESCC	positive regulation of protein catabolic process	167/8552	231/18723	1.47e-16	1.14e-14	167
GO:0010563111	Esophagus	ESCC	negative regulation of phosphorus metabolic process	274/8552	442/18723	2.32e-12	9.41e-11	274
GO:0045936111	Esophagus	ESCC	negative regulation of phosphate metabolic process	273/8552	441/18723	3.18e-12	1.25e-10	273
GO:00086544	Esophagus	ESCC	phospholipid biosynthetic process	162/8552	253/18723	2.59e-09	5.73e-08	162
GO:00464744	Esophagus	ESCC	glycerophospholipid biosynthetic process	135/8552	211/18723	5.75e-08	1.02e-06	135
GO:00450175	Esophagus	ESCC	glycerolipid biosynthetic process	154/8552	252/18723	5.20e-07	6.96e-06	154
GO:00066446	Esophagus	ESCC	phospholipid metabolic process	218/8552	383/18723	5.37e-06	5.59e-05	218
GO:00066561	Esophagus	ESCC	phosphatidylcholine biosynthetic process	24/8552	29/18723	4.50e-05	3.55e-04	24
GO:00066505	Esophagus	ESCC	glycerophospholipid metabolic process	174/8552	306/18723	4.92e-05	3.85e-04	174
GO:00066541	Esophagus	ESCC	phosphatidic acid biosynthetic process	26/8552	33/18723	1.06e-04	7.43e-04	26
GO:00464733	Esophagus	ESCC	phosphatidic acid metabolic process	28/8552	37/18723	2.00e-04	1.26e-03	28
GO:00464864	Esophagus	ESCC	glycerolipid metabolic process	211/8552	392/18723	6.51e-04	3.46e-03	211
GO:01501724	Esophagus	ESCC	regulation of phosphatidylcholine metabolic process	9/8552	10/18723	5.09e-03	1.92e-02	9
GO:00192168	Esophagus	ESCC	regulation of lipid metabolic process	172/8552	331/18723	1.20e-02	4.02e-02	172
GO:000989622	Liver	HCC	positive regulation of catabolic process	335/7958	492/18723	3.83e-31	1.87e-28	335
GO:004217622	Liver	HCC	regulation of protein catabolic process	267/7958	391/18723	2.45e-25	7.38e-23	267
GO:004573222	Liver	HCC	positive regulation of protein catabolic process	163/7958	231/18723	4.00e-18	4.69e-16	163
GO:001056322	Liver	HCC	negative regulation of phosphorus metabolic process	259/7958	442/18723	4.29e-12	1.92e-10	259

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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

LPCAT1

SNV

Missense_Mutation

novel

c.1351N>T

p.Val451Leu

p.V451L

Q8NF37

protein_coding

tolerated(0.1)

benign(0.031)

TCGA-B6-A0I1-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

LPCAT1

SNV

Missense_Mutation

c.1382N>A

p.Arg461Gln

p.R461Q

Q8NF37

protein_coding

tolerated(0.52)

benign(0.003)

TCGA-B6-A0WY-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

LPCAT1

SNV

Missense_Mutation

c.1600N>C

p.Asp534His

p.D534H

Q8NF37

protein_coding

deleterious_low_confidence(0)

possibly_damaging(0.781)

TCGA-BH-A0BP-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

LPCAT1

SNV

Missense_Mutation

c.1588C>T

p.Arg530Cys

p.R530C

Q8NF37

protein_coding

tolerated_low_confidence(0.26)

benign(0)

TCGA-D8-A1XK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicine+cyclophosphamide

LPCAT1

SNV

Missense_Mutation

novel

c.999A>T

p.Glu333Asp

p.E333D

Q8NF37

protein_coding

deleterious(0)

possibly_damaging(0.831)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

LPCAT1

SNV

Missense_Mutation

novel

c.559G>T

p.Val187Leu

p.V187L

Q8NF37

protein_coding

deleterious(0.04)

possibly_damaging(0.771)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

LPCAT1

SNV

Missense_Mutation

c.814N>C

p.Glu272Gln

p.E272Q

Q8NF37

protein_coding

deleterious(0.02)

probably_damaging(0.91)

TCGA-LP-A4AV-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

LPCAT1

SNV

Missense_Mutation

rs747860604

c.358N>T

p.Arg120Trp

p.R120W

Q8NF37

protein_coding

deleterious(0)

probably_damaging(0.93)

TCGA-4T-AA8H-01

Colorectum

colon adenocarcinoma

Female

<65

I/II

Unknown

LPCAT1

SNV

Missense_Mutation

novel

c.655A>G

p.Thr219Ala

p.T219A

Q8NF37

protein_coding

deleterious(0.02)

benign(0.081)

TCGA-5M-AAT6-01

Colorectum

colon adenocarcinoma

Female

<65

III/IV

Unknown

LPCAT1

SNV

Missense_Mutation

c.392N>T

p.Thr131Met

p.T131M

Q8NF37

protein_coding

deleterious(0.01)

possibly_damaging(0.829)

TCGA-AA-3819-01

Colorectum

colon adenocarcinoma

Female

<65

I/II

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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