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: HMGCS1

Gene summary for HMGCS1

Gene summary.

Gene information	Species	Human
	Gene symbol	HMGCS1
	Gene ID	3157
	Gene name	3-hydroxy-3-methylglutaryl-CoA synthase 1
	Gene Alias	HMGCS
	Cytomap	5p12
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	A0A024R059

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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
3157	HMGCS1	AEH-subject1	Human	Endometrium	AEH	1.65e-05	3.28e-01	-0.3059
3157	HMGCS1	AEH-subject4	Human	Endometrium	AEH	3.84e-03	2.76e-01	-0.2657
3157	HMGCS1	AEH-subject5	Human	Endometrium	AEH	3.35e-28	8.16e-01	-0.2953
3157	HMGCS1	EEC-subject3	Human	Endometrium	EEC	3.23e-04	-6.81e-02	-0.2525
3157	HMGCS1	EEC-subject4	Human	Endometrium	EEC	4.29e-02	2.59e-01	-0.2571
3157	HMGCS1	GSM6177620_NYU_UCEC1_lib1_lib1	Human	Endometrium	EEC	2.32e-03	-1.29e-01	-0.1869
3157	HMGCS1	GSM6177620_NYU_UCEC1_lib2_lib2	Human	Endometrium	EEC	2.43e-03	-1.01e-01	-0.1875
3157	HMGCS1	GSM6177620_NYU_UCEC1_lib3_lib3	Human	Endometrium	EEC	2.87e-03	-1.47e-01	-0.1883
3157	HMGCS1	GSM6177621_NYU_UCEC2_lib1_lib1	Human	Endometrium	EEC	4.20e-05	3.18e-02	-0.1934
3157	HMGCS1	GSM6177622_NYU_UCEC3_lib1_lib1	Human	Endometrium	EEC	5.29e-04	-1.36e-01	-0.1917
3157	HMGCS1	GSM6177622_NYU_UCEC3_lib2_lib2	Human	Endometrium	EEC	2.41e-06	-1.32e-01	-0.1916
3157	HMGCS1	LZE2T	Human	Esophagus	ESCC	1.09e-03	1.04e+00	0.082
3157	HMGCS1	LZE4T	Human	Esophagus	ESCC	5.68e-23	1.14e+00	0.0811
3157	HMGCS1	LZE5T	Human	Esophagus	ESCC	2.32e-03	1.30e+00	0.0514
3157	HMGCS1	LZE7T	Human	Esophagus	ESCC	3.38e-11	1.23e+00	0.0667
3157	HMGCS1	LZE8T	Human	Esophagus	ESCC	1.40e-15	5.67e-01	0.067
3157	HMGCS1	LZE20T	Human	Esophagus	ESCC	2.30e-09	6.90e-01	0.0662
3157	HMGCS1	LZE22D1	Human	Esophagus	HGIN	1.39e-05	8.44e-03	0.0595
3157	HMGCS1	LZE22T	Human	Esophagus	ESCC	4.74e-05	9.27e-01	0.068
3157	HMGCS1	LZE24T	Human	Esophagus	ESCC	2.24e-10	4.57e-01	0.0596

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
GC		CAG: Chronic atrophic gastritis
		CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
		CSG: Chronic superficial gastritis
		GC: Gastric cancer
		SIM: Severe intestinal metaplasia
		WIM: Wild intestinal metaplasia
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
Prostate		BPH: Benign Prostatic Hyperplasia
Skin		AK: Actinic keratosis
		cSCC: Cutaneous squamous cell carcinoma
		SCCIS:squamous cell carcinoma in situ
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:000911712	Liver	Cirrhotic	nucleotide metabolic process	187/4634	489/18723	1.55e-11	9.63e-10	187
GO:00082031	Liver	Cirrhotic	cholesterol metabolic process	70/4634	137/18723	2.59e-11	1.55e-09	70
GO:00161251	Liver	Cirrhotic	sterol metabolic process	75/4634	152/18723	4.54e-11	2.61e-09	75
GO:001969312	Liver	Cirrhotic	ribose phosphate metabolic process	156/4634	396/18723	5.83e-11	3.23e-09	156
GO:000606612	Liver	Cirrhotic	alcohol metabolic process	141/4634	353/18723	1.57e-10	8.03e-09	141
GO:000925912	Liver	Cirrhotic	ribonucleotide metabolic process	151/4634	385/18723	1.72e-10	8.70e-09	151
GO:003166712	Liver	Cirrhotic	response to nutrient levels	174/4634	474/18723	3.08e-09	1.27e-07	174
GO:007252112	Liver	Cirrhotic	purine-containing compound metabolic process	156/4634	416/18723	3.74e-09	1.52e-07	156
GO:000915012	Liver	Cirrhotic	purine ribonucleotide metabolic process	141/4634	368/18723	4.22e-09	1.70e-07	141
GO:00066941	Liver	Cirrhotic	steroid biosynthetic process	77/4634	173/18723	1.02e-08	3.91e-07	77
GO:0016126	Liver	Cirrhotic	sterol biosynthetic process	37/4634	64/18723	1.74e-08	6.32e-07	37
GO:0006695	Liver	Cirrhotic	cholesterol biosynthetic process	34/4634	57/18723	2.22e-08	7.77e-07	34
GO:1902653	Liver	Cirrhotic	secondary alcohol biosynthetic process	34/4634	57/18723	2.22e-08	7.77e-07	34
GO:000679011	Liver	Cirrhotic	sulfur compound metabolic process	129/4634	339/18723	3.06e-08	1.04e-06	129
GO:000616312	Liver	Cirrhotic	purine nucleotide metabolic process	146/4634	396/18723	4.12e-08	1.34e-06	146
GO:000941012	Liver	Cirrhotic	response to xenobiotic stimulus	165/4634	462/18723	6.82e-08	2.09e-06	165
GO:004873212	Liver	Cirrhotic	gland development	154/4634	436/18723	4.03e-07	9.42e-06	154
GO:009730512	Liver	Cirrhotic	response to alcohol	96/4634	253/18723	1.97e-06	3.65e-05	96
GO:000758411	Liver	Cirrhotic	response to nutrient	67/4634	174/18723	3.83e-05	4.59e-04	67
GO:0046165	Liver	Cirrhotic	alcohol biosynthetic process	55/4634	140/18723	9.74e-05	1.03e-03	55

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa009005	Esophagus	ESCC	Terpenoid backbone biosynthesis	20/4205	23/8465	2.14e-04	7.87e-04	4.03e-04	20
hsa002809	Esophagus	ESCC	Valine, leucine and isoleucine degradation	34/4205	48/8465	2.34e-03	6.54e-03	3.35e-03	34
hsa0090012	Esophagus	ESCC	Terpenoid backbone biosynthesis	20/4205	23/8465	2.14e-04	7.87e-04	4.03e-04	20
hsa0028014	Esophagus	ESCC	Valine, leucine and isoleucine degradation	34/4205	48/8465	2.34e-03	6.54e-03	3.35e-03	34
hsa0028021	Liver	Cirrhotic	Valine, leucine and isoleucine degradation	32/2530	48/8465	1.45e-07	2.02e-06	1.24e-06	32
hsa006502	Liver	Cirrhotic	Butanoate metabolism	15/2530	27/8465	4.71e-03	1.74e-02	1.07e-02	15
hsa0332021	Liver	Cirrhotic	PPAR signaling pathway	32/2530	75/8465	1.24e-02	3.92e-02	2.42e-02	32
hsa0028031	Liver	Cirrhotic	Valine, leucine and isoleucine degradation	32/2530	48/8465	1.45e-07	2.02e-06	1.24e-06	32
hsa006503	Liver	Cirrhotic	Butanoate metabolism	15/2530	27/8465	4.71e-03	1.74e-02	1.07e-02	15
hsa0332031	Liver	Cirrhotic	PPAR signaling pathway	32/2530	75/8465	1.24e-02	3.92e-02	2.42e-02	32
hsa0028041	Liver	HCC	Valine, leucine and isoleucine degradation	41/4020	48/8465	4.84e-08	7.05e-07	3.92e-07	41
hsa033204	Liver	HCC	PPAR signaling pathway	48/4020	75/8465	2.83e-03	9.37e-03	5.21e-03	48
hsa00900	Liver	HCC	Terpenoid backbone biosynthesis	17/4020	23/8465	9.26e-03	2.46e-02	1.37e-02	17
hsa006504	Liver	HCC	Butanoate metabolism	19/4020	27/8465	1.37e-02	3.33e-02	1.85e-02	19
hsa0028051	Liver	HCC	Valine, leucine and isoleucine degradation	41/4020	48/8465	4.84e-08	7.05e-07	3.92e-07	41
hsa033205	Liver	HCC	PPAR signaling pathway	48/4020	75/8465	2.83e-03	9.37e-03	5.21e-03	48
hsa009001	Liver	HCC	Terpenoid backbone biosynthesis	17/4020	23/8465	9.26e-03	2.46e-02	1.37e-02	17
hsa006505	Liver	HCC	Butanoate metabolism	19/4020	27/8465	1.37e-02	3.33e-02	1.85e-02	19
hsa009004	Oral cavity	OSCC	Terpenoid backbone biosynthesis	19/3704	23/8465	1.55e-04	5.34e-04	2.72e-04	19
hsa002808	Oral cavity	OSCC	Valine, leucine and isoleucine degradation	30/3704	48/8465	6.75e-03	1.57e-02	7.99e-03	30

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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

HMGCS1

SNV

Missense_Mutation

rs752479224

c.1409N>G

p.Pro470Arg

p.P470R

Q01581

protein_coding

deleterious(0)

possibly_damaging(0.848)

TCGA-A1-A0SP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

HMGCS1

SNV

Missense_Mutation

novel

c.236N>T

p.Arg79Ile

p.R79I

Q01581

protein_coding

deleterious(0)

probably_damaging(0.911)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

HMGCS1

SNV

Missense_Mutation

novel

c.17N>A

p.Pro6His

p.P6H

Q01581

protein_coding

deleterious(0)

possibly_damaging(0.885)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

HMGCS1

SNV

Missense_Mutation

c.717N>T

p.Lys239Asn

p.K239N

Q01581

protein_coding

deleterious(0.02)

probably_damaging(0.955)

TCGA-AR-A251-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

doxorubicin

HMGCS1

SNV

Missense_Mutation

c.506N>C

p.Arg169Thr

p.R169T

Q01581

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-C8-A26Y-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

HMGCS1

insertion

Nonsense_Mutation

novel

c.1376_1377insAAAAAGCTAAGACTAAGGGCTGGCAATCAAATAAGAGCAAATTTAG

p.Asp459GlufsTer4

p.D459Efs*4

Q01581

protein_coding

TCGA-A2-A0EO-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

HMGCS1

SNV

Missense_Mutation

c.1106N>C

p.Arg369Thr

p.R369T

Q01581

protein_coding

deleterious(0.03)

probably_damaging(0.997)

TCGA-DR-A0ZM-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Unspecific

Cisplatin

HMGCS1

SNV

Missense_Mutation

c.829C>T

p.Arg277Trp

p.R277W

Q01581

protein_coding

deleterious(0)

possibly_damaging(0.876)

TCGA-AA-3864-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

HMGCS1

SNV

Missense_Mutation

rs772131971

c.572N>A

p.Arg191Gln

p.R191Q

Q01581

protein_coding

tolerated(0.11)

possibly_damaging(0.558)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

HMGCS1

SNV

Missense_Mutation

novel

c.1033T>C

p.Tyr345His

p.Y345H

Q01581

protein_coding

deleterious(0)

probably_damaging(0.977)

TCGA-A5-A1OF-01

Endometrium

uterine corpus endometrioid carcinoma

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
3157	HMGCS1	DRUGGABLE GENOME, ENZYME	inhibitor	135651558

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