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:00614589	Endometrium	AEH	reproductive system development	88/2100	427/18723	9.50e-09	6.41e-07	88
GO:00486089	Endometrium	AEH	reproductive structure development	87/2100	424/18723	1.43e-08	9.12e-07	87
GO:004873216	Endometrium	AEH	gland development	83/2100	436/18723	8.62e-07	3.11e-05	83
GO:000915016	Endometrium	AEH	purine ribonucleotide metabolic process	68/2100	368/18723	2.26e-05	4.35e-04	68
GO:000616316	Endometrium	AEH	purine nucleotide metabolic process	70/2100	396/18723	7.46e-05	1.13e-03	70
GO:000925910	Endometrium	AEH	ribonucleotide metabolic process	68/2100	385/18723	9.63e-05	1.39e-03	68
GO:001969310	Endometrium	AEH	ribose phosphate metabolic process	69/2100	396/18723	1.31e-04	1.79e-03	69
GO:009730510	Endometrium	AEH	response to alcohol	48/2100	253/18723	1.80e-04	2.31e-03	48
GO:007252116	Endometrium	AEH	purine-containing compound metabolic process	71/2100	416/18723	2.01e-04	2.54e-03	71
GO:003166716	Endometrium	AEH	response to nutrient levels	78/2100	474/18723	3.26e-04	3.64e-03	78
GO:006100810	Endometrium	AEH	hepaticobiliary system development	31/2100	150/18723	5.41e-04	5.45e-03	31
GO:000911715	Endometrium	AEH	nucleotide metabolic process	78/2100	489/18723	8.39e-04	7.82e-03	78
GO:000675314	Endometrium	AEH	nucleoside phosphate metabolic process	78/2100	497/18723	1.34e-03	1.13e-02	78
GO:000188910	Endometrium	AEH	liver development	29/2100	147/18723	1.72e-03	1.38e-02	29
GO:000941010	Endometrium	AEH	response to xenobiotic stimulus	71/2100	462/18723	3.66e-03	2.50e-02	71
GO:00075482	Endometrium	AEH	sex differentiation	46/2100	276/18723	3.91e-03	2.64e-02	46
GO:000931410	Endometrium	AEH	response to radiation	70/2100	456/18723	3.99e-03	2.68e-02	70
GO:00451372	Endometrium	AEH	development of primary sexual characteristics	39/2100	227/18723	4.45e-03	2.92e-02	39
GO:00084062	Endometrium	AEH	gonad development	38/2100	221/18723	4.87e-03	3.08e-02	38
GO:001407414	Endometrium	AEH	response to purine-containing compound	27/2100	148/18723	7.34e-03	4.18e-02	27

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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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