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

Home

Download

Statistics

Help

Contact

	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: HMGCS2

Gene summary for HMGCS2

Gene summary.

Gene information	Species	Human
	Gene symbol	HMGCS2
	Gene ID	3158
	Gene name	3-hydroxy-3-methylglutaryl-CoA synthase 2
	Gene Alias	HMGCS2
	Cytomap	1p12
	Gene Type	protein-coding
	GO ID	GO:0006066
	UniProtAcc	P54868

Top

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
3158	HMGCS2	HTA11_3410_2000001011	Human	Colorectum	AD	5.01e-32	1.30e+00	0.0155
3158	HMGCS2	HTA11_2487_2000001011	Human	Colorectum	SER	2.69e-22	1.50e+00	-0.1808
3158	HMGCS2	HTA11_1938_2000001011	Human	Colorectum	AD	4.41e-40	2.56e+00	-0.0811
3158	HMGCS2	HTA11_78_2000001011	Human	Colorectum	AD	4.59e-23	1.91e+00	-0.1088
3158	HMGCS2	HTA11_347_2000001011	Human	Colorectum	AD	3.29e-83	3.02e+00	-0.1954
3158	HMGCS2	HTA11_411_2000001011	Human	Colorectum	SER	1.03e-03	6.38e-01	-0.2602
3158	HMGCS2	HTA11_2112_2000001011	Human	Colorectum	SER	2.93e-02	9.95e-01	-0.2196
3158	HMGCS2	HTA11_3361_2000001011	Human	Colorectum	AD	7.06e-22	1.71e+00	-0.1207
3158	HMGCS2	HTA11_83_2000001011	Human	Colorectum	SER	7.00e-41	2.73e+00	-0.1526
3158	HMGCS2	HTA11_696_2000001011	Human	Colorectum	AD	9.32e-21	1.08e+00	-0.1464
3158	HMGCS2	HTA11_866_2000001011	Human	Colorectum	AD	9.65e-47	1.85e+00	-0.1001
3158	HMGCS2	HTA11_1391_2000001011	Human	Colorectum	AD	2.26e-38	2.43e+00	-0.059
3158	HMGCS2	HTA11_2992_2000001011	Human	Colorectum	SER	4.76e-17	1.61e+00	-0.1706
3158	HMGCS2	HTA11_5212_2000001011	Human	Colorectum	AD	2.69e-20	1.69e+00	-0.2061
3158	HMGCS2	HTA11_5216_2000001011	Human	Colorectum	SER	9.40e-20	2.21e+00	-0.1462
3158	HMGCS2	HTA11_546_2000001011	Human	Colorectum	AD	7.81e-25	1.88e+00	-0.0842
3158	HMGCS2	HTA11_9341_2000001011	Human	Colorectum	SER	6.24e-18	1.58e+00	-0.00410000000000005
3158	HMGCS2	HTA11_7862_2000001011	Human	Colorectum	AD	4.06e-27	1.83e+00	-0.0179
3158	HMGCS2	HTA11_4255_2000001011	Human	Colorectum	SER	1.14e-25	1.85e+00	0.0446
3158	HMGCS2	HTA11_9408_2000001011	Human	Colorectum	AD	4.73e-08	1.02e+00	0.0451

Page: 1 2 3 4

Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Colorectum (GSE201348)		FAP: Familial adenomatous polyposis
		CRC: Colorectal cancer
Colorectum (HTA11)		AD: Adenomas
		SER: Sessile serrated lesions
		MSI-H: Microsatellite-high colorectal cancer
		MSS: Microsatellite stable colorectal cancer
Liver		HCC: Hepatocellular carcinoma
		NAFLD: Non-alcoholic fatty liver disease

∗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.

Top

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).

Page: 1 2 3 4 5 6 7 8 9

Enriched GO biological processes.

GO ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	Count
GO:0006091	Colorectum	AD	generation of precursor metabolites and energy	209/3918	490/18723	3.17e-28	6.61e-25	209
GO:0009150	Colorectum	AD	purine ribonucleotide metabolic process	142/3918	368/18723	4.29e-15	1.17e-12	142
GO:0006163	Colorectum	AD	purine nucleotide metabolic process	149/3918	396/18723	1.08e-14	2.80e-12	149
GO:0072521	Colorectum	AD	purine-containing compound metabolic process	153/3918	416/18723	4.34e-14	1.01e-11	153
GO:0009259	Colorectum	AD	ribonucleotide metabolic process	144/3918	385/18723	5.25e-14	1.13e-11	144
GO:0019693	Colorectum	AD	ribose phosphate metabolic process	145/3918	396/18723	3.01e-13	5.71e-11	145
GO:0009117	Colorectum	AD	nucleotide metabolic process	168/3918	489/18723	2.20e-12	3.36e-10	168
GO:0006753	Colorectum	AD	nucleoside phosphate metabolic process	169/3918	497/18723	4.99e-12	6.98e-10	169
GO:0006066	Colorectum	AD	alcohol metabolic process	106/3918	353/18723	3.02e-05	5.57e-04	106
GO:0006790	Colorectum	AD	sulfur compound metabolic process	101/3918	339/18723	6.46e-05	1.07e-03	101
GO:0033865	Colorectum	AD	nucleoside bisphosphate metabolic process	42/3918	128/18723	1.12e-03	1.02e-02	42
GO:0033875	Colorectum	AD	ribonucleoside bisphosphate metabolic process	42/3918	128/18723	1.12e-03	1.02e-02	42
GO:0034032	Colorectum	AD	purine nucleoside bisphosphate metabolic process	42/3918	128/18723	1.12e-03	1.02e-02	42
GO:0006644	Colorectum	AD	phospholipid metabolic process	101/3918	383/18723	5.80e-03	3.67e-02	101
GO:0008202	Colorectum	AD	steroid metabolic process	85/3918	319/18723	8.07e-03	4.75e-02	85
GO:00060911	Colorectum	SER	generation of precursor metabolites and energy	168/2897	490/18723	1.39e-25	1.70e-22	168
GO:00061631	Colorectum	SER	purine nucleotide metabolic process	109/2897	396/18723	4.26e-10	5.44e-08	109
GO:00091501	Colorectum	SER	purine ribonucleotide metabolic process	103/2897	368/18723	4.69e-10	5.68e-08	103
GO:00725211	Colorectum	SER	purine-containing compound metabolic process	113/2897	416/18723	4.80e-10	5.68e-08	113
GO:00092591	Colorectum	SER	ribonucleotide metabolic process	104/2897	385/18723	3.27e-09	3.04e-07	104

Page: 1 2 3 4 5 6 7

Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa00280	Colorectum	AD	Valine, leucine and isoleucine degradation	25/2092	48/8465	3.97e-05	3.41e-04	2.18e-04	25
hsa002801	Colorectum	AD	Valine, leucine and isoleucine degradation	25/2092	48/8465	3.97e-05	3.41e-04	2.18e-04	25
hsa002802	Colorectum	MSS	Valine, leucine and isoleucine degradation	21/1875	48/8465	6.73e-04	4.51e-03	2.76e-03	21
hsa002803	Colorectum	MSS	Valine, leucine and isoleucine degradation	21/1875	48/8465	6.73e-04	4.51e-03	2.76e-03	21
hsa002804	Colorectum	FAP	Valine, leucine and isoleucine degradation	18/1404	48/8465	3.94e-04	3.06e-03	1.86e-03	18
hsa002805	Colorectum	FAP	Valine, leucine and isoleucine degradation	18/1404	48/8465	3.94e-04	3.06e-03	1.86e-03	18
hsa002806	Liver	NAFLD	Valine, leucine and isoleucine degradation	20/1043	48/8465	3.03e-07	1.65e-05	1.33e-05	20
hsa033206	Liver	NAFLD	PPAR signaling pathway	25/1043	75/8465	1.61e-06	6.62e-05	5.33e-05	25
hsa0028011	Liver	NAFLD	Valine, leucine and isoleucine degradation	20/1043	48/8465	3.03e-07	1.65e-05	1.33e-05	20
hsa0332011	Liver	NAFLD	PPAR signaling pathway	25/1043	75/8465	1.61e-06	6.62e-05	5.33e-05	25
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

Page: 1 2

Top

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

Page: 1

Top

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.

Page: 1

Top

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

HMGCS2

SNV

Missense_Mutation

c.1144N>C

p.Tyr382His

p.Y382H

P54868

protein_coding

deleterious(0)

probably_damaging(0.987)

TCGA-A8-A09Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

HMGCS2

SNV

Missense_Mutation

rs770800317

c.1355G>A

p.Arg452Gln

p.R452Q

P54868

protein_coding

deleterious(0)

probably_damaging(0.997)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

HMGCS2

SNV

Missense_Mutation

c.1058N>T

p.Asp353Val

p.D353V

P54868

protein_coding

deleterious(0)

benign(0.204)

TCGA-AN-A0XU-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

HMGCS2

SNV

Missense_Mutation

c.35T>C

p.Leu12Pro

p.L12P

P54868

protein_coding

deleterious_low_confidence(0)

possibly_damaging(0.65)

TCGA-B6-A0I6-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

HMGCS2

SNV

Missense_Mutation

rs775277893

c.1015G>A

p.Gly339Arg

p.G339R

P54868

protein_coding

tolerated(1)

benign(0.001)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

HMGCS2

SNV

Missense_Mutation

novel

c.1392N>A

p.Met464Ile

p.M464I

P54868

protein_coding

tolerated(0.25)

possibly_damaging(0.514)

TCGA-JW-A5VJ-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

HMGCS2

SNV

Missense_Mutation

c.74N>A

p.Pro25His

p.P25H

P54868

protein_coding

deleterious_low_confidence(0.02)

benign(0.436)

TCGA-VS-A9UJ-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

HMGCS2

SNV

Missense_Mutation

rs61729865

c.1342N>T

p.Arg448Cys

p.R448C

P54868

protein_coding

deleterious(0.04)

probably_damaging(0.988)

TCGA-AA-3713-01

Colorectum

colon adenocarcinoma

Male

>=65

III/IV

Chemotherapy

5-fluorouracil

HMGCS2

SNV

Missense_Mutation

c.617N>A

p.Arg206His

p.R206H

P54868

protein_coding

deleterious(0.03)

probably_damaging(0.986)

TCGA-AU-6004-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

HMGCS2

SNV

Missense_Mutation

novel

c.1366N>C

p.Ser456Pro

p.S456P

P54868

protein_coding

tolerated(0.27)

benign(0.005)

TCGA-AZ-6598-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

Page: 1 2 3 4 5 6

Top

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
3158	HMGCS2	DRUGGABLE GENOME, ENZYME		hydrochlorothiazide	HYDROCHLOROTHIAZIDE	29523524
3158	HMGCS2	DRUGGABLE GENOME, ENZYME		chlorothiazide	CHLOROTHIAZIDE	29523524

Page: 1