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: SMCHD1

Gene summary for SMCHD1

Gene summary.

Gene information	Species	Human
	Gene symbol	SMCHD1
	Gene ID	23347
	Gene name	structural maintenance of chromosomes flexible hinge domain containing 1
	Gene Alias	BAMS
	Cytomap	18p11.32
	Gene Type	protein-coding
	GO ID	GO:0000018
	UniProtAcc	A6NHR9

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
23347	SMCHD1	CA_HPV_1	Human	Cervix	CC	2.63e-05	1.83e-01	0.0264
23347	SMCHD1	CA_HPV_2	Human	Cervix	CC	3.72e-04	2.82e-01	0.0391
23347	SMCHD1	CCI_2	Human	Cervix	CC	1.07e-07	1.20e+00	0.5249
23347	SMCHD1	CCI_3	Human	Cervix	CC	5.71e-04	6.59e-01	0.516
23347	SMCHD1	L1	Human	Cervix	CC	3.46e-02	-1.58e-01	0.0802
23347	SMCHD1	HTA11_3410_2000001011	Human	Colorectum	AD	2.41e-17	-7.13e-01	0.0155
23347	SMCHD1	HTA11_1938_2000001011	Human	Colorectum	AD	2.81e-03	-5.21e-01	-0.0811
23347	SMCHD1	HTA11_78_2000001011	Human	Colorectum	AD	1.24e-03	-5.33e-01	-0.1088
23347	SMCHD1	HTA11_3361_2000001011	Human	Colorectum	AD	2.75e-02	-5.63e-01	-0.1207
23347	SMCHD1	HTA11_696_2000001011	Human	Colorectum	AD	7.67e-14	-4.97e-01	-0.1464
23347	SMCHD1	HTA11_866_2000001011	Human	Colorectum	AD	2.67e-07	-4.61e-01	-0.1001
23347	SMCHD1	HTA11_7862_2000001011	Human	Colorectum	AD	8.57e-05	-7.50e-01	-0.0179
23347	SMCHD1	HTA11_866_3004761011	Human	Colorectum	AD	1.06e-11	-6.67e-01	0.096
23347	SMCHD1	HTA11_4255_2000001011	Human	Colorectum	SER	8.69e-04	-8.38e-01	0.0446
23347	SMCHD1	HTA11_8622_2000001021	Human	Colorectum	SER	3.50e-03	-7.32e-01	0.0528
23347	SMCHD1	HTA11_10623_2000001011	Human	Colorectum	AD	2.09e-02	-6.66e-01	-0.0177
23347	SMCHD1	HTA11_10711_2000001011	Human	Colorectum	AD	7.06e-03	-5.52e-01	0.0338
23347	SMCHD1	HTA11_7696_3000711011	Human	Colorectum	AD	4.47e-27	-6.99e-01	0.0674
23347	SMCHD1	HTA11_6818_2000001011	Human	Colorectum	AD	2.13e-03	-7.09e-01	0.0112
23347	SMCHD1	HTA11_6818_2000001021	Human	Colorectum	AD	1.31e-04	-6.30e-01	0.0588

Page: 1 2 3 4 5 6 7 8 9 10 11 12

Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Cervix		CC: Cervix cancer
		HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
		N_HPV: HPV-infected normal cervix
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
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
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
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.

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:00063257	Cervix	CC	chromatin organization	78/2311	409/18723	5.40e-05	8.02e-04	78
GO:20010209	Cervix	CC	regulation of response to DNA damage stimulus	46/2311	219/18723	1.92e-04	2.23e-03	46
GO:00510528	Cervix	CC	regulation of DNA metabolic process	65/2311	359/18723	9.25e-04	7.84e-03	65
GO:00605413	Cervix	CC	respiratory system development	39/2311	203/18723	3.18e-03	2.07e-02	39
GO:0051052	Colorectum	AD	regulation of DNA metabolic process	116/3918	359/18723	2.47e-07	1.00e-05	116
GO:0051054	Colorectum	AD	positive regulation of DNA metabolic process	73/3918	201/18723	3.27e-07	1.29e-05	73
GO:2001020	Colorectum	AD	regulation of response to DNA damage stimulus	71/3918	219/18723	4.38e-05	7.65e-04	71
GO:0006325	Colorectum	AD	chromatin organization	119/3918	409/18723	4.85e-05	8.33e-04	119
GO:2001022	Colorectum	AD	positive regulation of response to DNA damage stimulus	36/3918	105/18723	1.02e-03	9.47e-03	36
GO:0006282	Colorectum	AD	regulation of DNA repair	42/3918	130/18723	1.57e-03	1.32e-02	42
GO:00510541	Colorectum	SER	positive regulation of DNA metabolic process	53/2897	201/18723	4.51e-05	1.13e-03	53
GO:00510521	Colorectum	SER	regulation of DNA metabolic process	83/2897	359/18723	8.03e-05	1.77e-03	83
GO:00063251	Colorectum	SER	chromatin organization	89/2897	409/18723	4.15e-04	6.17e-03	89
GO:20010201	Colorectum	SER	regulation of response to DNA damage stimulus	49/2897	219/18723	4.24e-03	3.45e-02	49
GO:00510522	Colorectum	MSS	regulation of DNA metabolic process	108/3467	359/18723	5.86e-08	3.10e-06	108
GO:00510542	Colorectum	MSS	positive regulation of DNA metabolic process	69/3467	201/18723	6.33e-08	3.26e-06	69
GO:20010202	Colorectum	MSS	regulation of response to DNA damage stimulus	64/3467	219/18723	7.20e-05	1.21e-03	64
GO:00063252	Colorectum	MSS	chromatin organization	107/3467	409/18723	7.22e-05	1.21e-03	107
GO:20010221	Colorectum	MSS	positive regulation of response to DNA damage stimulus	33/3467	105/18723	9.83e-04	9.86e-03	33
GO:00062821	Colorectum	MSS	regulation of DNA repair	38/3467	130/18723	1.93e-03	1.67e-02	38

Page: 1 2 3 4 5 6 7 8 9 10 11

Enriched KEGG pathways.

Pathway ID

Tissue

Disease Stage

Description

Gene Ratio

Bg Ratio

pvalue

p.adjust

qvalue

Count

Page: 1

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

SMCHD1

SNV

Missense_Mutation

c.4108N>T

p.Arg1370Cys

p.R1370C

A6NHR9

protein_coding

tolerated(0.22)

benign(0.013)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SMCHD1

SNV

Missense_Mutation

c.1436G>A

p.Arg479Gln

p.R479Q

A6NHR9

protein_coding

deleterious(0)

probably_damaging(0.992)

TCGA-AR-A0TX-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SMCHD1

SNV

Missense_Mutation

novel

c.907G>A

p.Glu303Lys

p.E303K

A6NHR9

protein_coding

deleterious(0)

probably_damaging(0.985)

TCGA-AR-A254-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

paclitaxel

SMCHD1

SNV

Missense_Mutation

c.2509G>T

p.Val837Phe

p.V837F

A6NHR9

protein_coding

deleterious(0)

possibly_damaging(0.873)

TCGA-BH-A0DS-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

cyclophosphamide

SMCHD1

SNV

Missense_Mutation

c.1483N>T

p.Pro495Ser

p.P495S

A6NHR9

protein_coding

deleterious(0.01)

probably_damaging(0.996)

TCGA-BH-A0H6-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SMCHD1

SNV

Missense_Mutation

c.3824N>T

p.Arg1275Ile

p.R1275I

A6NHR9

protein_coding

tolerated(0.18)

benign(0)

TCGA-BH-A0HO-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

SMCHD1

SNV

Missense_Mutation

novel

c.3286A>C

p.Thr1096Pro

p.T1096P

A6NHR9

protein_coding

deleterious(0.04)

probably_damaging(0.916)

TCGA-C8-A12Y-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SMCHD1

SNV

Missense_Mutation

c.3176N>G

p.Asn1059Ser

p.N1059S

A6NHR9

protein_coding

tolerated(0.57)

benign(0.003)

TCGA-D8-A1XK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicine+cyclophosphamide

SMCHD1

SNV

Missense_Mutation

c.4154N>C

p.Gly1385Ala

p.G1385A

A6NHR9

protein_coding

deleterious(0.04)

benign(0.024)

TCGA-E9-A22G-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

SMCHD1

SNV

Missense_Mutation

novel

c.2432N>G

p.Ser811Cys

p.S811C

A6NHR9

protein_coding

tolerated(0.08)

benign(0.011)

TCGA-EW-A6SA-01

Breast

breast invasive carcinoma

Male

<65

I/II

Unknown

Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

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

Page: 1