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: MBD4

Gene summary for MBD4

Gene summary.

Gene information	Species	Human
	Gene symbol	MBD4
	Gene ID	8930
	Gene name	methyl-CpG binding domain 4, DNA glycosylase
	Gene Alias	MED1
	Cytomap	3q21.3
	Gene Type	protein-coding
	GO ID	GO:0006139
	UniProtAcc	O95243

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
8930	MBD4	LZE2D	Human	Esophagus	HGIN	1.16e-02	1.65e-01	0.0642
8930	MBD4	LZE2T	Human	Esophagus	ESCC	1.30e-05	9.10e-01	0.082
8930	MBD4	LZE4T	Human	Esophagus	ESCC	5.29e-15	5.38e-01	0.0811
8930	MBD4	LZE5T	Human	Esophagus	ESCC	1.48e-04	3.58e-01	0.0514
8930	MBD4	LZE7T	Human	Esophagus	ESCC	2.30e-12	1.12e+00	0.0667
8930	MBD4	LZE8T	Human	Esophagus	ESCC	5.61e-11	2.29e-01	0.067
8930	MBD4	LZE20T	Human	Esophagus	ESCC	3.49e-04	1.14e-01	0.0662
8930	MBD4	LZE22T	Human	Esophagus	ESCC	1.09e-02	3.82e-01	0.068
8930	MBD4	LZE24T	Human	Esophagus	ESCC	7.05e-18	4.97e-01	0.0596
8930	MBD4	LZE6T	Human	Esophagus	ESCC	3.79e-04	4.70e-01	0.0845
8930	MBD4	P1T-E	Human	Esophagus	ESCC	3.09e-17	7.30e-01	0.0875
8930	MBD4	P2T-E	Human	Esophagus	ESCC	9.97e-73	1.24e+00	0.1177
8930	MBD4	P4T-E	Human	Esophagus	ESCC	3.12e-41	8.77e-01	0.1323
8930	MBD4	P5T-E	Human	Esophagus	ESCC	9.04e-26	5.55e-01	0.1327
8930	MBD4	P8T-E	Human	Esophagus	ESCC	1.45e-31	6.00e-01	0.0889
8930	MBD4	P9T-E	Human	Esophagus	ESCC	2.09e-21	5.03e-01	0.1131
8930	MBD4	P10T-E	Human	Esophagus	ESCC	1.11e-41	7.81e-01	0.116
8930	MBD4	P11T-E	Human	Esophagus	ESCC	1.72e-14	5.70e-01	0.1426
8930	MBD4	P12T-E	Human	Esophagus	ESCC	2.34e-22	4.67e-01	0.1122
8930	MBD4	P15T-E	Human	Esophagus	ESCC	3.04e-28	6.14e-01	0.1149

Page: 1 2 3 4 5 6

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
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
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:003465519	Esophagus	HGIN	nucleobase-containing compound catabolic process	98/2587	407/18723	1.44e-08	8.94e-07	98
GO:004670017	Esophagus	HGIN	heterocycle catabolic process	103/2587	445/18723	5.44e-08	2.99e-06	103
GO:004427018	Esophagus	HGIN	cellular nitrogen compound catabolic process	103/2587	451/18723	1.10e-07	5.56e-06	103
GO:001943917	Esophagus	HGIN	aromatic compound catabolic process	105/2587	467/18723	1.89e-07	9.31e-06	105
GO:190136117	Esophagus	HGIN	organic cyclic compound catabolic process	106/2587	495/18723	1.94e-06	7.13e-05	106
GO:00196924	Esophagus	HGIN	deoxyribose phosphate metabolic process	16/2587	42/18723	7.90e-05	1.76e-03	16
GO:00092624	Esophagus	HGIN	deoxyribonucleotide metabolic process	16/2587	44/18723	1.51e-04	2.97e-03	16
GO:00093944	Esophagus	HGIN	2'-deoxyribonucleotide metabolic process	15/2587	40/18723	1.62e-04	3.16e-03	15
GO:00092643	Esophagus	HGIN	deoxyribonucleotide catabolic process	12/2587	30/18723	3.62e-04	5.68e-03	12
GO:00463863	Esophagus	HGIN	deoxyribose phosphate catabolic process	12/2587	31/18723	5.17e-04	7.46e-03	12
GO:000911720	Esophagus	HGIN	nucleotide metabolic process	92/2587	489/18723	1.11e-03	1.36e-02	92
GO:000675320	Esophagus	HGIN	nucleoside phosphate metabolic process	93/2587	497/18723	1.25e-03	1.49e-02	93
GO:00092233	Esophagus	HGIN	pyrimidine deoxyribonucleotide catabolic process	8/2587	19/18723	2.40e-03	2.41e-02	8
GO:0006285	Esophagus	HGIN	base-excision repair, AP site formation	6/2587	12/18723	3.03e-03	2.88e-02	6
GO:00092193	Esophagus	HGIN	pyrimidine deoxyribonucleotide metabolic process	9/2587	24/18723	3.33e-03	3.12e-02	9
GO:00062442	Esophagus	HGIN	pyrimidine nucleotide catabolic process	8/2587	21/18723	5.00e-03	4.19e-02	8
GO:0034655110	Esophagus	ESCC	nucleobase-containing compound catabolic process	272/8552	407/18723	2.92e-18	2.90e-16	272
GO:004670018	Esophagus	ESCC	heterocycle catabolic process	286/8552	445/18723	1.12e-15	7.47e-14	286
GO:004427019	Esophagus	ESCC	cellular nitrogen compound catabolic process	288/8552	451/18723	3.03e-15	1.79e-13	288
GO:001943918	Esophagus	ESCC	aromatic compound catabolic process	295/8552	467/18723	1.09e-14	5.98e-13	295

Page: 1 2 3 4 5 6 7 8

Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa034104	Esophagus	ESCC	Base excision repair	38/4205	44/8465	3.59e-07	2.62e-06	1.34e-06	38
hsa0341011	Esophagus	ESCC	Base excision repair	38/4205	44/8465	3.59e-07	2.62e-06	1.34e-06	38
hsa03410	Oral cavity	OSCC	Base excision repair	32/3704	44/8465	9.11e-05	3.25e-04	1.65e-04	32
hsa034101	Oral cavity	OSCC	Base excision repair	32/3704	44/8465	9.11e-05	3.25e-04	1.65e-04	32
hsa034102	Oral cavity	LP	Base excision repair	23/2418	44/8465	7.66e-04	3.75e-03	2.42e-03	23
hsa034103	Oral cavity	LP	Base excision repair	23/2418	44/8465	7.66e-04	3.75e-03	2.42e-03	23

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

TF	Cell Type	Tissue	Disease Stage	Target Gene	RSS	Regulon Activity
MBD4	CFIB	Colorectum	AD	RAP2C-AS1,PXDC1,CNIH4, etc.	9.59e-02
MBD4	CFIB	Colorectum	CRC	RAP2C-AS1,PXDC1,CNIH4, etc.	8.60e-02
MBD4	PCV	Colorectum	CRC	RAP2C-AS1,PXDC1,CNIH4, etc.	2.64e-02
MBD4	LYMEND	Colorectum	MSS	RAP2C-AS1,PXDC1,CNIH4, etc.	4.81e-02
MBD4	TRANS	Esophagus	ADJ	CD38,TMEM45A,CNBP, etc.	3.72e-01
MBD4	MMC	Lung	Healthy	MBD6,ID2,ARL8A, etc.	1.42e-03
MBD4	CD8TEREX	Lung	MIAC	CREB3L2,HMGCS1,ANKRD42, etc.	4.24e-02
MBD4	END	Oral cavity	OSCC	HMGA1,CYB5R1,TNFSF10, etc.	1.79e-01
MBD4	STM	Pancreas	ADJ	AL121839.2,AKIP1,RND1, etc.	9.56e-03
MBD4	DUCT2	Pancreas	ADJ	AL121839.2,AKIP1,RND1, etc.	5.29e-03

∗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 2

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

MBD4

SNV

Missense_Mutation

novel

c.1637N>A

p.Arg546Gln

p.R546Q

O95243

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MBD4

SNV

Missense_Mutation

c.1483G>C

p.Asp495His

p.D495H

O95243

protein_coding

deleterious(0)

benign(0.311)

TCGA-C8-A8HQ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

MBD4

SNV

Missense_Mutation

c.58N>A

p.Val20Ile

p.V20I

O95243

protein_coding

tolerated_low_confidence(0.23)

benign(0)

TCGA-EW-A1IZ-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

taxotere

MBD4

insertion

Frame_Shift_Ins

novel

c.710_711insCCCCAAACCACAGTCTCCCACTGACCTA

p.Leu238ProfsTer16

p.L238Pfs*16

O95243

protein_coding

TCGA-B6-A0I6-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

MBD4

SNV

Missense_Mutation

rs776001887

c.208G>A

p.Ala70Thr

p.A70T

O95243

protein_coding

deleterious(0.04)

benign(0.005)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

MBD4

SNV

Missense_Mutation

c.932N>C

p.Lys311Thr

p.K311T

O95243

protein_coding

tolerated(0.36)

benign(0.021)

TCGA-FU-A3HZ-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

MBD4

SNV

Missense_Mutation

rs776001887

c.208N>A

p.Ala70Thr

p.A70T

O95243

protein_coding

deleterious(0.04)

benign(0.005)

TCGA-VS-A94Z-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

MBD4

SNV

Missense_Mutation

novel

c.1460N>T

p.Ser487Leu

p.S487L

O95243

protein_coding

deleterious(0)

probably_damaging(0.986)

TCGA-ZJ-AAXT-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Unknown

MBD4

SNV

Missense_Mutation

rs755035506

c.139N>A

p.Gly47Arg

p.G47R

O95243

protein_coding

tolerated(0.77)

benign(0)

TCGA-A6-6137-01

Colorectum

colon adenocarcinoma

Male

<65

III/IV

Chemotherapy

fluorouracil

MBD4

SNV

Missense_Mutation

novel

c.1666G>A

p.Val556Met

p.V556M

O95243

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AA-3971-01

Colorectum

colon adenocarcinoma

Male

<65

III/IV

Chemotherapy

folinic

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
8930	MBD4	DNA REPAIR		PD1 INHIBITOR		29760383

Page: 1