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: PDGFRB

Gene summary for PDGFRB

Gene summary.

Gene information	Species	Human
	Gene symbol	PDGFRB
	Gene ID	5159
	Gene name	platelet derived growth factor receptor beta
	Gene Alias	CD140B
	Cytomap	5q32
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	P09619

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
5159	PDGFRB	C43	Human	Oral cavity	OSCC	8.75e-05	-2.51e-01	0.1704
5159	PDGFRB	C46	Human	Oral cavity	OSCC	2.62e-03	-2.51e-01	0.1673
5159	PDGFRB	C08	Human	Oral cavity	OSCC	1.54e-02	-2.42e-01	0.1919
5159	PDGFRB	EOLP-1	Human	Oral cavity	EOLP	7.30e-11	5.37e-01	-0.0202
5159	PDGFRB	NEOLP-2	Human	Oral cavity	NEOLP	6.72e-13	4.40e-01	-0.0196
5159	PDGFRB	NEOLP-3	Human	Oral cavity	NEOLP	2.52e-10	5.29e-01	-0.0191
5159	PDGFRB	SYSMH1	Human	Oral cavity	OSCC	9.07e-06	-2.49e-01	0.1127
5159	PDGFRB	SYSMH2	Human	Oral cavity	OSCC	7.62e-04	-2.32e-01	0.2326
5159	PDGFRB	SYSMH3	Human	Oral cavity	OSCC	3.64e-03	-2.46e-01	0.2442
5159	PDGFRB	SYSMH4	Human	Oral cavity	OSCC	9.07e-06	-2.51e-01	0.1226
5159	PDGFRB	SYSMH5	Human	Oral cavity	OSCC	9.27e-03	-2.46e-01	0.0647
5159	PDGFRB	SYSMH6	Human	Oral cavity	OSCC	3.54e-03	-2.40e-01	0.1275
5159	PDGFRB	ATC11	Human	Thyroid	ATC	1.70e-05	7.68e-01	0.3386
5159	PDGFRB	ATC12	Human	Thyroid	ATC	2.22e-85	2.51e+00	0.34
5159	PDGFRB	ATC13	Human	Thyroid	ATC	8.31e-80	1.72e+00	0.34
5159	PDGFRB	ATC2	Human	Thyroid	ATC	3.05e-24	1.41e+00	0.34
5159	PDGFRB	ATC3	Human	Thyroid	ATC	2.30e-16	1.16e+00	0.338
5159	PDGFRB	ATC4	Human	Thyroid	ATC	3.71e-93	2.80e+00	0.34
5159	PDGFRB	ATC5	Human	Thyroid	ATC	1.96e-97	1.79e+00	0.34

Page: 1

Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
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:000697920	Oral cavity	OSCC	response to oxidative stress	273/7305	446/18723	8.35e-22	1.65e-19	273
GO:01400145	Oral cavity	OSCC	mitotic nuclear division	191/7305	287/18723	1.99e-21	3.70e-19	191
GO:00073469	Oral cavity	OSCC	regulation of mitotic cell cycle	266/7305	457/18723	3.87e-17	3.41e-15	266
GO:000030220	Oral cavity	OSCC	response to reactive oxygen species	143/7305	222/18723	1.32e-14	7.88e-13	143
GO:004254219	Oral cavity	OSCC	response to hydrogen peroxide	101/7305	146/18723	1.30e-13	6.66e-12	101
GO:005105210	Oral cavity	OSCC	regulation of DNA metabolic process	207/7305	359/18723	4.45e-13	2.17e-11	207
GO:004206020	Oral cavity	OSCC	wound healing	237/7305	422/18723	4.51e-13	2.18e-11	237
GO:007048219	Oral cavity	OSCC	response to oxygen levels	200/7305	347/18723	1.17e-12	5.13e-11	200
GO:00482852	Oral cavity	OSCC	organelle fission	265/7305	488/18723	3.22e-12	1.27e-10	265
GO:000756818	Oral cavity	OSCC	aging	194/7305	339/18723	6.18e-12	2.33e-10	194
GO:005105414	Oral cavity	OSCC	positive regulation of DNA metabolic process	126/7305	201/18723	8.12e-12	3.01e-10	126
GO:007190010	Oral cavity	OSCC	regulation of protein serine/threonine kinase activity	201/7305	359/18723	3.90e-11	1.27e-09	201
GO:00002801	Oral cavity	OSCC	nuclear division	237/7305	439/18723	9.62e-11	2.90e-09	237
GO:000647015	Oral cavity	OSCC	protein dephosphorylation	162/7305	281/18723	1.56e-10	4.56e-09	162
GO:00072659	Oral cavity	OSCC	Ras protein signal transduction	185/7305	337/18723	1.95e-09	4.60e-08	185
GO:00457879	Oral cavity	OSCC	positive regulation of cell cycle	173/7305	313/18723	3.28e-09	7.44e-08	173
GO:00163119	Oral cavity	OSCC	dephosphorylation	220/7305	417/18723	6.33e-09	1.34e-07	220
GO:003297020	Oral cavity	OSCC	regulation of actin filament-based process	209/7305	397/18723	1.89e-08	3.72e-07	209
GO:00718979	Oral cavity	OSCC	DNA biosynthetic process	106/7305	180/18723	4.86e-08	8.95e-07	106
GO:003530319	Oral cavity	OSCC	regulation of dephosphorylation	80/7305	128/18723	6.10e-08	1.10e-06	80

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

Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa051659	Oral cavity	OSCC	Human papillomavirus infection	200/3704	331/8465	3.83e-10	4.93e-09	2.51e-09	200
hsa0451019	Oral cavity	OSCC	Focal adhesion	128/3704	203/8465	1.71e-08	1.63e-07	8.31e-08	128
hsa0521510	Oral cavity	OSCC	Prostate cancer	66/3704	97/8465	1.05e-06	5.89e-06	3.00e-06	66
hsa0523016	Oral cavity	OSCC	Central carbon metabolism in cancer	49/3704	70/8465	7.57e-06	3.59e-05	1.83e-05	49
hsa0401014	Oral cavity	OSCC	MAPK signaling pathway	165/3704	302/8465	7.11e-05	2.74e-04	1.40e-04	165
hsa0481026	Oral cavity	OSCC	Regulation of actin cytoskeleton	129/3704	229/8465	7.14e-05	2.74e-04	1.40e-04	129
hsa041516	Oral cavity	OSCC	PI3K-Akt signaling pathway	185/3704	354/8465	6.26e-04	1.86e-03	9.49e-04	185
hsa0401518	Oral cavity	OSCC	Rap1 signaling pathway	107/3704	210/8465	2.01e-02	4.34e-02	2.21e-02	107
hsa0516514	Oral cavity	OSCC	Human papillomavirus infection	200/3704	331/8465	3.83e-10	4.93e-09	2.51e-09	200
hsa04510110	Oral cavity	OSCC	Focal adhesion	128/3704	203/8465	1.71e-08	1.63e-07	8.31e-08	128
hsa0521515	Oral cavity	OSCC	Prostate cancer	66/3704	97/8465	1.05e-06	5.89e-06	3.00e-06	66
hsa0523017	Oral cavity	OSCC	Central carbon metabolism in cancer	49/3704	70/8465	7.57e-06	3.59e-05	1.83e-05	49
hsa0401015	Oral cavity	OSCC	MAPK signaling pathway	165/3704	302/8465	7.11e-05	2.74e-04	1.40e-04	165
hsa04810111	Oral cavity	OSCC	Regulation of actin cytoskeleton	129/3704	229/8465	7.14e-05	2.74e-04	1.40e-04	129
hsa0415113	Oral cavity	OSCC	PI3K-Akt signaling pathway	185/3704	354/8465	6.26e-04	1.86e-03	9.49e-04	185
hsa0401519	Oral cavity	OSCC	Rap1 signaling pathway	107/3704	210/8465	2.01e-02	4.34e-02	2.21e-02	107
hsa0451026	Oral cavity	EOLP	Focal adhesion	60/1218	203/8465	1.42e-08	1.83e-07	1.08e-07	60
hsa0516541	Oral cavity	EOLP	Human papillomavirus infection	79/1218	331/8465	1.96e-06	1.63e-05	9.60e-06	79
hsa0521524	Oral cavity	EOLP	Prostate cancer	31/1218	97/8465	7.90e-06	4.73e-05	2.79e-05	31
hsa0152124	Oral cavity	EOLP	EGFR tyrosine kinase inhibitor resistance	25/1218	79/8465	7.03e-05	3.25e-04	1.91e-04	25

Page: 1 2 3

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
PDGFA	PDGFRB	PDGFA_PDGFRB	PDGF	Breast	ADJ
PDGFB	PDGFRB	PDGFB_PDGFRB	PDGF	Breast	ADJ
PDGFD	PDGFRB	PDGFD_PDGFRB	PDGF	Breast	ADJ
PDGFA	PDGFRB	PDGFA_PDGFRB	PDGF	Breast	DCIS
PDGFB	PDGFRB	PDGFB_PDGFRB	PDGF	Breast	DCIS
PDGFD	PDGFRB	PDGFD_PDGFRB	PDGF	Breast	DCIS
PDGFA	PDGFRB	PDGFA_PDGFRB	PDGF	Breast	Healthy
PDGFD	PDGFRB	PDGFD_PDGFRB	PDGF	Breast	Healthy
PDGFA	PDGFRB	PDGFA_PDGFRB	PDGF	Breast	IDC
PDGFA	PDGFRB	PDGFA_PDGFRB	PDGF	Cervix	ADJ
PDGFD	PDGFRB	PDGFD_PDGFRB	PDGF	Cervix	ADJ
PDGFA	PDGFRB	PDGFA_PDGFRB	PDGF	Cervix	CC
PDGFA	PDGFRB	PDGFA_PDGFRB	PDGF	Cervix	Precancer
PDGFD	PDGFRB	PDGFD_PDGFRB	PDGF	Cervix	Precancer
PDGFB	PDGFRB	PDGFB_PDGFRB	PDGF	CRC	AD
PDGFD	PDGFRB	PDGFD_PDGFRB	PDGF	CRC	AD
PDGFD	PDGFRB	PDGFD_PDGFRB	PDGF	CRC	ADJ
PDGFA	PDGFRB	PDGFA_PDGFRB	PDGF	CRC	CRC
PDGFD	PDGFRB	PDGFD_PDGFRB	PDGF	CRC	CRC
PDGFA	PDGFRB	PDGFA_PDGFRB	PDGF	CRC	FAP

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

PDGFRB

SNV

Missense_Mutation

rs756509220

c.1339N>G

p.Ile447Val

p.I447V

P09619

protein_coding

tolerated(0.21)

benign(0)

TCGA-A2-A0EU-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

PDGFRB

SNV

Missense_Mutation

novel

c.2668N>T

p.Gly890Trp

p.G890W

P09619

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-A7-A6VX-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

docetaxel

PDGFRB

SNV

Missense_Mutation

rs757668250

c.751N>T

p.Arg251Cys

p.R251C

P09619

protein_coding

deleterious(0.04)

probably_damaging(0.982)

TCGA-A8-A09Q-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

anastrozole

PDGFRB

SNV

Missense_Mutation

rs751904503

c.2326N>A

p.Asp776Asn

p.D776N

P09619

protein_coding

deleterious(0.01)

possibly_damaging(0.738)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

PDGFRB

SNV

Missense_Mutation

c.1310N>A

p.Arg437His

p.R437H

P09619

protein_coding

tolerated(0.47)

possibly_damaging(0.769)

TCGA-B6-A0RH-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

PDGFRB

SNV

Missense_Mutation

novel

c.871T>C

p.Cys291Arg

p.C291R

P09619

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-BH-A201-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

PDGFRB

SNV

Missense_Mutation

novel

c.3211G>A

p.Glu1071Lys

p.E1071K

P09619

protein_coding

deleterious(0.03)

benign(0.091)

TCGA-BH-A2L8-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

PDGFRB

SNV

Missense_Mutation

novel

c.1359C>A

p.Asp453Glu

p.D453E

P09619

protein_coding

deleterious(0.01)

benign(0.4)

TCGA-E2-A1B5-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

PDGFRB

SNV

Missense_Mutation

c.1858N>T

p.His620Tyr

p.H620Y

P09619

protein_coding

tolerated(1)

benign(0.194)

TCGA-GM-A2D9-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

PDGFRB

insertion

Nonsense_Mutation

novel

c.725_726insTTTTTAAGATGGAGTCTGGCTCTGTTGCCCAGGCTGGAGTGCA

p.Val243PhefsTer2

p.V243Ffs*2

P09619

protein_coding

TCGA-A2-A0CP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

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

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
5159	PDGFRB	KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TYROSINE KINASE, CELL SURFACE	inhibitor	CHEMBL576982	QUIZARTINIB
5159	PDGFRB	KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TYROSINE KINASE, CELL SURFACE	inhibitor	PAZOPANIB	PAZOPANIB
5159	PDGFRB	KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TYROSINE KINASE, CELL SURFACE		SOTRASTAURIN	SOTRASTAURIN
5159	PDGFRB	KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TYROSINE KINASE, CELL SURFACE		SORAFENIB	SORAFENIB
5159	PDGFRB	KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TYROSINE KINASE, CELL SURFACE		Imatinib	IMATINIB
5159	PDGFRB	KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TYROSINE KINASE, CELL SURFACE		PMID25656651-Compound-21a
5159	PDGFRB	KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TYROSINE KINASE, CELL SURFACE	inhibitor	249565577	FAMITINIB
5159	PDGFRB	KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TYROSINE KINASE, CELL SURFACE	inhibitor	CHEMBL2105728	CRENOLANIB
5159	PDGFRB	KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TYROSINE KINASE, CELL SURFACE	inhibitor	385612234
5159	PDGFRB	KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TYROSINE KINASE, CELL SURFACE	inhibitor	CEDIRANIB	CEDIRANIB

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