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: F2R

Gene summary for F2R

Gene summary.

Gene information	Species	Human
	Gene symbol	F2R
	Gene ID	2149
	Gene name	coagulation factor II thrombin receptor
	Gene Alias	CF2R
	Cytomap	5q13.3
	Gene Type	protein-coding
	GO ID	GO:0000165
	UniProtAcc	P25116

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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
2149	F2R	LZE4T	Human	Esophagus	ESCC	6.58e-09	9.37e-02	0.0811
2149	F2R	LZE24T	Human	Esophagus	ESCC	8.04e-04	7.79e-02	0.0596
2149	F2R	P2T-E	Human	Esophagus	ESCC	4.63e-04	5.74e-02	0.1177
2149	F2R	P9T-E	Human	Esophagus	ESCC	5.05e-13	3.89e-01	0.1131
2149	F2R	P10T-E	Human	Esophagus	ESCC	4.05e-16	2.78e-01	0.116
2149	F2R	P11T-E	Human	Esophagus	ESCC	2.51e-04	4.12e-01	0.1426
2149	F2R	P12T-E	Human	Esophagus	ESCC	4.19e-09	2.64e-01	0.1122
2149	F2R	P15T-E	Human	Esophagus	ESCC	1.45e-03	2.26e-01	0.1149
2149	F2R	P19T-E	Human	Esophagus	ESCC	1.41e-05	7.12e-01	0.1662
2149	F2R	P20T-E	Human	Esophagus	ESCC	1.20e-02	1.42e-01	0.1124
2149	F2R	P21T-E	Human	Esophagus	ESCC	1.04e-19	4.74e-01	0.1617
2149	F2R	P22T-E	Human	Esophagus	ESCC	1.66e-10	1.63e-01	0.1236
2149	F2R	P26T-E	Human	Esophagus	ESCC	6.03e-03	4.83e-02	0.1276
2149	F2R	P28T-E	Human	Esophagus	ESCC	2.74e-09	1.37e-01	0.1149
2149	F2R	P30T-E	Human	Esophagus	ESCC	1.35e-02	3.82e-01	0.137
2149	F2R	P31T-E	Human	Esophagus	ESCC	2.35e-19	3.27e-01	0.1251
2149	F2R	P49T-E	Human	Esophagus	ESCC	2.52e-11	1.10e+00	0.1768
2149	F2R	P57T-E	Human	Esophagus	ESCC	1.92e-03	1.43e-01	0.0926
2149	F2R	P62T-E	Human	Esophagus	ESCC	1.33e-03	4.05e-02	0.1302
2149	F2R	P75T-E	Human	Esophagus	ESCC	5.92e-05	2.28e-02	0.1125

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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
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:0016032	Colorectum	AD	viral process	168/3918	415/18723	4.67e-20	3.66e-17	168
GO:0048732	Colorectum	AD	gland development	149/3918	436/18723	6.07e-11	6.33e-09	149
GO:0044403	Colorectum	AD	biological process involved in symbiotic interaction	99/3918	290/18723	1.02e-07	4.93e-06	99
GO:0007034	Colorectum	AD	vacuolar transport	60/3918	157/18723	4.97e-07	1.85e-05	60
GO:0061008	Colorectum	AD	hepaticobiliary system development	55/3918	150/18723	6.34e-06	1.59e-04	55
GO:0001889	Colorectum	AD	liver development	54/3918	147/18723	7.20e-06	1.77e-04	54
GO:0007041	Colorectum	AD	lysosomal transport	42/3918	114/18723	6.61e-05	1.07e-03	42
GO:0006898	Colorectum	AD	receptor-mediated endocytosis	76/3918	244/18723	1.07e-04	1.59e-03	76
GO:0009791	Colorectum	AD	post-embryonic development	29/3918	80/18723	1.13e-03	1.03e-02	29
GO:0035821	Colorectum	AD	modulation of process of other organism	34/3918	106/18723	4.73e-03	3.22e-02	34
GO:0031100	Colorectum	AD	animal organ regeneration	26/3918	76/18723	4.94e-03	3.32e-02	26
GO:00160321	Colorectum	SER	viral process	118/2897	415/18723	8.36e-12	1.65e-09	118
GO:00487321	Colorectum	SER	gland development	112/2897	436/18723	1.75e-08	1.28e-06	112
GO:00610081	Colorectum	SER	hepaticobiliary system development	45/2897	150/18723	4.98e-06	1.85e-04	45
GO:00018891	Colorectum	SER	liver development	44/2897	147/18723	6.73e-06	2.35e-04	44
GO:00444031	Colorectum	SER	biological process involved in symbiotic interaction	72/2897	290/18723	2.08e-05	6.02e-04	72
GO:00070341	Colorectum	SER	vacuolar transport	43/2897	157/18723	8.92e-05	1.93e-03	43
GO:0048009	Colorectum	SER	insulin-like growth factor receptor signaling pathway	14/2897	37/18723	7.80e-04	9.87e-03	14
GO:00097911	Colorectum	SER	post-embryonic development	22/2897	80/18723	4.12e-03	3.36e-02	22
GO:00160322	Colorectum	MSS	viral process	157/3467	415/18723	7.94e-21	6.19e-18	157

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa05130211	Esophagus	ESCC	Pathogenic Escherichia coli infection	142/4205	197/8465	8.21e-11	1.06e-09	5.42e-10	142
hsa0481028	Esophagus	ESCC	Regulation of actin cytoskeleton	133/4205	229/8465	5.94e-03	1.48e-02	7.56e-03	133
hsa041517	Esophagus	ESCC	PI3K-Akt signaling pathway	197/4205	354/8465	1.24e-02	2.83e-02	1.45e-02	197
hsa05130310	Esophagus	ESCC	Pathogenic Escherichia coli infection	142/4205	197/8465	8.21e-11	1.06e-09	5.42e-10	142
hsa04810112	Esophagus	ESCC	Regulation of actin cytoskeleton	133/4205	229/8465	5.94e-03	1.48e-02	7.56e-03	133
hsa0415114	Esophagus	ESCC	PI3K-Akt signaling pathway	197/4205	354/8465	1.24e-02	2.83e-02	1.45e-02	197
hsa0481021	Liver	Cirrhotic	Regulation of actin cytoskeleton	100/2530	229/8465	5.28e-06	5.50e-05	3.39e-05	100
hsa0513022	Liver	Cirrhotic	Pathogenic Escherichia coli infection	88/2530	197/8465	6.48e-06	6.24e-05	3.84e-05	88
hsa0481031	Liver	Cirrhotic	Regulation of actin cytoskeleton	100/2530	229/8465	5.28e-06	5.50e-05	3.39e-05	100
hsa0513032	Liver	Cirrhotic	Pathogenic Escherichia coli infection	88/2530	197/8465	6.48e-06	6.24e-05	3.84e-05	88
hsa0513042	Liver	HCC	Pathogenic Escherichia coli infection	129/4020	197/8465	2.02e-07	2.50e-06	1.39e-06	129
hsa046104	Liver	HCC	Complement and coagulation cascades	57/4020	86/8465	3.19e-04	1.45e-03	8.04e-04	57
hsa0481041	Liver	HCC	Regulation of actin cytoskeleton	134/4020	229/8465	4.48e-04	1.94e-03	1.08e-03	134
hsa046112	Liver	HCC	Platelet activation	71/4020	124/8465	1.77e-02	4.15e-02	2.31e-02	71
hsa0513052	Liver	HCC	Pathogenic Escherichia coli infection	129/4020	197/8465	2.02e-07	2.50e-06	1.39e-06	129
hsa046105	Liver	HCC	Complement and coagulation cascades	57/4020	86/8465	3.19e-04	1.45e-03	8.04e-04	57
hsa0481051	Liver	HCC	Regulation of actin cytoskeleton	134/4020	229/8465	4.48e-04	1.94e-03	1.08e-03	134
hsa0461111	Liver	HCC	Platelet activation	71/4020	124/8465	1.77e-02	4.15e-02	2.31e-02	71

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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
GZMA	F2R	GZMA_F2R	PARs	Breast	ADJ
GZMA	F2RL2	GZMA_F2RL2	PARs	Breast	ADJ
GZMA	F2R	GZMA_F2R	PARs	Breast	DCIS
CTSG	F2RL3	CTSG_F2RL3	PARs	Breast	Healthy
GZMA	F2RL3	GZMA_F2RL3	PARs	Breast	Healthy
GZMA	F2R	GZMA_F2R	PARs	Breast	IDC
CTSG	F2R	CTSG_F2R	PARs	Cervix	ADJ
GZMA	F2R	GZMA_F2R	PARs	Cervix	ADJ
PRSS3	F2R	PRSS3_F2R	PARs	Cervix	CC
CTSG	F2R	CTSG_F2R	PARs	Cervix	CC
GZMA	F2R	GZMA_F2R	PARs	Cervix	CC
GZMA	F2R	GZMA_F2R	PARs	Cervix	Healthy
CTSG	F2R	CTSG_F2R	PARs	Cervix	Precancer
GZMA	F2R	GZMA_F2R	PARs	Cervix	Precancer
PRSS3	F2R	PRSS3_F2R	PARs	CRC	AD
CTSG	F2R	CTSG_F2R	PARs	CRC	AD
GZMA	F2R	GZMA_F2R	PARs	CRC	AD
PRSS3	F2RL3	PRSS3_F2RL3	PARs	CRC	AD
CTSG	F2RL3	CTSG_F2RL3	PARs	CRC	AD
GZMA	F2RL3	GZMA_F2RL3	PARs	CRC	AD

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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

F2R

SNV

Missense_Mutation

c.978N>G

p.Phe326Leu

p.F326L

P25116

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-A7-A13D-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

F2R

SNV

Missense_Mutation

c.253N>A

p.Pro85Thr

p.P85T

P25116

protein_coding

tolerated(0.39)

benign(0.005)

TCGA-AO-A03R-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

F2R

SNV

Missense_Mutation

novel

c.1106N>C

p.Leu369Pro

p.L369P

P25116

protein_coding

deleterious(0)

probably_damaging(0.983)

TCGA-AO-A0JI-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

F2R

SNV

Missense_Mutation

c.250N>T

p.Leu84Phe

p.L84F

P25116

protein_coding

tolerated(0.69)

benign(0.063)

TCGA-BH-A0HF-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

F2R

SNV

Missense_Mutation

c.238N>G

p.Leu80Val

p.L80V

P25116

protein_coding

tolerated(0.55)

benign(0.039)

TCGA-BH-A1FM-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

F2R

insertion

Frame_Shift_Ins

novel

c.391_392insACACTACCAGGCTCTGCTCTGCTGTCTCTGAGTTGGTACTACTC

p.Met131AsnfsTer16

p.M131Nfs*16

P25116

protein_coding

TCGA-BH-A0B1-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

adriamycin

F2R

SNV

Missense_Mutation

c.299N>C

p.Trp100Ser

p.W100S

P25116

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-C5-A1BI-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Chemotherapy

cisplatin

F2R

SNV

Missense_Mutation

novel

c.727N>C

p.Thr243Pro

p.T243P

P25116

protein_coding

deleterious(0)

probably_damaging(0.936)

TCGA-FU-A3HZ-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

F2R

SNV

Missense_Mutation

novel

c.517N>A

p.Glu173Lys

p.E173K

P25116

protein_coding

tolerated(0.57)

benign(0.096)

TCGA-HM-A4S6-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Chemotherapy

cisplatin

F2R

SNV

Missense_Mutation

c.1210N>G

p.Met404Val

p.M404V

P25116

protein_coding

tolerated(0.19)

benign(0)

TCGA-A6-6780-01

Colorectum

colon adenocarcinoma

Male

>=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
2149	F2R	G PROTEIN COUPLED RECEPTOR, DRUGGABLE GENOME, CELL SURFACE	inhibitor	CHEMBL2013119	RIGOSERTIB SODIUM
2149	F2R	G PROTEIN COUPLED RECEPTOR, DRUGGABLE GENOME, CELL SURFACE		TYROSINE KINASE INHIBITOR		15383630
2149	F2R	G PROTEIN COUPLED RECEPTOR, DRUGGABLE GENOME, CELL SURFACE		MORPHINE	MORPHINE	12373743
2149	F2R	G PROTEIN COUPLED RECEPTOR, DRUGGABLE GENOME, CELL SURFACE		ETHANOL	ALCOHOL	16930224
2149	F2R	G PROTEIN COUPLED RECEPTOR, DRUGGABLE GENOME, CELL SURFACE	antagonist	405560412
2149	F2R	G PROTEIN COUPLED RECEPTOR, DRUGGABLE GENOME, CELL SURFACE	antagonist	CHEMBL2103856	ATOPAXAR
2149	F2R	G PROTEIN COUPLED RECEPTOR, DRUGGABLE GENOME, CELL SURFACE	antagonist	CHEMBL2107386	VORAPAXAR SULFATE
2149	F2R	G PROTEIN COUPLED RECEPTOR, DRUGGABLE GENOME, CELL SURFACE		WORTMANNIN	WORTMANNIN	10318860,7559410,8955143
2149	F2R	G PROTEIN COUPLED RECEPTOR, DRUGGABLE GENOME, CELL SURFACE	antagonist	178100871	VORAPAXAR
2149	F2R	G PROTEIN COUPLED RECEPTOR, DRUGGABLE GENOME, CELL SURFACE	agonist	178100667

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