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: BCR

Gene summary for BCR

Gene summary.

Gene information	Species	Human
	Gene symbol	BCR
	Gene ID	613
	Gene name	BCR activator of RhoGEF and GTPase
	Gene Alias	ALL
	Cytomap	22q11.23
	Gene Type	protein-coding
	GO ID	GO:0006464
	UniProtAcc	P11274

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
613	BCR	HTA11_3410_2000001011	Human	Colorectum	AD	4.34e-05	3.87e-01	0.0155
613	BCR	HTA11_1938_2000001011	Human	Colorectum	AD	1.40e-08	8.14e-01	-0.0811
613	BCR	HTA11_347_2000001011	Human	Colorectum	AD	1.68e-02	3.19e-01	-0.1954
613	BCR	HTA11_411_2000001011	Human	Colorectum	SER	1.63e-05	1.03e+00	-0.2602
613	BCR	HTA11_3361_2000001011	Human	Colorectum	AD	3.25e-05	6.01e-01	-0.1207
613	BCR	HTA11_83_2000001011	Human	Colorectum	SER	2.63e-06	7.65e-01	-0.1526
613	BCR	HTA11_696_2000001011	Human	Colorectum	AD	1.49e-25	1.02e+00	-0.1464
613	BCR	HTA11_866_2000001011	Human	Colorectum	AD	7.28e-03	3.74e-01	-0.1001
613	BCR	HTA11_1391_2000001011	Human	Colorectum	AD	2.13e-04	5.44e-01	-0.059
613	BCR	HTA11_2992_2000001011	Human	Colorectum	SER	1.30e-07	1.03e+00	-0.1706
613	BCR	HTA11_5212_2000001011	Human	Colorectum	AD	6.26e-07	8.79e-01	-0.2061
613	BCR	HTA11_5216_2000001011	Human	Colorectum	SER	1.55e-05	9.51e-01	-0.1462
613	BCR	HTA11_546_2000001011	Human	Colorectum	AD	1.11e-11	1.06e+00	-0.0842
613	BCR	A015-C-203	Human	Colorectum	FAP	3.77e-12	-1.68e-01	-0.1294
613	BCR	A002-C-201	Human	Colorectum	FAP	4.04e-04	-7.30e-02	0.0324
613	BCR	A001-C-119	Human	Colorectum	FAP	2.74e-02	-1.01e-01	-0.1557
613	BCR	A001-C-108	Human	Colorectum	FAP	2.41e-05	-1.36e-01	-0.0272
613	BCR	A002-C-205	Human	Colorectum	FAP	1.67e-09	-2.09e-01	-0.1236
613	BCR	A015-C-006	Human	Colorectum	FAP	1.07e-06	-1.45e-01	-0.0994
613	BCR	A015-C-106	Human	Colorectum	FAP	1.69e-04	-2.11e-01	-0.0511

Page: 1 2 3 4 5 6

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
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
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:0034329	Colorectum	AD	cell junction assembly	136/3918	420/18723	2.02e-08	1.15e-06	136
GO:0150115	Colorectum	AD	cell-substrate junction organization	44/3918	101/18723	2.38e-07	9.81e-06	44
GO:0031589	Colorectum	AD	cell-substrate adhesion	116/3918	363/18723	4.68e-07	1.76e-05	116
GO:0007044	Colorectum	AD	cell-substrate junction assembly	41/3918	95/18723	8.20e-07	2.85e-05	41
GO:0043087	Colorectum	AD	regulation of GTPase activity	110/3918	348/18723	1.64e-06	5.03e-05	110
GO:0007265	Colorectum	AD	Ras protein signal transduction	104/3918	337/18723	1.01e-05	2.35e-04	104
GO:0051056	Colorectum	AD	regulation of small GTPase mediated signal transduction	94/3918	302/18723	1.81e-05	3.76e-04	94
GO:0046777	Colorectum	AD	protein autophosphorylation	74/3918	227/18723	2.48e-05	4.76e-04	74
GO:0007160	Colorectum	AD	cell-matrix adhesion	75/3918	233/18723	3.56e-05	6.45e-04	75
GO:0048041	Colorectum	AD	focal adhesion assembly	34/3918	87/18723	8.30e-05	1.30e-03	34
GO:0043547	Colorectum	AD	positive regulation of GTPase activity	75/3918	255/18723	7.95e-04	7.91e-03	75
GO:0046578	Colorectum	AD	regulation of Ras protein signal transduction	56/3918	189/18723	2.85e-03	2.14e-02	56
GO:0007266	Colorectum	AD	Rho protein signal transduction	42/3918	137/18723	4.64e-03	3.16e-02	42
GO:0009913	Colorectum	AD	epidermal cell differentiation	58/3918	202/18723	5.16e-03	3.42e-02	58
GO:0008544	Colorectum	AD	epidermis development	87/3918	324/18723	5.99e-03	3.76e-02	87
GO:00343291	Colorectum	SER	cell junction assembly	100/2897	420/18723	4.23e-06	1.61e-04	100
GO:01501151	Colorectum	SER	cell-substrate junction organization	34/2897	101/18723	4.46e-06	1.67e-04	34
GO:00467771	Colorectum	SER	protein autophosphorylation	60/2897	227/18723	1.36e-05	4.25e-04	60
GO:00070441	Colorectum	SER	cell-substrate junction assembly	31/2897	95/18723	2.34e-05	6.64e-04	31
GO:00315891	Colorectum	SER	cell-substrate adhesion	86/2897	363/18723	2.36e-05	6.64e-04	86

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
hsa05220	Colorectum	AD	Chronic myeloid leukemia	31/2092	76/8465	1.41e-03	8.46e-03	5.39e-03	31
hsa052201	Colorectum	AD	Chronic myeloid leukemia	31/2092	76/8465	1.41e-03	8.46e-03	5.39e-03	31
hsa052204	Colorectum	FAP	Chronic myeloid leukemia	23/1404	76/8465	2.14e-03	1.05e-02	6.39e-03	23
hsa052205	Colorectum	FAP	Chronic myeloid leukemia	23/1404	76/8465	2.14e-03	1.05e-02	6.39e-03	23
hsa052206	Colorectum	CRC	Chronic myeloid leukemia	18/1091	76/8465	6.86e-03	3.37e-02	2.28e-02	18
hsa052207	Colorectum	CRC	Chronic myeloid leukemia	18/1091	76/8465	6.86e-03	3.37e-02	2.28e-02	18
hsa0522021	Liver	HCC	Chronic myeloid leukemia	55/4020	76/8465	8.67e-06	6.91e-05	3.84e-05	55
hsa0522031	Liver	HCC	Chronic myeloid leukemia	55/4020	76/8465	8.67e-06	6.91e-05	3.84e-05	55
hsa0522018	Oral cavity	OSCC	Chronic myeloid leukemia	56/3704	76/8465	1.04e-07	7.43e-07	3.78e-07	56
hsa0522019	Oral cavity	OSCC	Chronic myeloid leukemia	56/3704	76/8465	1.04e-07	7.43e-07	3.78e-07	56
hsa0522025	Oral cavity	LP	Chronic myeloid leukemia	37/2418	76/8465	1.53e-04	9.08e-04	5.86e-04	37
hsa0522035	Oral cavity	LP	Chronic myeloid leukemia	37/2418	76/8465	1.53e-04	9.08e-04	5.86e-04	37

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

BCR

SNV

Missense_Mutation

c.900G>C

p.Gln300His

p.Q300H

P11274

protein_coding

tolerated_low_confidence(0.47)

benign(0.275)

TCGA-AN-A0FT-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

BCR

SNV

Missense_Mutation

c.2311N>C

p.Glu771Gln

p.E771Q

P11274

protein_coding

deleterious(0.04)

possibly_damaging(0.688)

TCGA-BH-A209-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

BCR

SNV

Missense_Mutation

novel

c.3671N>C

p.Asn1224Thr

p.N1224T

P11274

protein_coding

tolerated(0.15)

benign(0.001)

TCGA-D8-A1JU-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

BCR

SNV

Missense_Mutation

c.2710N>A

p.Asp904Asn

p.D904N

P11274

protein_coding

deleterious(0.03)

benign(0.41)

TCGA-GM-A2D9-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

BCR

insertion

In_Frame_Ins

novel

c.2067_2068insTTAGTACCAGGAATTAATCTCAGCTCCTTCCCA

p.Asn689_Glu690insLeuValProGlyIleAsnLeuSerSerPhePro

p.N689_E690insLVPGINLSSFP

P11274

protein_coding

TCGA-B6-A0IE-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

BCR

deletion

Frame_Shift_Del

novel

c.2203delC

p.Leu735PhefsTer53

p.L735Ffs*53

P11274

protein_coding

TCGA-D8-A27V-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

BCR

SNV

Missense_Mutation

rs775101020

c.1607N>T

p.Pro536Leu

p.P536L

P11274

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

BCR

SNV

Missense_Mutation

novel

c.3656N>A

p.Ser1219Asn

p.S1219N

P11274

protein_coding

deleterious(0.03)

benign(0.104)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

BCR

SNV

Missense_Mutation

c.1816N>C

p.Glu606Gln

p.E606Q

P11274

protein_coding

tolerated(0.1)

benign(0.217)

TCGA-C5-A1BQ-01

Cervix

cervical & endocervical cancer

Female

>=65

III/IV

Chemotherapy

cisplatin

BCR

SNV

Missense_Mutation

c.1816N>C

p.Glu606Gln

p.E606Q

P11274

protein_coding

tolerated(0.1)

benign(0.217)

TCGA-C5-A3HL-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Unknown

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

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
613	BCR	TUMOR SUPPRESSOR, SERINE THREONINE KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, KINASE, ENZYME, DRUGGABLE GENOME		ponatinib	PONATINIB
613	BCR	TUMOR SUPPRESSOR, SERINE THREONINE KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, KINASE, ENZYME, DRUGGABLE GENOME		Nilotinib	NILOTINIB
613	BCR	TUMOR SUPPRESSOR, SERINE THREONINE KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, KINASE, ENZYME, DRUGGABLE GENOME		Ponatinib	PONATINIB
613	BCR	TUMOR SUPPRESSOR, SERINE THREONINE KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, KINASE, ENZYME, DRUGGABLE GENOME		nilotinib	NILOTINIB
613	BCR	TUMOR SUPPRESSOR, SERINE THREONINE KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, KINASE, ENZYME, DRUGGABLE GENOME		IMATINIB	IMATINIB	22148584,24681986
613	BCR	TUMOR SUPPRESSOR, SERINE THREONINE KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, KINASE, ENZYME, DRUGGABLE GENOME		Imatinib	IMATINIB
613	BCR	TUMOR SUPPRESSOR, SERINE THREONINE KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, KINASE, ENZYME, DRUGGABLE GENOME		busulfan	BUSULFAN
613	BCR	TUMOR SUPPRESSOR, SERINE THREONINE KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, KINASE, ENZYME, DRUGGABLE GENOME		Bosutinib	BOSUTINIB
613	BCR	TUMOR SUPPRESSOR, SERINE THREONINE KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, KINASE, ENZYME, DRUGGABLE GENOME		GNF-2	CHEMBL483847	16415863
613	BCR	TUMOR SUPPRESSOR, SERINE THREONINE KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE, KINASE, ENZYME, DRUGGABLE GENOME		vincristine	VINCRISTINE

Page: 1 2 3