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: COPB2

Gene summary for COPB2

Gene summary.

Gene information	Species	Human
	Gene symbol	COPB2
	Gene ID	9276
	Gene name	COPI coat complex subunit beta 2
	Gene Alias	MCPH19
	Cytomap	3q23
	Gene Type	protein-coding
	GO ID	GO:0006810
	UniProtAcc	P35606

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
9276	COPB2	GSM4909281	Human	Breast	IDC	5.69e-06	3.50e-01	0.21
9276	COPB2	GSM4909285	Human	Breast	IDC	2.80e-10	4.07e-01	0.21
9276	COPB2	GSM4909293	Human	Breast	IDC	2.20e-12	4.03e-01	0.1581
9276	COPB2	GSM4909296	Human	Breast	IDC	6.81e-05	-1.55e-01	0.1524
9276	COPB2	GSM4909297	Human	Breast	IDC	6.52e-04	-1.14e-01	0.1517
9276	COPB2	GSM4909304	Human	Breast	IDC	5.49e-03	2.65e-01	0.1636
9276	COPB2	GSM4909311	Human	Breast	IDC	2.15e-14	-1.26e-01	0.1534
9276	COPB2	GSM4909312	Human	Breast	IDC	1.44e-05	4.00e-02	0.1552
9276	COPB2	GSM4909319	Human	Breast	IDC	1.38e-14	-1.64e-01	0.1563
9276	COPB2	GSM4909321	Human	Breast	IDC	1.75e-06	-1.36e-01	0.1559
9276	COPB2	brca2	Human	Breast	Precancer	1.37e-09	3.29e-01	-0.024
9276	COPB2	brca3	Human	Breast	Precancer	2.79e-03	2.58e-01	-0.0263
9276	COPB2	NCCBC14	Human	Breast	DCIS	2.54e-14	5.67e-01	0.2021
9276	COPB2	P1	Human	Breast	IDC	1.11e-03	-1.50e-02	0.1527
9276	COPB2	P2	Human	Breast	IDC	6.53e-07	4.89e-01	0.21
9276	COPB2	DCIS2	Human	Breast	DCIS	4.64e-60	3.00e-01	0.0085
9276	COPB2	HTA11_347_2000001011	Human	Colorectum	AD	7.55e-06	4.27e-01	-0.1954
9276	COPB2	HTA11_99999970781_79442	Human	Colorectum	MSS	2.46e-05	4.72e-01	0.294
9276	COPB2	A015-C-203	Human	Colorectum	FAP	2.64e-08	-1.64e-01	-0.1294
9276	COPB2	A001-C-108	Human	Colorectum	FAP	1.73e-02	1.15e-02	-0.0272

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

Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Breast		IDC: Invasive ductal carcinoma
		DCIS: Ductal carcinoma in situ
		Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
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
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:19019983	Breast	Precancer	toxin transport	9/1080	40/18723	3.69e-04	5.03e-03	9
GO:19019981	Breast	IDC	toxin transport	9/1434	40/18723	2.76e-03	2.42e-02	9
GO:00068906	Breast	IDC	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	10/1434	52/18723	5.49e-03	4.03e-02	10
GO:19019982	Breast	DCIS	toxin transport	9/1390	40/18723	2.23e-03	2.04e-02	9
GO:000689012	Breast	DCIS	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	10/1390	52/18723	4.41e-03	3.41e-02	10
GO:0048193	Colorectum	AD	Golgi vesicle transport	109/3918	296/18723	1.80e-10	1.68e-08	109
GO:0006890	Colorectum	AD	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	27/3918	52/18723	7.67e-07	2.70e-05	27
GO:0006888	Colorectum	AD	endoplasmic reticulum to Golgi vesicle-mediated transport	44/3918	130/18723	4.13e-04	4.68e-03	44
GO:00481932	Colorectum	MSS	Golgi vesicle transport	101/3467	296/18723	9.09e-11	9.77e-09	101
GO:00068902	Colorectum	MSS	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	26/3467	52/18723	2.66e-07	1.10e-05	26
GO:00068882	Colorectum	MSS	endoplasmic reticulum to Golgi vesicle-mediated transport	44/3467	130/18723	2.17e-05	4.60e-04	44
GO:00481934	Colorectum	FAP	Golgi vesicle transport	77/2622	296/18723	2.86e-08	2.62e-06	77
GO:00068904	Colorectum	FAP	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	18/2622	52/18723	1.48e-04	2.29e-03	18
GO:00068884	Colorectum	FAP	endoplasmic reticulum to Golgi vesicle-mediated transport	30/2622	130/18723	3.51e-03	2.53e-02	30
GO:004819317	Esophagus	HGIN	Golgi vesicle transport	83/2587	296/18723	8.59e-11	8.89e-09	83
GO:00068889	Esophagus	HGIN	endoplasmic reticulum to Golgi vesicle-mediated transport	40/2587	130/18723	4.67e-07	2.07e-05	40
GO:000689016	Esophagus	HGIN	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	19/2587	52/18723	3.44e-05	8.67e-04	19
GO:004819318	Esophagus	ESCC	Golgi vesicle transport	231/8552	296/18723	1.82e-30	9.63e-28	231
GO:000688815	Esophagus	ESCC	endoplasmic reticulum to Golgi vesicle-mediated transport	102/8552	130/18723	1.73e-14	9.22e-13	102
GO:000689017	Esophagus	ESCC	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	46/8552	52/18723	1.23e-10	3.66e-09	46

Page: 1 2 3 4

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

COPB2

SNV

Missense_Mutation

novel

c.1682T>G

p.Met561Arg

p.M561R

P35606

protein_coding

deleterious(0)

possibly_damaging(0.61)

TCGA-A7-A0CJ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

COPB2

SNV

Missense_Mutation

novel

c.2240N>T

p.Arg747Ile

p.R747I

P35606

protein_coding

deleterious(0.02)

benign(0.062)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COPB2

SNV

Missense_Mutation

novel

c.1894N>A

p.Gln632Lys

p.Q632K

P35606

protein_coding

tolerated(0.17)

benign(0.01)

TCGA-BH-A0AV-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

COPB2

SNV

Missense_Mutation

c.935G>A

p.Gly312Glu

p.G312E

P35606

protein_coding

deleterious(0)

probably_damaging(0.95)

TCGA-D8-A142-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

cyclophosphamid

COPB2

SNV

Missense_Mutation

novel

c.547N>A

p.Gly183Arg

p.G183R

P35606

protein_coding

deleterious(0)

probably_damaging(0.997)

TCGA-LL-A8F5-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

COPB2

insertion

Frame_Shift_Ins

novel

c.1679_1680insTTCTCCTTTCTCAGTGCCCCCTTTAAATGTTG

p.Met561SerfsTer15

p.M561Sfs*15

P35606

protein_coding

TCGA-A7-A0CJ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

COPB2

deletion

Frame_Shift_Del

novel

c.2349delN

p.Ala784GlnfsTer18

p.A784Qfs*18

P35606

protein_coding

TCGA-D8-A27V-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

COPB2

insertion

In_Frame_Ins

rs766565677

c.592_593insGGA

p.Asp198delinsGlyAsn

p.D198delinsGN

P35606

protein_coding

TCGA-E9-A1NG-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

letrozole

COPB2

SNV

Missense_Mutation

c.2582N>T

p.Thr861Ile

p.T861I

P35606

protein_coding

tolerated(0.29)

benign(0.034)

TCGA-HM-A4S6-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Chemotherapy

cisplatin

COPB2

SNV

Missense_Mutation

rs745412053

c.902N>A

p.Arg301Gln

p.R301Q

P35606

protein_coding

deleterious(0.02)

benign(0.241)

TCGA-MA-AA42-01

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

Page: 1