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: COPG1

Gene summary for COPG1

Gene summary.

Gene information	Species	Human
	Gene symbol	COPG1
	Gene ID	22820
	Gene name	COPI coat complex subunit gamma 1
	Gene Alias	COPG
	Cytomap	3q21.3
	Gene Type	protein-coding
	GO ID	GO:0006810
	UniProtAcc	Q9Y678

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
22820	COPG1	P40T-E	Human	Esophagus	ESCC	2.75e-20	7.21e-01	0.109
22820	COPG1	P42T-E	Human	Esophagus	ESCC	5.28e-27	7.01e-01	0.1175
22820	COPG1	P44T-E	Human	Esophagus	ESCC	1.03e-22	5.67e-01	0.1096
22820	COPG1	P47T-E	Human	Esophagus	ESCC	3.41e-41	7.53e-01	0.1067
22820	COPG1	P48T-E	Human	Esophagus	ESCC	2.81e-21	4.07e-01	0.0959
22820	COPG1	P49T-E	Human	Esophagus	ESCC	2.11e-17	1.67e+00	0.1768
22820	COPG1	P52T-E	Human	Esophagus	ESCC	2.92e-40	8.56e-01	0.1555
22820	COPG1	P54T-E	Human	Esophagus	ESCC	1.49e-34	7.61e-01	0.0975
22820	COPG1	P56T-E	Human	Esophagus	ESCC	3.29e-15	1.57e+00	0.1613
22820	COPG1	P57T-E	Human	Esophagus	ESCC	1.05e-23	4.25e-01	0.0926
22820	COPG1	P61T-E	Human	Esophagus	ESCC	4.74e-45	1.13e+00	0.099
22820	COPG1	P62T-E	Human	Esophagus	ESCC	7.99e-64	1.06e+00	0.1302
22820	COPG1	P65T-E	Human	Esophagus	ESCC	8.08e-37	8.10e-01	0.0978
22820	COPG1	P74T-E	Human	Esophagus	ESCC	1.75e-59	1.36e+00	0.1479
22820	COPG1	P75T-E	Human	Esophagus	ESCC	2.34e-34	8.27e-01	0.1125
22820	COPG1	P76T-E	Human	Esophagus	ESCC	3.41e-54	8.43e-01	0.1207
22820	COPG1	P79T-E	Human	Esophagus	ESCC	1.27e-51	9.46e-01	0.1154
22820	COPG1	P80T-E	Human	Esophagus	ESCC	9.79e-45	1.12e+00	0.155
22820	COPG1	P82T-E	Human	Esophagus	ESCC	3.07e-27	1.01e+00	0.1072
22820	COPG1	P83T-E	Human	Esophagus	ESCC	1.54e-38	9.94e-01	0.1738

Page: 1 2 3 4 5 6 7 8

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
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:0048193	Colorectum	AD	Golgi vesicle transport	109/3918	296/18723	1.80e-10	1.68e-08	109
GO:0051656	Colorectum	AD	establishment of organelle localization	131/3918	390/18723	3.00e-09	2.06e-07	131
GO:0009306	Colorectum	AD	protein secretion	105/3918	359/18723	1.05e-04	1.57e-03	105
GO:0035592	Colorectum	AD	establishment of protein localization to extracellular region	105/3918	360/18723	1.18e-04	1.73e-03	105
GO:0071692	Colorectum	AD	protein localization to extracellular region	106/3918	368/18723	1.86e-04	2.49e-03	106
GO:0006888	Colorectum	AD	endoplasmic reticulum to Golgi vesicle-mediated transport	44/3918	130/18723	4.13e-04	4.68e-03	44
GO:0030705	Colorectum	AD	cytoskeleton-dependent intracellular transport	60/3918	195/18723	7.56e-04	7.59e-03	60
GO:0072384	Colorectum	AD	organelle transport along microtubule	28/3918	85/18723	6.55e-03	4.07e-02	28
GO:00516561	Colorectum	SER	establishment of organelle localization	100/2897	390/18723	1.11e-07	6.79e-06	100
GO:00481931	Colorectum	SER	Golgi vesicle transport	79/2897	296/18723	4.20e-07	2.15e-05	79
GO:00093061	Colorectum	SER	protein secretion	79/2897	359/18723	5.99e-04	8.19e-03	79
GO:00355921	Colorectum	SER	establishment of protein localization to extracellular region	79/2897	360/18723	6.54e-04	8.77e-03	79
GO:00716921	Colorectum	SER	protein localization to extracellular region	80/2897	368/18723	8.13e-04	1.01e-02	80
GO:00068881	Colorectum	SER	endoplasmic reticulum to Golgi vesicle-mediated transport	34/2897	130/18723	1.13e-03	1.29e-02	34
GO:00307051	Colorectum	SER	cytoskeleton-dependent intracellular transport	44/2897	195/18723	5.53e-03	4.09e-02	44
GO:00481932	Colorectum	MSS	Golgi vesicle transport	101/3467	296/18723	9.09e-11	9.77e-09	101
GO:00516562	Colorectum	MSS	establishment of organelle localization	115/3467	390/18723	7.30e-08	3.67e-06	115
GO:00068882	Colorectum	MSS	endoplasmic reticulum to Golgi vesicle-mediated transport	44/3467	130/18723	2.17e-05	4.60e-04	44
GO:00093062	Colorectum	MSS	protein secretion	98/3467	359/18723	2.43e-05	5.09e-04	98
GO:00355922	Colorectum	MSS	establishment of protein localization to extracellular region	98/3467	360/18723	2.75e-05	5.58e-04	98

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

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

COPG1

SNV

Missense_Mutation

novel

c.1942N>T

p.Ile648Phe

p.I648F

Q9Y678

protein_coding

deleterious(0)

benign(0.415)

TCGA-A7-A3J0-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

anastrazole

COPG1

SNV

Missense_Mutation

c.1339N>A

p.Glu447Lys

p.E447K

Q9Y678

protein_coding

deleterious(0.02)

probably_damaging(0.983)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COPG1

SNV

Missense_Mutation

novel

c.706N>A

p.Ala236Thr

p.A236T

Q9Y678

protein_coding

tolerated(0.21)

benign(0.078)

TCGA-AN-A0AK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COPG1

SNV

Missense_Mutation

novel

c.1907N>A

p.Pro636His

p.P636H

Q9Y678

protein_coding

deleterious(0)

possibly_damaging(0.783)

TCGA-AN-A0AK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COPG1

SNV

Missense_Mutation

novel

c.425G>C

p.Arg142Pro

p.R142P

Q9Y678

protein_coding

deleterious(0)

probably_damaging(0.992)

TCGA-B6-A0X1-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

COPG1

SNV

Missense_Mutation

rs762136146

c.611G>A

p.Arg204His

p.R204H

Q9Y678

protein_coding

deleterious(0)

probably_damaging(0.991)

TCGA-BH-A0B0-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

COPG1

SNV

Missense_Mutation

novel

c.2494N>T

p.Gly832Cys

p.G832C

Q9Y678

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-D8-A27M-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

methotrexate+5

COPG1

SNV

Missense_Mutation

novel

c.510N>A

p.Ser170Arg

p.S170R

Q9Y678

protein_coding

deleterious(0.01)

probably_damaging(0.985)

TCGA-E2-A1L6-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

COPG1

SNV

Missense_Mutation

novel

c.1582G>T

p.Ala528Ser

p.A528S

Q9Y678

protein_coding

deleterious(0.02)

benign(0.033)

TCGA-E9-A247-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

COPG1

insertion

Nonsense_Mutation

novel

c.2555_2556insAAATAAGACAGATATATAAATAGAGAAAATAACT

p.Thr853AsnfsTer6

p.T853Nfs*6

Q9Y678

protein_coding

TCGA-A7-A0CJ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

Page: 1 2 3 4 5 6 7 8 9

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