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: COPS5

Gene summary for COPS5

Gene summary.

Gene information	Species	Human
	Gene symbol	COPS5
	Gene ID	10987
	Gene name	COP9 signalosome subunit 5
	Gene Alias	CSN5
	Cytomap	8q13.1
	Gene Type	protein-coding
	GO ID	GO:0000165
	UniProtAcc	A0A024R7W9

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
10987	COPS5	HTA11_2487_2000001011	Human	Colorectum	SER	4.07e-02	1.83e-01	-0.1808
10987	COPS5	HTA11_78_2000001011	Human	Colorectum	AD	1.53e-03	3.29e-01	-0.1088
10987	COPS5	HTA11_347_2000001011	Human	Colorectum	AD	2.96e-07	2.54e-01	-0.1954
10987	COPS5	HTA11_866_3004761011	Human	Colorectum	AD	6.99e-03	1.79e-01	0.096
10987	COPS5	HTA11_6801_2000001011	Human	Colorectum	SER	9.65e-03	3.66e-01	0.0171
10987	COPS5	HTA11_99999970781_79442	Human	Colorectum	MSS	2.04e-06	2.61e-01	0.294
10987	COPS5	HTA11_99999965062_69753	Human	Colorectum	MSI-H	1.17e-02	5.83e-01	0.3487
10987	COPS5	HTA11_99999971662_82457	Human	Colorectum	MSS	1.20e-13	4.72e-01	0.3859
10987	COPS5	HTA11_99999974143_84620	Human	Colorectum	MSS	4.73e-02	1.49e-01	0.3005
10987	COPS5	LZE4T	Human	Esophagus	ESCC	3.43e-24	8.28e-01	0.0811
10987	COPS5	LZE5T	Human	Esophagus	ESCC	6.45e-03	3.05e-01	0.0514
10987	COPS5	LZE7T	Human	Esophagus	ESCC	5.70e-09	4.03e-01	0.0667
10987	COPS5	LZE8T	Human	Esophagus	ESCC	2.35e-17	6.14e-01	0.067
10987	COPS5	LZE20T	Human	Esophagus	ESCC	1.05e-15	7.09e-01	0.0662
10987	COPS5	LZE22D1	Human	Esophagus	HGIN	3.03e-04	1.83e-01	0.0595
10987	COPS5	LZE22T	Human	Esophagus	ESCC	3.21e-02	3.54e-01	0.068
10987	COPS5	LZE24T	Human	Esophagus	ESCC	1.41e-35	1.16e+00	0.0596
10987	COPS5	LZE21T	Human	Esophagus	ESCC	6.89e-03	2.47e-01	0.0655
10987	COPS5	LZE6T	Human	Esophagus	ESCC	4.84e-10	4.78e-01	0.0845
10987	COPS5	P1T-E	Human	Esophagus	ESCC	1.34e-15	8.50e-01	0.0875

Page: 1 2 3 4 5 6 7

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
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:0032872110	Thyroid	PTC	regulation of stress-activated MAPK cascade	81/5968	192/18723	1.62e-03	8.95e-03	81
GO:00165794	Thyroid	PTC	protein deubiquitination	59/5968	139/18723	5.50e-03	2.50e-02	59
GO:003497633	Thyroid	ATC	response to endoplasmic reticulum stress	167/6293	256/18723	2.62e-25	1.03e-22	167
GO:000641334	Thyroid	ATC	translational initiation	83/6293	118/18723	3.44e-16	2.88e-14	83
GO:003596633	Thyroid	ATC	response to topologically incorrect protein	102/6293	159/18723	2.87e-15	1.99e-13	102
GO:000698633	Thyroid	ATC	response to unfolded protein	88/6293	137/18723	2.04e-13	9.91e-12	88
GO:003596733	Thyroid	ATC	cellular response to topologically incorrect protein	74/6293	116/18723	2.69e-11	9.20e-10	74
GO:003462033	Thyroid	ATC	cellular response to unfolded protein	61/6293	96/18723	1.84e-09	4.52e-08	61
GO:190589728	Thyroid	ATC	regulation of response to endoplasmic reticulum stress	54/6293	82/18723	2.34e-09	5.58e-08	54
GO:003096823	Thyroid	ATC	endoplasmic reticulum unfolded protein response	49/6293	74/18723	9.75e-09	2.03e-07	49
GO:003109826	Thyroid	ATC	stress-activated protein kinase signaling cascade	120/6293	247/18723	7.06e-07	9.46e-06	120
GO:005140326	Thyroid	ATC	stress-activated MAPK cascade	115/6293	239/18723	2.17e-06	2.58e-05	115
GO:199018216	Thyroid	ATC	exosomal secretion	17/6293	20/18723	3.20e-06	3.62e-05	17
GO:009773416	Thyroid	ATC	extracellular exosome biogenesis	17/6293	21/18723	1.15e-05	1.12e-04	17
GO:014011214	Thyroid	ATC	extracellular vesicle biogenesis	18/6293	23/18723	1.47e-05	1.39e-04	18
GO:005109022	Thyroid	ATC	regulation of DNA-binding transcription factor activity	190/6293	440/18723	1.49e-05	1.39e-04	190
GO:190010118	Thyroid	ATC	regulation of endoplasmic reticulum unfolded protein response	20/6293	30/18723	2.18e-04	1.43e-03	20
GO:007030226	Thyroid	ATC	regulation of stress-activated protein kinase signaling cascade	89/6293	195/18723	3.05e-04	1.93e-03	89
GO:003287226	Thyroid	ATC	regulation of stress-activated MAPK cascade	87/6293	192/18723	4.72e-04	2.77e-03	87
GO:190389411	Thyroid	ATC	regulation of IRE1-mediated unfolded protein response	11/6293	14/18723	7.46e-04	4.14e-03	11

Page: 1 2 3 4 5 6 7 8 9 10 11 12 13

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

COPS5

insertion

Frame_Shift_Ins

novel

c.98_99insC

p.Lys33AsnfsTer15

p.K33Nfs*15

Q92905

protein_coding

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COPS5

insertion

In_Frame_Ins

novel

c.96_97insCTTGAGCCCAGTGTCGACATGCACCTTGTTTGGGTCTTC

p.Asp32_Lys33insLeuGluProSerValAspMetHisLeuValTrpValPhe

p.D32_K33insLEPSVDMHLVWVF

Q92905

protein_coding

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COPS5

SNV

Missense_Mutation

c.592N>A

p.Glu198Lys

p.E198K

Q92905

protein_coding

tolerated(0.26)

benign(0.367)

TCGA-C5-A1BQ-01

Cervix

cervical & endocervical cancer

Female

>=65

III/IV

Chemotherapy

cisplatin

COPS5

SNV

Missense_Mutation

novel

c.94N>A

p.Asp32Asn

p.D32N

Q92905

protein_coding

tolerated(0.11)

benign(0.056)

TCGA-C5-A2LZ-01

Cervix

cervical & endocervical cancer

Female

>=65

III/IV

Unknown

COPS5

SNV

Missense_Mutation

novel

c.715N>C

p.Glu239Gln

p.E239Q

Q92905

protein_coding

tolerated(0.05)

benign(0.027)

TCGA-MA-AA41-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

COPS5

SNV

Missense_Mutation

novel

c.86N>G

p.Tyr29Cys

p.Y29C

Q92905

protein_coding

deleterious(0)

possibly_damaging(0.873)

TCGA-AD-6964-01

Colorectum

colon adenocarcinoma

Male

<65

III/IV

Chemotherapy

folfox

COPS5

SNV

Missense_Mutation

rs143525514

c.872C>T

p.Thr291Met

p.T291M

Q92905

protein_coding

tolerated(0.13)

benign(0.15)

TCGA-AG-3902-01

Colorectum

rectum adenocarcinoma

Male

<65

I/II

Unknown

COPS5

SNV

Missense_Mutation

c.881N>A

p.Arg294Gln

p.R294Q

Q92905

protein_coding

tolerated(0.16)

benign(0.048)

TCGA-EI-6882-01

Colorectum

rectum adenocarcinoma

Male

<65

I/II

Unknown

COPS5

SNV

Missense_Mutation

c.804T>A

p.Asp268Glu

p.D268E

Q92905

protein_coding

deleterious(0.02)

probably_damaging(0.976)

TCGA-A5-A0GA-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

III/IV

Chemotherapy

taxol

COPS5

SNV

Missense_Mutation

c.34N>G

p.Thr12Ala

p.T12A

Q92905

protein_coding

tolerated(0.19)

benign(0.006)

TCGA-AP-A056-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

Page: 1 2 3 4

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