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: USP1

Gene summary for USP1

Gene summary.

Gene information	Species	Human
	Gene symbol	USP1
	Gene ID	7398
	Gene name	ubiquitin specific peptidase 1
	Gene Alias	UBP
	Cytomap	1p31.3
	Gene Type	protein-coding
	GO ID	GO:0001501
	UniProtAcc	O94782

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
7398	USP1	GSM4909281	Human	Breast	IDC	1.99e-15	5.59e-01	0.21
7398	USP1	GSM4909282	Human	Breast	IDC	6.34e-11	4.95e-01	-0.0288
7398	USP1	GSM4909285	Human	Breast	IDC	4.08e-19	4.50e-01	0.21
7398	USP1	GSM4909286	Human	Breast	IDC	1.90e-11	4.78e-01	0.1081
7398	USP1	GSM4909287	Human	Breast	IDC	3.37e-10	5.37e-01	0.2057
7398	USP1	GSM4909293	Human	Breast	IDC	4.70e-02	1.68e-01	0.1581
7398	USP1	GSM4909311	Human	Breast	IDC	1.09e-07	-1.44e-01	0.1534
7398	USP1	GSM4909319	Human	Breast	IDC	2.99e-09	-6.62e-02	0.1563
7398	USP1	DCIS2	Human	Breast	DCIS	9.40e-42	2.07e-01	0.0085
7398	USP1	LZE2D	Human	Esophagus	HGIN	8.33e-05	2.54e-01	0.0642
7398	USP1	LZE2T	Human	Esophagus	ESCC	2.09e-06	7.14e-01	0.082
7398	USP1	LZE3D	Human	Esophagus	HGIN	1.74e-02	4.99e-01	0.0668
7398	USP1	LZE4T	Human	Esophagus	ESCC	1.36e-06	2.61e-01	0.0811
7398	USP1	LZE7T	Human	Esophagus	ESCC	3.96e-10	6.55e-01	0.0667
7398	USP1	LZE20T	Human	Esophagus	ESCC	2.62e-04	2.01e-01	0.0662
7398	USP1	LZE24T	Human	Esophagus	ESCC	9.63e-18	5.05e-01	0.0596
7398	USP1	LZE6T	Human	Esophagus	ESCC	4.43e-05	2.03e-01	0.0845
7398	USP1	P1T-E	Human	Esophagus	ESCC	5.22e-03	4.35e-01	0.0875
7398	USP1	P2T-E	Human	Esophagus	ESCC	1.80e-51	1.17e+00	0.1177
7398	USP1	P4T-E	Human	Esophagus	ESCC	2.36e-16	6.02e-01	0.1323

Page: 1 2 3 4 5 6 7

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
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:000691316	Prostate	Tumor	nucleocytoplasmic transport	97/3246	301/18723	1.78e-10	1.05e-08	97
GO:005116916	Prostate	Tumor	nuclear transport	97/3246	301/18723	1.78e-10	1.05e-08	97
GO:190165418	Prostate	Tumor	response to ketone	70/3246	194/18723	2.69e-10	1.48e-08	70
GO:004254218	Prostate	Tumor	response to hydrogen peroxide	57/3246	146/18723	3.91e-10	2.06e-08	57
GO:005254819	Prostate	Tumor	regulation of endopeptidase activity	126/3246	432/18723	5.86e-10	3.01e-08	126
GO:000030219	Prostate	Tumor	response to reactive oxygen species	76/3246	222/18723	7.85e-10	3.84e-08	76
GO:004217718	Prostate	Tumor	negative regulation of protein catabolic process	49/3246	121/18723	1.53e-09	7.19e-08	49
GO:004232618	Prostate	Tumor	negative regulation of phosphorylation	112/3246	385/18723	6.17e-09	2.42e-07	112
GO:004593619	Prostate	Tumor	negative regulation of phosphate metabolic process	124/3246	441/18723	9.08e-09	3.44e-07	124
GO:001056319	Prostate	Tumor	negative regulation of phosphorus metabolic process	124/3246	442/18723	1.05e-08	3.88e-07	124
GO:000989518	Prostate	Tumor	negative regulation of catabolic process	96/3246	320/18723	1.40e-08	5.07e-07	96
GO:001003819	Prostate	Tumor	response to metal ion	107/3246	373/18723	3.02e-08	9.77e-07	107
GO:004586119	Prostate	Tumor	negative regulation of proteolysis	102/3246	351/18723	3.09e-08	9.94e-07	102
GO:003133019	Prostate	Tumor	negative regulation of cellular catabolic process	81/3246	262/18723	4.42e-08	1.37e-06	81
GO:001657013	Prostate	Tumor	histone modification	126/3246	463/18723	5.51e-08	1.65e-06	126
GO:190589719	Prostate	Tumor	regulation of response to endoplasmic reticulum stress	35/3246	82/18723	6.76e-08	1.95e-06	35
GO:003196017	Prostate	Tumor	response to corticosteroid	57/3246	167/18723	1.11e-07	2.94e-06	57
GO:005134819	Prostate	Tumor	negative regulation of transferase activity	81/3246	268/18723	1.30e-07	3.35e-06	81
GO:005138417	Prostate	Tumor	response to glucocorticoid	52/3246	148/18723	1.38e-07	3.50e-06	52
GO:200005918	Prostate	Tumor	negative regulation of ubiquitin-dependent protein catabolic process	24/3246	48/18723	2.17e-07	5.26e-06	24

Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147

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

USP1

SNV

Missense_Mutation

c.1516N>A

p.Cys506Ser

p.C506S

O94782

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-A2-A04U-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

USP1

SNV

Missense_Mutation

c.1058N>T

p.Ser353Phe

p.S353F

O94782

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-A2-A0YK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

USP1

SNV

Missense_Mutation

novel

c.127C>G

p.Gln43Glu

p.Q43E

O94782

protein_coding

tolerated(0.18)

benign(0.104)

TCGA-AC-A3W6-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

USP1

SNV

Missense_Mutation

rs772351967

c.962N>G

p.Tyr321Cys

p.Y321C

O94782

protein_coding

tolerated(0.19)

benign(0)

TCGA-AC-A8OR-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

USP1

SNV

Missense_Mutation

c.670N>G

p.Lys224Glu

p.K224E

O94782

protein_coding

tolerated(0.82)

benign(0.033)

TCGA-AN-A0AL-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

USP1

SNV

Missense_Mutation

c.1881N>T

p.Leu627Phe

p.L627F

O94782

protein_coding

deleterious(0.04)

benign(0.376)

TCGA-BH-A0C0-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

carboplatin

USP1

SNV

Missense_Mutation

novel

c.219G>C

p.Lys73Asn

p.K73N

O94782

protein_coding

deleterious(0.01)

probably_damaging(0.997)

TCGA-BH-A0DX-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

USP1

insertion

In_Frame_Ins

novel

c.395_396insCGTTACTTCCAA

p.Asp131_Lys132insAsnValThrSer

p.D131_K132insNVTS

O94782

protein_coding

TCGA-AR-A0TU-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Doxorubicin

USP1

insertion

Frame_Shift_Ins

novel

c.2072_2073insCTGCAGGTGCCCACCACCACGCCCGGCTAATTTTTTGTATTTT

p.Ser692CysfsTer15

p.S692Cfs*15

O94782

protein_coding

TCGA-BH-A0HF-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

USP1

SNV

Missense_Mutation

novel

c.748G>A

p.Glu250Lys

p.E250K

O94782

protein_coding

tolerated(0.21)

benign(0.341)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

Page: 1 2 3 4 5 6 7 8

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
7398	USP1	DNA REPAIR, PROTEASE, ENZYME		GNF-PF-5510	CHEMBL578741
7398	USP1	DNA REPAIR, PROTEASE, ENZYME		CLOFENOXYDE	CLOFENOXYDE
7398	USP1	DNA REPAIR, PROTEASE, ENZYME		GW7074	CHEMBL72365
7398	USP1	DNA REPAIR, PROTEASE, ENZYME		CETRIMIDE	CETRIMIDE
7398	USP1	DNA REPAIR, PROTEASE, ENZYME		BENZIODARONE	BENZIODARONE
7398	USP1	DNA REPAIR, PROTEASE, ENZYME		GNF-PF-4579	CHEMBL584626
7398	USP1	DNA REPAIR, PROTEASE, ENZYME		AMYLMETACRESOL	AMYLMETACRESOL
7398	USP1	DNA REPAIR, PROTEASE, ENZYME		DIHYDROGAMBOGIC ACID	DIHYDROGAMBOGIC ACID
7398	USP1	DNA REPAIR, PROTEASE, ENZYME		BEXAROTENE	BEXAROTENE
7398	USP1	DNA REPAIR, PROTEASE, ENZYME		DITHIAZANINE	DITHIAZANINE

Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21