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: RPN1

Gene summary for RPN1

Gene summary.

Gene information	Species	Human
	Gene symbol	RPN1
	Gene ID	6184
	Gene name	ribophorin I
	Gene Alias	OST1
	Cytomap	3q21.3
	Gene Type	protein-coding
	GO ID	GO:0006464
	UniProtAcc	P04843

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
6184	RPN1	HTA11_2487_2000001011	Human	Colorectum	SER	4.27e-13	6.01e-01	-0.1808
6184	RPN1	HTA11_1938_2000001011	Human	Colorectum	AD	1.36e-14	6.78e-01	-0.0811
6184	RPN1	HTA11_78_2000001011	Human	Colorectum	AD	3.10e-18	6.10e-01	-0.1088
6184	RPN1	HTA11_347_2000001011	Human	Colorectum	AD	3.86e-33	8.09e-01	-0.1954
6184	RPN1	HTA11_411_2000001011	Human	Colorectum	SER	3.13e-15	1.36e+00	-0.2602
6184	RPN1	HTA11_2112_2000001011	Human	Colorectum	SER	3.30e-03	6.21e-01	-0.2196
6184	RPN1	HTA11_3361_2000001011	Human	Colorectum	AD	1.81e-02	4.05e-01	-0.1207
6184	RPN1	HTA11_83_2000001011	Human	Colorectum	SER	1.62e-05	4.81e-01	-0.1526
6184	RPN1	HTA11_696_2000001011	Human	Colorectum	AD	1.85e-25	7.98e-01	-0.1464
6184	RPN1	HTA11_866_2000001011	Human	Colorectum	AD	1.77e-09	4.91e-01	-0.1001
6184	RPN1	HTA11_1391_2000001011	Human	Colorectum	AD	1.19e-25	9.51e-01	-0.059
6184	RPN1	HTA11_2992_2000001011	Human	Colorectum	SER	2.81e-05	7.04e-01	-0.1706
6184	RPN1	HTA11_5212_2000001011	Human	Colorectum	AD	3.13e-02	4.43e-01	-0.2061
6184	RPN1	HTA11_546_2000001011	Human	Colorectum	AD	3.11e-04	4.62e-01	-0.0842
6184	RPN1	HTA11_9341_2000001011	Human	Colorectum	SER	7.29e-04	6.52e-01	-0.00410000000000005
6184	RPN1	HTA11_7862_2000001011	Human	Colorectum	AD	5.03e-03	4.37e-01	-0.0179
6184	RPN1	HTA11_866_3004761011	Human	Colorectum	AD	8.01e-18	6.07e-01	0.096
6184	RPN1	HTA11_4255_2000001011	Human	Colorectum	SER	1.98e-02	6.22e-01	0.0446
6184	RPN1	HTA11_8622_2000001021	Human	Colorectum	SER	2.65e-04	4.96e-01	0.0528
6184	RPN1	HTA11_7663_2000001011	Human	Colorectum	SER	9.07e-08	9.59e-01	0.0131

Page: 1 2 3 4 5 6 7 8 9

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
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
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:0018279	Colorectum	AD	protein N-linked glycosylation via asparagine	15/3918	23/18723	5.47e-06	1.40e-04	15
GO:0018196	Colorectum	AD	peptidyl-asparagine modification	15/3918	24/18723	1.18e-05	2.62e-04	15
GO:0006487	Colorectum	AD	protein N-linked glycosylation	25/3918	65/18723	9.12e-04	8.71e-03	25
GO:0006486	Colorectum	AD	protein glycosylation	64/3918	226/18723	4.86e-03	3.27e-02	64
GO:0043413	Colorectum	AD	macromolecule glycosylation	64/3918	226/18723	4.86e-03	3.27e-02	64
GO:0070085	Colorectum	AD	glycosylation	67/3918	240/18723	5.78e-03	3.67e-02	67
GO:00182791	Colorectum	SER	protein N-linked glycosylation via asparagine	9/2897	23/18723	5.20e-03	3.95e-02	9
GO:00181961	Colorectum	SER	peptidyl-asparagine modification	9/2897	24/18723	7.19e-03	4.99e-02	9
GO:00182792	Colorectum	MSS	protein N-linked glycosylation via asparagine	13/3467	23/18723	5.21e-05	9.31e-04	13
GO:00181962	Colorectum	MSS	peptidyl-asparagine modification	13/3467	24/18723	9.44e-05	1.49e-03	13
GO:00064871	Colorectum	MSS	protein N-linked glycosylation	23/3467	65/18723	9.47e-04	9.54e-03	23
GO:00182793	Colorectum	MSI-H	protein N-linked glycosylation via asparagine	7/1319	23/18723	7.62e-04	1.42e-02	7
GO:00181963	Colorectum	MSI-H	peptidyl-asparagine modification	7/1319	24/18723	1.01e-03	1.73e-02	7
GO:00182794	Colorectum	FAP	protein N-linked glycosylation via asparagine	10/2622	23/18723	5.68e-04	6.33e-03	10
GO:00181964	Colorectum	FAP	peptidyl-asparagine modification	10/2622	24/18723	8.53e-04	8.79e-03	10
GO:00064861	Colorectum	FAP	protein glycosylation	48/2622	226/18723	1.85e-03	1.57e-02	48
GO:00434131	Colorectum	FAP	macromolecule glycosylation	48/2622	226/18723	1.85e-03	1.57e-02	48
GO:00700851	Colorectum	FAP	glycosylation	50/2622	240/18723	2.30e-03	1.85e-02	50
GO:0009101	Colorectum	FAP	glycoprotein biosynthetic process	63/2622	317/18723	2.31e-03	1.86e-02	63
GO:00064872	Colorectum	FAP	protein N-linked glycosylation	18/2622	65/18723	2.85e-03	2.19e-02	18

Page: 1 2 3 4

Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa04141	Colorectum	AD	Protein processing in endoplasmic reticulum	80/2092	174/8465	5.96e-10	1.25e-08	7.96e-09	80
hsa00510	Colorectum	AD	N-Glycan biosynthesis	21/2092	53/8465	1.15e-02	4.24e-02	2.71e-02	21
hsa041411	Colorectum	AD	Protein processing in endoplasmic reticulum	80/2092	174/8465	5.96e-10	1.25e-08	7.96e-09	80
hsa005101	Colorectum	AD	N-Glycan biosynthesis	21/2092	53/8465	1.15e-02	4.24e-02	2.71e-02	21
hsa041412	Colorectum	SER	Protein processing in endoplasmic reticulum	60/1580	174/8465	4.20e-07	7.33e-06	5.32e-06	60
hsa041413	Colorectum	SER	Protein processing in endoplasmic reticulum	60/1580	174/8465	4.20e-07	7.33e-06	5.32e-06	60
hsa041414	Colorectum	MSS	Protein processing in endoplasmic reticulum	75/1875	174/8465	3.78e-10	8.44e-09	5.17e-09	75
hsa005102	Colorectum	MSS	N-Glycan biosynthesis	20/1875	53/8465	7.17e-03	2.83e-02	1.73e-02	20
hsa00513	Colorectum	MSS	Various types of N-glycan biosynthesis	16/1875	42/8465	1.39e-02	4.53e-02	2.77e-02	16
hsa041415	Colorectum	MSS	Protein processing in endoplasmic reticulum	75/1875	174/8465	3.78e-10	8.44e-09	5.17e-09	75
hsa005103	Colorectum	MSS	N-Glycan biosynthesis	20/1875	53/8465	7.17e-03	2.83e-02	1.73e-02	20
hsa005131	Colorectum	MSS	Various types of N-glycan biosynthesis	16/1875	42/8465	1.39e-02	4.53e-02	2.77e-02	16
hsa041416	Colorectum	MSI-H	Protein processing in endoplasmic reticulum	46/797	174/8465	4.53e-11	9.78e-10	8.19e-10	46
hsa041417	Colorectum	MSI-H	Protein processing in endoplasmic reticulum	46/797	174/8465	4.53e-11	9.78e-10	8.19e-10	46
hsa041418	Colorectum	FAP	Protein processing in endoplasmic reticulum	50/1404	174/8465	3.64e-05	3.68e-04	2.24e-04	50
hsa041419	Colorectum	FAP	Protein processing in endoplasmic reticulum	50/1404	174/8465	3.64e-05	3.68e-04	2.24e-04	50
hsa0414139	Esophagus	HGIN	Protein processing in endoplasmic reticulum	67/1383	174/8465	1.06e-12	2.16e-11	1.72e-11	67
hsa005106	Esophagus	HGIN	N-Glycan biosynthesis	17/1383	53/8465	3.43e-03	2.54e-02	2.02e-02	17
hsa04141114	Esophagus	HGIN	Protein processing in endoplasmic reticulum	67/1383	174/8465	1.06e-12	2.16e-11	1.72e-11	67
hsa0051013	Esophagus	HGIN	N-Glycan biosynthesis	17/1383	53/8465	3.43e-03	2.54e-02	2.02e-02	17

Page: 1 2 3 4

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

RPN1

SNV

Missense_Mutation

c.391G>A

p.Val131Met

p.V131M

P04843

protein_coding

deleterious(0)

probably_damaging(0.961)

TCGA-BH-A0BM-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

RPN1

SNV

Missense_Mutation

c.1636N>C

p.Asp546His

p.D546H

P04843

protein_coding

deleterious(0)

probably_damaging(0.948)

TCGA-BH-A18T-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RPN1

SNV

Missense_Mutation

novel

c.473N>A

p.Gly158Glu

p.G158E

P04843

protein_coding

deleterious(0)

probably_damaging(0.967)

TCGA-E9-A3X8-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphane

RPN1

insertion

Nonsense_Mutation

novel

c.497_498insAAAGAAAAAAAAAGAAAAACCTCT

p.Tyr166delinsTer

p.Y166delins*

P04843

protein_coding

TCGA-AR-A0TY-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Paclitaxel

RPN1

SNV

Missense_Mutation

novel

c.1466G>T

p.Arg489Ile

p.R489I

P04843

protein_coding

deleterious(0)

probably_damaging(0.994)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

RPN1

SNV

Missense_Mutation

novel

c.34C>A

p.Leu12Met

p.L12M

P04843

protein_coding

tolerated(0.09)

possibly_damaging(0.601)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

RPN1

SNV

Missense_Mutation

rs762506765

c.1712N>A

p.Arg571His

p.R571H

P04843

protein_coding

deleterious(0.01)

possibly_damaging(0.634)

TCGA-EA-A3HU-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

RPN1

SNV

Missense_Mutation

c.283N>C

p.Glu95Gln

p.E95Q

P04843

protein_coding

tolerated(0.51)

benign(0.033)

TCGA-JW-A5VJ-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

RPN1

SNV

Missense_Mutation

novel

c.379N>G

p.Ile127Val

p.I127V

P04843

protein_coding

tolerated(1)

benign(0.006)

TCGA-AA-3984-01

Colorectum

colon adenocarcinoma

Female

<65

I/II

Unknown

RPN1

SNV

Missense_Mutation

c.673N>A

p.Leu225Met

p.L225M

P04843

protein_coding

tolerated(0.05)

probably_damaging(0.955)

TCGA-AZ-6598-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

Page: 1 2 3 4 5

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