Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	Gene Summary
	Phenotypic Information (metabolism pathway, cancer, disease, phenome)
	Mutations : SVs, CNVs, SNVs
	Gene expression: GE, Protein, DEGE, CNV vs GE
	Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG
	Pharmacological Information: Drug-Gene Network
	Cross referenced IDs

Gene Summary for RPN1

Basic gene info.	Gene symbol	RPN1
	Gene name	ribophorin I
	Synonyms	OST1\|RBPH1
	Cytomap	UCSC genome browser: 3q21.3
	Genomic location	chr3 :128338812-128369719
	Type of gene	protein-coding
	RefGenes	NM_002950.3,
	Ensembl id	ENSG00000163902
	Description	RPN-Idolichyl-diphosphooligosaccharide--protein glycosyltransferase 67 kDa subunitdolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1dolichyl-diphosphooligosaccharide-protein glycosyltransferase 67 kDa subunitoligosaccharyltransfe
	Modification date	20141207
dbXrefs	MIM : 180470
	HGNC : HGNC
	Ensembl : ENSG00000163902
	HPRD : 01598
	Vega : OTTHUMG00000159691
Protein	UniProt: P04843 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPN1
	BioGPS: 6184
	Gene Expression Atlas: ENSG00000163902
	The Human Protein Atlas: ENSG00000163902
Pathway	NCI Pathway Interaction Database: RPN1
	KEGG: RPN1
	REACTOME: RPN1
	ConsensusPathDB
	Pathway Commons: RPN1
Metabolism	MetaCyc: RPN1
	HUMANCyc: RPN1
Regulation	Ensembl's Regulation: ENSG00000163902
	miRBase: chr3 :128,338,812-128,369,719
	TargetScan: NM_002950
	cisRED: ENSG00000163902
Context	iHOP: RPN1
	cancer metabolism search in PubMed: RPN1
	UCL Cancer Institute: RPN1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for RPN1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPN1
	Familial Cancer Database: RPN1

* This gene is included in those cancer gene databases.

						.
Oncogene ¹	Tumor Suppressor gene ²	Cancer Gene Census ³	CancerGenes ⁴	Network of Cancer Gene ⁵	Significant driver gene in	Therapeutic Vulnerabilities in Cancer¹

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM	180470; gene.
Orphanet
Disease	KEGG Disease: RPN1
	MedGen: RPN1 (Human Medical Genetics with Condition)
	ClinVar: RPN1
Phenotype	MGI: RPN1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPN1

Mutations for RPN1

* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	RPN1	chr3	128341367	128341567	RPN1	chr3	128351578	128351778
ovary	RPN1	chr3	128341414	128341434	RPN1	chr3	128341732	128341752

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RPN1 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
CD370735	RPLP2	21	436	11	809999	812873	RPN1	433	666	3	128339108	128339342
BM838536	MALAT1	1	84	11	65271319	65271402	RPN1	85	558	3	128341096	128345633
AF310158	RPN1	1	111	3	128369383	128369493	MECOM	110	140	3	168849291	168849321
BE873777	RPN1	285	311	3	128385395	128385421	GATAD2B	293	314	1	153894765	153894786
AW067818	RPN1	9	79	3	128339335	128339405	RPN1	73	480	3	128338867	128339270

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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SNV Counts per Each Loci in COSMIC data : go to COSMIC point mutation

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=30)	Stat. for Synonymous SNVs (# total SNVs=14)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=1)
There's no deleted snv.

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Top 10 SNVs Having the Most Samples in COSMIC data

* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.

GRCh37 position	Mutation(aa)	Unique sampleID count
chr3:128363791-128363791	p.E99E	3
chr3:128369626-128369626	p.A6A	2
chr3:128350847-128350847	p.R263C	2
chr3:128348840-128348840	p.Y330Y	2
chr3:128339335-128339335	p.T581T	2
chr3:128356662-128356662	p.D205Y	2
chr3:128344786-128344786	p.D402D	2
chr3:128344800-128344800	p.Y398H	1
chr3:128369614-128369614	p.L10L	1
chr3:128350832-128350832	p.R268*	1

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SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=4

Point Mutation/ Tissue ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	2		9	1		1		1	1		3	1	1			3	4		4
# mutation	1	2		6	1		1		1	1		3	1	1			3	4		4
nonsynonymous SNV		2		4	1		1		1	1		2	1	1				2		3
synonymous SNV	1			2								1					3	2		1

cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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Top 10 SNVs Having the Most Samples in TCGA data

* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.

Genomic Position	Mutation(aa)	Unique sampleID count
chr3:128363791	p.E99E	3
chr3:128341088	p.E520E	2
chr3:128350836	p.Y398D	1
chr3:128344411	p.E99K	1
chr3:128350847	p.P386P	1
chr3:128344420	p.S62P	1
chr3:128350918	p.I365M	1
chr3:128344441	p.D347H	1
chr3:128350961	p.V332I	1
chr3:128339278	p.I600I	1

Other DBs for Point Mutations

Point Mutation Table of Ensembl: go to Ensembl variation table

Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

Copy Number for RPN1 in TCGA

* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.

cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for RPN1

Gene Expression in Cancer Cell-lines (CCLE)

* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

Differential Gene Expression in Primary Tumors (TCGA)

* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))

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CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

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Gene-Gene Network Information

Co-Expressed gene's network Plot

* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types


ACAD9,ALG3,TIMMDC1,HMCES,CALR,CCDC58,COPG1, DDOST,DNAJB11,ISY1,MCM2,MRPL3,MRPS22,PDIA5, PDIA6,PRDX4,RPN1,RUVBL1,SEC61A1,SRPRB,TPRA1	ARF1,ATP6V0B,BSCL2,CALR,CFL1,HM13,LAMP1, LMAN2,MANF,NANS,PDIA3,PPIB,RHOC,RPN1, SDF2,SEC61B,SRPRB,SUMF2,TMED9,TMEM179B,UFC1

C19orf10,CALR,COPE,COPG1,DNAJB11,EIF5A,FAM162A, GMPPA,MANF,MRPL47,P4HB,POLR2L,PPIB,PSMC3, RPN1,SDF2L1,SEC13,SERP1,SRPRB,SSR3,TMEM179B	ACTR3,C19orf10,CALR,CCT5,DNAJB11,EIF4A1,GMPPB, HNRNPF,LRRC59,MANF,NUDT5,PDIA4,PDIA6,PPIB, PSMB2,PSMC4,RPN1,SDF2L1,SEC61B,SPCS2,TMED9

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for RPN1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA34777; -.
Organism-specific databases	CTD	6184; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00171	ribophorin I	approved; nutraceutical	Adenosine triphosphate

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Cross referenced IDs for RPN1

* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information