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 RPN2

Basic gene info.	Gene symbol	RPN2
	Gene name	ribophorin II
	Synonyms	RIBIIR\|RPN-II\|RPNII\|SWP1
	Cytomap	UCSC genome browser: 20q12-q13.1
	Genomic location	chr20 :35807455-35870025
	Type of gene	protein-coding
	RefGenes	NM_001135771.1, NM_002951.3,
	Ensembl id	ENSG00000118705
	Description	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 63 kDa subunitdolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2oligosaccharyltransferase complex subunit (non-catalytic)ribophorin-2
	Modification date	20141222
dbXrefs	MIM : 180490
	HGNC : HGNC
	Ensembl : ENSG00000118705
	HPRD : 01609
	Vega : OTTHUMG00000032409
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPN2
	BioGPS: 6185
	Gene Expression Atlas: ENSG00000118705
	The Human Protein Atlas: ENSG00000118705
Pathway	NCI Pathway Interaction Database: RPN2
	KEGG: RPN2
	REACTOME: RPN2
	ConsensusPathDB
	Pathway Commons: RPN2
Metabolism	MetaCyc: RPN2
	HUMANCyc: RPN2
Regulation	Ensembl's Regulation: ENSG00000118705
	miRBase: chr20 :35,807,455-35,870,025
	TargetScan: NM_001135771
	cisRED: ENSG00000118705
Context	iHOP: RPN2
	cancer metabolism search in PubMed: RPN2
	UCL Cancer Institute: RPN2
Assigned class in ccmGDB	C

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Phenotypic Information for RPN2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPN2
	Familial Cancer Database: RPN2

* 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
Orphanet
Disease	KEGG Disease: RPN2
	MedGen: RPN2 (Human Medical Genetics with Condition)
	ClinVar: RPN2
Phenotype	MGI: RPN2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPN2

Mutations for RPN2

* 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
pancreas	RPN2	chr20	35819010	35819030	RPN2	chr20	35822245	35822265

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 RPN2 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
CF125171	RPN2	1	104	20	35835739	35835842	MED15	97	666	22	20861958	20918847
AA740310	GPX3	1	227	5	150408293	150408522	RPN2	219	437	20	35812585	35826827
BC009430	GAPDH	61	997	12	6646122	6647537	RPN2	997	1744	20	35857110	35870026
AA367913	C5orf42	1	105	5	37201714	37201819	RPN2	105	339	20	35812749	35827562
BE075537	RPN2	13	481	20	35842162	35857107	RPN2	482	606	20	35833209	35835703
BI051087	RPN2	6	90	20	35826836	35827477	RPN2	86	323	20	35833177	35835785
BG390108	RPN2	15	66	20	35857081	35857132	RPN2	62	483	20	35857114	35869832

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=34)	Stat. for Synonymous SNVs (# total SNVs=16)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted 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
chr20:35827443-35827443	p.?	3
chr20:35835810-35835810	p.P275P	2
chr20:35833268-35833268	p.L218L	2
chr20:35865068-35865068	p.T613T	2
chr20:35835736-35835736	p.E251K	2
chr20:35862445-35862445	p.V567A	2
chr20:35862446-35862446	p.V567V	2
chr20:35826803-35826803	p.A71S	1
chr20:35852284-35852284	p.R366G	1
chr20:35832307-35832307	p.T167A	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=2

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			10	2		1		4			5		3			8	4		6
# mutation	1			10	2		1		4			6		3			8	4		6
nonsynonymous SNV				6					2			4		2			2	3		5
synonymous SNV	1			4	2		1		2			2		1			6	1		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
chr20:35862445	p.V535A,RPN2	2
chr20:35862446	p.V535V,RPN2	2
chr20:35856957	p.F382F,RPN2	1
chr20:35827572	p.T581T,RPN2	1
chr20:35862467	p.A143G,RPN2	1
chr20:35835810	p.A157A,RPN2	1
chr20:35857024	p.F403S,RPN2	1
chr20:35827584	p.V594V,RPN2	1
chr20:35862471	p.R158S,RPN2	1
chr20:35838528	p.N425N,RPN2	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 RPN2 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 RPN2

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


ACTR5,BLCAP,C20orf24,NDUFAF5,CTNNBL1,ESF1,TTI1, LOC100130274,MANBAL,MKKS,NDRG3,RALGAPB,RBL1,RPN2, RPRD1B,SNHG11,SNRPB2,SRC,SRXN1,TOMM34,YWHAB	AGA,C14orf1,ABRACL,DAP,DPAGT1,GSS,HSPA5, MYCBP,PDIA3,PDIA3P1,PDIA6,PRDX1,SLC50A1,RNPEP, RPN1,RPN2,SLC35A2,SRPRB,TM9SF1,TMED3,YIPF1

AAR2,RTFDC1,CTNNBL1,DHX35,EIF2S2,ERGIC3,MTG2, HM13,TTI1,MAPRE1,NFS1,PIGU,RALY,RPN2, RPRD1B,STAU1,NELFCD,TP53RK,TRPC4AP,UQCC1,YTHDF1	CCNE1,COPB2,CRELD2,DNAJB11,GINS4,GMPPB,HM13, HSP90B1,HSPA5,HYOU1,LRRC59,MCM10,PDIA3,PDIA3P1, PDIA4,RPN2,RRM2,SEC23B,SEC61A1,SSR1,STT3A

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 RPN2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB01248	ribophorin II	approved; investigational	Docetaxel
DB00171	ribophorin II	approved; nutraceutical	Adenosine triphosphate

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Cross referenced IDs for RPN2

* 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