Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolRPN1
Gene nameribophorin I
SynonymsOST1|RBPH1
CytomapUCSC genome browser: 3q21.3
Genomic locationchr3 :128338812-128369719
Type of geneprotein-coding
RefGenesNM_002950.3,
Ensembl idENSG00000163902
DescriptionRPN-Idolichyl-diphosphooligosaccharide--protein glycosyltransferase 67 kDa subunitdolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1dolichyl-diphosphooligosaccharide-protein glycosyltransferase 67 kDa subunitoligosaccharyltransfe
Modification date20141207
dbXrefs MIM : 180470
HGNC : HGNC
Ensembl : ENSG00000163902
HPRD : 01598
Vega : OTTHUMG00000159691
ProteinUniProt: P04843
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPN1
BioGPS: 6184
Gene Expression Atlas: ENSG00000163902
The Human Protein Atlas: ENSG00000163902
PathwayNCI Pathway Interaction Database: RPN1
KEGG: RPN1
REACTOME: RPN1
ConsensusPathDB
Pathway Commons: RPN1
MetabolismMetaCyc: RPN1
HUMANCyc: RPN1
RegulationEnsembl's Regulation: ENSG00000163902
miRBase: chr3 :128,338,812-128,369,719
TargetScan: NM_002950
cisRED: ENSG00000163902
ContextiHOP: RPN1
cancer metabolism search in PubMed: RPN1
UCL Cancer Institute: RPN1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for RPN1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM 180470; gene.
Orphanet
DiseaseKEGG Disease: RPN1
MedGen: RPN1 (Human Medical Genetics with Condition)
ClinVar: RPN1
PhenotypeMGI: RPN1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryRPN1chr3128341367128341567RPN1chr3128351578128351778
ovaryRPN1chr3128341414128341434RPN1chr3128341732128341752
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RPN1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CD370735RPLP22143611809999812873RPN14336663128339108128339342
BM838536MALAT1184116527131965271402RPN1855583128341096128345633
AF310158RPN111113128369383128369493MECOM1101403168849291168849321
BE873777RPN12853113128385395128385421GATAD2B2933141153894765153894786
AW067818RPN19793128339335128339405RPN1734803128338867128339270

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample      1 1        
GAIN (# sample)                 
LOSS (# sample)      1 1        
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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr3:128363791-128363791p.E99E3
chr3:128348840-128348840p.Y330Y2
chr3:128339335-128339335p.T581T2
chr3:128356662-128356662p.D205Y2
chr3:128344786-128344786p.D402D2
chr3:128369626-128369626p.A6A2
chr3:128350847-128350847p.R263C2
chr3:128348836-128348836p.V332I1
chr3:128339300-128339300p.R593H1
chr3:128350888-128350888p.D249G1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample12 91 1 11 311  34 4
# mutation12 61 1 11 311  34 4
nonsynonymous SNV 2 41 1 11 211   2 3
synonymous SNV1  2       1    32 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr3:128363791p.E99E3
chr3:128341088p.E520E2
chr3:128356662p.A566V1
chr3:128339335p.Y266Y1
chr3:128344834p.S565S1
chr3:128356705p.R263C1
chr3:128339381p.D546H1
chr3:128345617p.W239L1
chr3:128356884p.L544M1
chr3:128339383p.L225M1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA34777; -.
Organism-specific databasesCTD 6184; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00171ribophorin Iapproved; nutraceuticalAdenosine 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



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