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 DPM1
Basic gene info.Gene symbolDPM1
Gene namedolichyl-phosphate mannosyltransferase polypeptide 1, catalytic subunit
SynonymsCDGIE|MPDS
CytomapUCSC genome browser: 20q13.13
Genomic locationchr20 :49551404-49575060
Type of geneprotein-coding
RefGenesNM_003859.1,
Ensembl idENSG00000000419
DescriptionDPM synthase complex, catalytic subunitDPM synthase subunit 1MPD synthase subunit 1dolichol monophosphate mannose synthasedolichol-phosphate mannose synthase subunit 1dolichol-phosphate mannosyltransferase subunit 1dolichyl-phosphate beta-D-mannosyl
Modification date20141219
dbXrefs MIM : 603503
HGNC : HGNC
Ensembl : ENSG00000000419
HPRD : 04613
Vega : OTTHUMG00000032742
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DPM1
BioGPS: 8813
Gene Expression Atlas: ENSG00000000419
The Human Protein Atlas: ENSG00000000419
PathwayNCI Pathway Interaction Database: DPM1
KEGG: DPM1
REACTOME: DPM1
ConsensusPathDB
Pathway Commons: DPM1
MetabolismMetaCyc: DPM1
HUMANCyc: DPM1
RegulationEnsembl's Regulation: ENSG00000000419
miRBase: chr20 :49,551,404-49,575,060
TargetScan: NM_003859
cisRED: ENSG00000000419
ContextiHOP: DPM1
cancer metabolism search in PubMed: DPM1
UCL Cancer Institute: DPM1
Assigned class in ccmGDBC

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Phenotypic Information for DPM1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DPM1
Familial Cancer Database: DPM1
* 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
Orphanet
DiseaseKEGG Disease: DPM1
MedGen: DPM1 (Human Medical Genetics with Condition)
ClinVar: DPM1
PhenotypeMGI: DPM1 (International Mouse Phenotyping Consortium)
PhenomicDB: DPM1

Mutations for DPM1
* 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
ovaryDPM1chr204957220449572224chr204958275249582772
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 DPM1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW937417DPM110251204956571749565958DPM1250552204956685249567154
CB241933DPM111331204955142949551749DPM1329459204955767649558627

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)          1  1   
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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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=24)
Stat. for Synonymous SNVs
(# total SNVs=4)
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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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
chr20:49574949-49574949p.E38K3
chr20:49574931-49574931p.V44M2
chr20:49575039-49575039p.R8S2
chr20:49575042-49575042p.S7G2
chr20:49552759-49552759p.C202G1
chr20:49571760-49571760p.A75V1
chr20:49575045-49575045p.V6L1
chr20:49552777-49552777p.E196Q1
chr20:49571794-49571794p.D64N1
chr20:49575052-49575052p.S3S1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12 31 2 1  411  32 3
# mutation12 31 2 1  411  32 4
nonsynonymous SNV12 21 2 1  411  11 3
synonymous SNV   1            21 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
chr20:49574949p.E38Q2
chr20:49552777p.D141N1
chr20:49574937p.F131C1
chr20:49552786p.L121F1
chr20:49574946p.D118N1
chr20:49552791p.P91P1
chr20:49558641p.A75V1
chr20:49575037p.D64N1
chr20:49562280p.F249L1
chr20:49575039p.V44M1

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 DPM1 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 DPM1

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

AURKA,GID8,C20orf24,AAR2,DDX27,DPM1,DSN1,
EIF6,MOCS3,OSBPL2,PIGU,PSMA7,RNF114,SLMO2,
NELFCD,TMEM189,TPD52L2,UBE2V1,UQCC1,YTHDF1,ZFP64
ACTR10,ANAPC10,BCAS2,SFR1,C11orf58,TEX30,C1D,
CGRRF1,DPM1,GTF2A2,IER3IP1,MED4,MOB4,OCIAD1,
PPP2CA,TRMT10C,TAF9,TM2D1,UBE2D2,UBE2D3,VAPA

ATP5E,C20orf24,AAR2,RTFDC1,COMMD7,CSE1L,DPM1,
DSN1,EIF2S2,MAPRE1,MOCS3,PDRG1,PFDN4,PSMA7,
RAE1,RNF114,SLMO2,NELFCD,TP53RK,UBE2V1,VAPB
ALG5,ATG3,C14orf119,EMC7,TRAPPC13,TMA7,DPM1,
EMG1,GLRX3,LAMTOR5,HSBP1,OSTC,PHF5A,PSMC6,
PTS,SELK,SELT,SEP15,SNRPG,TOMM5,TOMM6
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 DPM1


There's no related Drug.
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Cross referenced IDs for DPM1
* 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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