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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for DPM2 |
Basic gene info. | Gene symbol | DPM2 |
Gene name | dolichyl-phosphate mannosyltransferase polypeptide 2, regulatory subunit | |
Synonyms | CDG1U | |
Cytomap | UCSC genome browser: 9q34.13 | |
Genomic location | chr9 :130697373-130700763 | |
Type of gene | protein-coding | |
RefGenes | NM_003863.3, NM_152690.1, | |
Ensembl id | ENSG00000136908 | |
Description | DPM synthase complex subunitDPM synthase subunit 2dolichol phosphate-mannose biosynthesis regulatory proteindolichol-phosphate mannose synthase subunit 2 | |
Modification date | 20141219 | |
dbXrefs | MIM : 603564 | |
HGNC : HGNC | ||
Ensembl : ENSG00000136908 | ||
HPRD : 16028 | ||
Vega : OTTHUMG00000020725 | ||
Protein | UniProt: O94777 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_DPM2 | |
BioGPS: 8818 | ||
Gene Expression Atlas: ENSG00000136908 | ||
The Human Protein Atlas: ENSG00000136908 | ||
Pathway | NCI Pathway Interaction Database: DPM2 | |
KEGG: DPM2 | ||
REACTOME: DPM2 | ||
ConsensusPathDB | ||
Pathway Commons: DPM2 | ||
Metabolism | MetaCyc: DPM2 | |
HUMANCyc: DPM2 | ||
Regulation | Ensembl's Regulation: ENSG00000136908 | |
miRBase: chr9 :130,697,373-130,700,763 | ||
TargetScan: NM_003863 | ||
cisRED: ENSG00000136908 | ||
Context | iHOP: DPM2 | |
cancer metabolism search in PubMed: DPM2 | ||
UCL Cancer Institute: DPM2 | ||
Assigned class in ccmGDB | A - This gene has a literature evidence and it belongs to cancer gene. | |
References showing role of DPM2 in cancer cell metabolism | 1. Hu Y, Li ZF, Wu X, Lu Q (2011) Large induces functional glycans in an O-mannosylation dependent manner and targets GlcNAc terminals on alpha-dystroglycan. PLoS One 6: e16866. doi: 10.1371/journal.pone.0016866. pmid: 3036717. go to article |
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Phenotypic Information for DPM2(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: DPM2 |
Familial Cancer Database: DPM2 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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 | 603564; gene. 615042; phenotype. |
Orphanet | 329178; Congenital muscular dystrophy with intellectual disability and severe epilepsy. |
Disease | KEGG Disease: DPM2 |
MedGen: DPM2 (Human Medical Genetics with Condition) | |
ClinVar: DPM2 | |
Phenotype | MGI: DPM2 (International Mouse Phenotyping Consortium) |
PhenomicDB: DPM2 |
Mutations for DPM2 |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DPM2 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 |
BF088423 | MIR548H2 | 202 | 222 | 3 | 151398031 | 151398051 | DPM2 | 223 | 456 | 9 | 130697892 | 130698897 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=6) | (# total SNVs=2) |
(# total SNVs=0) | (# total SNVs=1) |
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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 |
chr9:130698858-130698858 | p.A57V | 1 |
chr9:130698880-130698880 | p.A50T | 1 |
chr9:130699718-130699718 | p.L30I | 1 |
chr9:130699733-130699734 | p.Y24_T25insY | 1 |
chr9:130699741-130699741 | p.T22N | 1 |
chr9:130699785-130699785 | p.Q7H | 1 |
chr9:130699797-130699797 | p.T3T | 1 |
chr9:130698020-130698020 | p.V79A | 1 |
chr9:130698029-130698029 | p.T76S | 1 |
chr9:130698031-130698031 | p.K75K | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |   |   |   |   | 1 |   |   | 1 | 1 |   |   |   | 1 |   |   | 1 |
# mutation |   |   |   | 1 |   |   |   |   | 1 |   |   | 1 | 1 |   |   |   | 1 |   |   | 1 |
nonsynonymous SNV |   |   |   | 1 |   |   |   |   | 1 |   |   |   |   |   |   |   | 1 |   |   | 1 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   | 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 |
chr9:130699785 | p.T3T | 1 |
chr9:130699797 | p.F64C | 1 |
chr9:130698837 | p.A57V | 1 |
chr9:130698858 | p.L30I | 1 |
chr9:130699718 | p.I19I | 1 |
chr9:130699749 | p.Q7H | 1 |
Other DBs for Point Mutations |
Copy Number for DPM2 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 DPM2 |
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. |
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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 |
AK1,LAMTOR4,SWI5,C9orf142,COQ4,DPM2,EDF1, ENDOG,FPGS,MRPL41,NDUFA8,PHPT1,PTGES2,PTRH1, SSNA1,SURF2,TMEM141,TOR2A,UCK1,URM1,ZDHHC12 | ALG3,C17orf49,R3HDM4,WDR83OS,CNFN,BLOC1S4,CUTA, DGUOK,DPM2,ETHE1,EEF2KMT,LSM2,MOSPD3,OVCA2, PDCD6,PSENEN,SF3B4,TMEM179B,TMEM54,TRAPPC1,TSEN34 |
ARPC5L,UQCC2,SWI5,C9orf142,DPM2,EDF1,NUDT1, PFDN6,PMPCA,PSMB7,PSMG3,PSMG4,PTGES2,SSNA1, SURF2,TMEM203,TMEM208,TXN,WDR34,ZDHHC12,ZMYND19 | APRT,B4GALT7,UQCC3,C19orf24,C9orf16,CHCHD5,DPM2, EXOSC5,JTB,KRTCAP3,LSM7,MLST8,NUDT8,RPL8, SF3B5,SYNGR2,THOC6,TIMM13,TMEM11,URM1,YIPF2 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for DPM2 |
There's no related Drug. |
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Cross referenced IDs for DPM2 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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