|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for DPM3 |
Basic gene info. | Gene symbol | DPM3 |
Gene name | dolichyl-phosphate mannosyltransferase polypeptide 3 | |
Synonyms | CDG1O | |
Cytomap | UCSC genome browser: 1q22 | |
Genomic location | chr1 :155112366-155112996 | |
Type of gene | protein-coding | |
RefGenes | NM_018973.3, NM_153741.1, | |
Ensembl id | ENSG00000179085 | |
Description | DPM synthase complex subunit 3DPM synthase subunit 3MPD synthase subunit 3dolichol-phosphate mannose synthase subunit 3dolichol-phosphate mannosyltransferase subunit 3dolichyl-phosphate beta-D-mannosyltransferase subunit 3mannose-P-dolichol synthase | |
Modification date | 20141219 | |
dbXrefs | MIM : 605951 | |
HGNC : HGNC | ||
Ensembl : ENSG00000179085 | ||
HPRD : 16179 | ||
Vega : OTTHUMG00000035335 | ||
Protein | UniProt: Q9P2X0 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_DPM3 | |
BioGPS: 54344 | ||
Gene Expression Atlas: ENSG00000179085 | ||
The Human Protein Atlas: ENSG00000179085 | ||
Pathway | NCI Pathway Interaction Database: DPM3 | |
KEGG: DPM3 | ||
REACTOME: DPM3 | ||
ConsensusPathDB | ||
Pathway Commons: DPM3 | ||
Metabolism | MetaCyc: DPM3 | |
HUMANCyc: DPM3 | ||
Regulation | Ensembl's Regulation: ENSG00000179085 | |
miRBase: chr1 :155,112,366-155,112,996 | ||
TargetScan: NM_018973 | ||
cisRED: ENSG00000179085 | ||
Context | iHOP: DPM3 | |
cancer metabolism search in PubMed: DPM3 | ||
UCL Cancer Institute: DPM3 | ||
Assigned class in ccmGDB | A - This gene has a literature evidence and it belongs to cancer gene. | |
References showing role of DPM3 in cancer cell metabolism | 1. Manos EJ, Kim ML, Kassis J, Chang PY, Wells A, et al. (2001) Dolichol-phosphate-mannose-3 (DPM3)/prostin-1 is a novel phospholipase C-gamma regulated gene negatively associated with prostate tumor invasion. Oncogene 20: 2781-2790. doi: 10.1038/sj.onc.1204379. go to article |
Top |
Phenotypic Information for DPM3(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: DPM3 |
Familial Cancer Database: DPM3 |
* This gene is included in those cancer gene databases. |
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 | 605951; gene. 612937; phenotype. |
Orphanet | 263494; DPM3-CDG. |
Disease | KEGG Disease: DPM3 |
MedGen: DPM3 (Human Medical Genetics with Condition) | |
ClinVar: DPM3 | |
Phenotype | MGI: DPM3 (International Mouse Phenotyping Consortium) |
PhenomicDB: DPM3 |
Mutations for DPM3 |
* 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 DPM3 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 |
Other DBs for Structural Variants |
Top |
Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
Top |
SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
|
Top |
Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=1) | (# total SNVs=4) |
(# total SNVs=0) | (# total SNVs=0) |
Top |
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 |
chr1:155112686-155112686 | p.L41L | 1 |
chr1:155112711-155112711 | p.T32T | 1 |
chr1:155112444-155112444 | p.R121R | 1 |
chr1:155112463-155112463 | p.L115* | 1 |
chr1:155112476-155112476 | p.A111S | 1 |
chr1:155112492-155112492 | p.Q105Q | 1 |
chr1:155112591-155112591 | p.P72P | 1 |
chr1:155112648-155112648 | p.T53T | 1 |
chr1:155112671-155112671 | p.S46P | 1 |
Top |
SNV Counts per Each Loci in TCGA data |
|
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 |   | 2 |
# mutation | 1 |   |   | 1 |   |   |   |   |   |   |   |   |   | 1 |   |   |   | 1 |   | 2 |
nonsynonymous SNV |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |
synonymous SNV | 1 |   |   | 1 |   |   |   |   |   |   |   |   |   | 1 |   |   |   | 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]) |
Top |
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 |
chr1:155112444 | p.R121R,DPM3 | 1 |
chr1:155112492 | p.Q105Q,DPM3 | 1 |
chr1:155112591 | p.P72P,DPM3 | 1 |
chr1:155112671 | p.S46P,DPM3 | 1 |
chr1:155112686 | p.L41L,DPM3 | 1 |
chr1:155112711 | p.T32T,DPM3 | 1 |
Other DBs for Point Mutations |
Copy Number for DPM3 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] |
Top |
Gene Expression for DPM3 |
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)) |
Top |
CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
Top |
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 |
AURKAIP1,BCL7C,C19orf24,C1orf35,PPP1R35,LAMTOR4,C9orf142, CCDC12,DPM3,EDF1,GADD45GIP1,KRTCAP2,NAA38,MRPL55, MTX1,NENF,LAMTOR2,TCEB2,THAP3,ZNF593,ZNHIT1 | BAD,UQCC3,C19orf24,C19orf53,LAMTOR4,DGCR6L,DPM3, MPG,MRPL28,MRPL55,NDUFA11,NME3,PRDX5,RBM42, ROMO1,RPP21,SCAND1,SSNA1,TMUB1,TRAPPC5,ZNF524 |
BOLA1,C7orf55,RPP25L,CHCHD1,COX4I1,COX7A2,DPM3, GUK1,NAA38,MRPL54,NDUFA13,NDUFA2,NDUFB1,NDUFB7, PSMB4,SERF2,SF3B5,TIMM8B,TMEM183A,TRAPPC5,TSPO | ABT1,ANAPC11,ARF5,BUD31,TIMMDC1,C7orf55,CHCHD5, DPM3,GPX1,MRPL57,MRPL43,MRPL49,MRPL54,LINC00116, NDUFA7,NDUFB7,NUBP2,PSMD9,RPL35,SERF2,SIVA1 |
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 |
Top |
Interacting Genes (from Pathway Commons) |
Top |
Pharmacological Information for DPM3 |
There's no related Drug. |
Top |
Cross referenced IDs for DPM3 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |