Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 PGM3
Basic gene info.Gene symbolPGM3
Gene namephosphoglucomutase 3
SynonymsAGM1|IMD23|PAGM|PGM 3
CytomapUCSC genome browser: 6q14.1-q15
Genomic locationchr6 :83874592-83903012
Type of geneprotein-coding
RefGenesNM_001199917.1,
NM_001199918.1,NM_001199919.1,NM_015599.2,
Ensembl idENSG00000013375
DescriptionN-acetylglucosamine-phosphate mutase 1acetylglucosamine phosphomutasephosphoacetylglucosamine mutase
Modification date20141207
dbXrefs MIM : 172100
HGNC : HGNC
Ensembl : ENSG00000013375
HPRD : 01390
Vega : OTTHUMG00000015110
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PGM3
BioGPS: 5238
Gene Expression Atlas: ENSG00000013375
The Human Protein Atlas: ENSG00000013375
PathwayNCI Pathway Interaction Database: PGM3
KEGG: PGM3
REACTOME: PGM3
ConsensusPathDB
Pathway Commons: PGM3
MetabolismMetaCyc: PGM3
HUMANCyc: PGM3
RegulationEnsembl's Regulation: ENSG00000013375
miRBase: chr6 :83,874,592-83,903,012
TargetScan: NM_001199917
cisRED: ENSG00000013375
ContextiHOP: PGM3
cancer metabolism search in PubMed: PGM3
UCL Cancer Institute: PGM3
Assigned class in ccmGDBC

Top
Phenotypic Information for PGM3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PGM3
Familial Cancer Database: PGM3
* 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
KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PGM3
MedGen: PGM3 (Human Medical Genetics with Condition)
ClinVar: PGM3
PhenotypeMGI: PGM3 (International Mouse Phenotyping Consortium)
PhenomicDB: PGM3

Mutations for PGM3
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PGM3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP314848HIST1H2BE146862618398926184456PGM346758368390069883902978

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

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

Top
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=5

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=34)
Stat. for Synonymous SNVs
(# total SNVs=6)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
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
chr6:83892687-83892687p.L156F5
chr6:83898387-83898387p.K112I2
chr6:83898499-83898499p.L75V2
chr6:83892684-83892684p.L157F2
chr6:83900643-83900643p.T30M1
chr6:83889582-83889582p.G298*1
chr6:83892563-83892563p.?1
chr6:83880116-83880116p.D483Y1
chr6:83898385-83898385p.E113Q1
chr6:83884176-83884176p.I387V1

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 7  1 1 14   1310 5
# mutation 1 8  1 1 15   1311 6
nonsynonymous SNV 1 7  1   15   118 3
synonymous SNV   1    1       23 3
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
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
chr6:83896745p.S175G,PGM31
chr6:83900643p.T30M,PGM31
chr6:83880190p.D377G,PGM31
chr6:83889536p.N165N,PGM31
chr6:83896760p.G24W,PGM31
chr6:83900662p.D365E,PGM31
chr6:83881683p.E123K,PGM31
chr6:83889564p.Y23Y,PGM31
chr6:83896771p.L343L,PGM31
chr6:83900663p.T90T,PGM31

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 PGM3 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 PGM3

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

ACBD3,ARCN1,ASCC3,CCNC,COPB2,DOPEY1,EIF2AK3,
FUCA2,HCCS,IBTK,UFL1,ME1,PGM3,PHACTR2,
PIGA,RARS2,RNGTT,RWDD2A,SEC24A,SNX14,SYNCRIP
ACADL,BNIP3L,COL4A3BP,CRYBG3,DDHD1,EHHADH,EYS,
FNIP2,GFPT1,GNAI1,IGF1,KCTD20,LIMA1,PGM3,
PREX2,PTENP1,PTPDC1,SLC25A16,TMEM135,TRHDE,TTLL7

AGR2,ARCN1,ARF4,TMEM263,SLC18B1,COPB2,FAM46A,
GSTTP2,HSPA5,IBTK,KDELR3,NUCB2,NUS1,PGM3,
RWDD2A,SEC24D,SLC30A7,SLC31A1,SLC39A7,SSR1,SSR3
C19orf10,CLINT1,COPB1,DDOST,GNPNAT1,KDELR3,MTHFD2,
NEK6,NUDT5,PDIA6,PGM3,PPIB,PYCR1,RPL22L1,
SEC22B,SLC10A7,SLC38A5,TMED2,TMEM39A,TSTA3,UBXN4
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for PGM3


There's no related Drug.
Top
Cross referenced IDs for PGM3
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas