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 PGM1
Basic gene info.Gene symbolPGM1
Gene namephosphoglucomutase 1
SynonymsCDG1T|GSD14
CytomapUCSC genome browser: 1p31
Genomic locationchr1 :64088886-64125916
Type of geneprotein-coding
RefGenesNM_001172818.1,
NM_001172819.1,NM_002633.2,
Ensembl idENSG00000079739
DescriptionPGM 1glucose phosphomutase 1phosphoglucomutase-1
Modification date20141219
dbXrefs MIM : 171900
HGNC : HGNC
Ensembl : ENSG00000079739
HPRD : 01389
Vega : OTTHUMG00000008968
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PGM1
BioGPS: 5236
Gene Expression Atlas: ENSG00000079739
The Human Protein Atlas: ENSG00000079739
PathwayNCI Pathway Interaction Database: PGM1
KEGG: PGM1
REACTOME: PGM1
ConsensusPathDB
Pathway Commons: PGM1
MetabolismMetaCyc: PGM1
HUMANCyc: PGM1
RegulationEnsembl's Regulation: ENSG00000079739
miRBase: chr1 :64,088,886-64,125,916
TargetScan: NM_001172818
cisRED: ENSG00000079739
ContextiHOP: PGM1
cancer metabolism search in PubMed: PGM1
UCL Cancer Institute: PGM1
Assigned class in ccmGDBC

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Phenotypic Information for PGM1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PGM1
Familial Cancer Database: PGM1
* 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_GLYCOLYSIS_GLUCONEOGENESIS
KEGG_GALACTOSE_METABOLISM
KEGG_STARCH_AND_SUCROSE_METABOLISM
KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PGM1
MedGen: PGM1 (Human Medical Genetics with Condition)
ClinVar: PGM1
PhenotypeMGI: PGM1 (International Mouse Phenotyping Consortium)
PhenomicDB: PGM1

Mutations for PGM1
* 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
ovaryPGM1chr16412521764125237PGM1chr16408720064087220
pancreasPGM1chr16410352164103541EFCAB7chr16402390064023920
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 PGM1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI830657PGM1118116412574164125974CPSF2182378149262892392629119
BE836713XG52174X26937182693841PGM117034316410060664101993
AI798979PGM117116412527664125346PGM16830116412541964125652

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             
LOSS (# sample) 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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=49)
Stat. for Synonymous SNVs
(# total SNVs=11)
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
chr1:64097432-64097432p.R221C3
chr1:64095186-64095186p.I113F2
chr1:64114301-64114301p.Y420H2
chr1:64125315-64125315p.T553M2
chr1:64120041-64120041p.V501V2
chr1:64059353-64059353p.F65C2
chr1:64095098-64095098p.I83I2
chr1:64100614-64100614p.L266H2
chr1:64125258-64125258p.V534G1
chr1:64095185-64095185p.I112I1

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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
# sample31171 1 11 511 154 8
# mutation31191 1 11 611 154 8
nonsynonymous SNV21181 1 11 31  112 6
synonymous SNV1  1       3 1  42 2
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
chr1:64095098p.I101I,PGM12
chr1:64095185p.W411C,PGM11
chr1:64120081p.F223L,PGM11
chr1:64100595p.E428K,PGM11
chr1:64059224p.G232G,PGM11
chr1:64114274p.D429H,PGM11
chr1:64095186p.L22P1
chr1:64120092p.I238I,PGM11
chr1:64100648p.R440Q,PGM11
chr1:64059309p.A50A1

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 PGM1 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 PGM1

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

CDC20,CMPK1,FAF1,CCDC71L,IFRD1,KTI12,LRP8,
LRRC41,LRRC42,MED8,MPP6,MRPL37,NRD1,ORC1,
PDIA6,PGM1,RHBDL2,SERBP1,STEAP3,TTC7A,UQCRHL
ACAT1,ACO2,ALPK3,ATP5B,C6orf106,CHCHD3,DLD,
ETFDH,HADHB,HOXA10,HSPB6,NRD1,OGDH,OPTN,
PGM1,PHYH,SGCG,SLC2A4,SNTA1,SOX6,TBX15

ABCD3,ACADS,ACO2,ADH6,SOWAHB,CPT2,FABP1,
GIPC2,HK2,ITM2C,LDHD,NR3C2,P2RY2,PGM1,
PIGR,RETSAT,RIMKLA,SLC35A3,UGP2,UGT1A10,UGT2B15
ACOT4,ACSS2,AGFG2,SOWAHB,AP1M2,BDH1,BTBD3,
CCNJL,RHOV___CHP1,DTX4,FUT3,IHH,MARVELD3,MYO1D,
PFKL,PGM1,PPARG,TNK1,TPRN,TRAF3IP2,WDR78
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 PGM1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00515phosphoglucomutase 1approvedCisplatin


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Cross referenced IDs for PGM1
* 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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