Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 PGAM1

Basic gene info.	Gene symbol	PGAM1
	Gene name	phosphoglycerate mutase 1 (brain)
	Synonyms	HEL-S-35\|PGAM-B\|PGAMA
	Cytomap	UCSC genome browser: 10q25.3
	Genomic location	chr10 :99186026-99193198
	Type of gene	protein-coding
	RefGenes	NM_002629.2,
	Ensembl id	ENSG00000171314
	Description	BPG-dependent PGAM 1epididymis secretory protein Li 35phosphoglycerate mutase 1phosphoglycerate mutase A, nonmuscle formphosphoglycerate mutase isozyme B
	Modification date	20141207
dbXrefs	MIM : 172250
	HGNC : HGNC
	Ensembl : ENSG00000171314
	HPRD : 01392
	Vega : OTTHUMG00000018846
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PGAM1
	BioGPS: 5223
	Gene Expression Atlas: ENSG00000171314
	The Human Protein Atlas: ENSG00000171314
Pathway	NCI Pathway Interaction Database: PGAM1
	KEGG: PGAM1
	REACTOME: PGAM1
	ConsensusPathDB
	Pathway Commons: PGAM1
Metabolism	MetaCyc: PGAM1
	HUMANCyc: PGAM1
Regulation	Ensembl's Regulation: ENSG00000171314
	miRBase: chr10 :99,186,026-99,193,198
	TargetScan: NM_002629
	cisRED: ENSG00000171314
Context	iHOP: PGAM1
	cancer metabolism search in PubMed: PGAM1
	UCL Cancer Institute: PGAM1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PGAM1 in cancer cell metabolism	1. Obre E, Rossignol R (2015) Emerging concepts in bioenergetics and cancer research: metabolic flexibility, coupling, symbiosis, switch, oxidative tumors, metabolic remodeling, signaling and bioenergetic therapy. Int J Biochem Cell Biol 59: 167-181. doi: 10.1016/j.biocel.2014.12.008. go to article 2. Jiang X, Sun Q, Li H, Li K, Ren X (2014) The role of phosphoglycerate mutase 1 in tumor aerobic glycolysis and its potential therapeutic implications. Int J Cancer 135: 1991-1996. doi: 10.1002/ijc.28637. go to article 3. Stine ZE, Dang CV (2013) Stress eating and tuning out: cancer cells re-wire metabolism to counter stress. Crit Rev Biochem Mol Biol 48: 609-619. doi: 10.3109/10409238.2013.844093. pmid: 4063414. go to article 4. Hitosugi T, Zhou L, Fan J, Elf S, Zhang L, et al. (2013) Tyr26 phosphorylation of PGAM1 provides a metabolic advantage to tumours by stabilizing the active conformation. Nat Commun 4: 1790. doi: 10.1038/ncomms2759. pmid: 3648882. go to article 5. Chaneton B, Gottlieb E (2012) PGAMgnam style: a glycolytic switch controls biosynthesis. Cancer Cell 22: 565-566. doi: 10.1016/j.ccr.2012.10.014. go to article

Top

Phenotypic Information for PGAM1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PGAM1
	Familial Cancer Database: PGAM1

* 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/

Metabolic Pathway Description
KEGG_GLYCOLYSIS_GLUCONEOGENESIS BIOCARTA_GLYCOLYSIS_PATHWAY REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: PGAM1
	MedGen: PGAM1 (Human Medical Genetics with Condition)
	ClinVar: PGAM1
Phenotype	MGI: PGAM1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PGAM1

Mutations for PGAM1

* 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 PGAM1 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
AK125057	SMAD2	1	1430	18	45453116	45454544	PGAM1	1431	3139	10	99186037	99193197
CN393630	ATP7A	1	63	X	77223635	77223697	PGAM1	64	581	10	99192262	99192779

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=2

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=9)	Stat. for Synonymous SNVs (# total SNVs=2)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

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
chr10:99192235-99192235	p.R240H	2
chr10:99190263-99190263	p.E89E	1
chr10:99190264-99190264	p.R90W	1
chr10:99190719-99190719	p.R141M	1
chr10:99190736-99190736	p.E147K	1
chr10:99190742-99190742	p.Q149E	1
chr10:99190894-99190894	p.?	1
chr10:99192182-99192182	p.K222N	1
chr10:99186086-99186086	p.L8V	1
chr10:99190184-99190184	p.A63V	1

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1		1	4					1			2								4
# mutation	1		1	3					1			2								4
nonsynonymous SNV	1		1	3					1			1								3
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])

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
chr10:99192235	p.R240H	2
chr10:99190257	p.R90W	1
chr10:99190263	p.R141M	1
chr10:99190264	p.E147K	1
chr10:99190719	p.Q149E	1
chr10:99190736	p.P173S	1
chr10:99190742	p.E198Q	1
chr10:99190814	p.A3S	1
chr10:99186071	p.L8V	1
chr10:99190889	p.A63V	1

Other 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

Copy Number for PGAM1 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 PGAM1

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.

: Open all plots for all cancer types

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

: Open all plots for all cancer types


ACTR1A,ARPC2,AVEN,BNIP3,ENO1,GAPDH,GLRX3, GOT1,GPI,GSTO1,LDHA,PGAM1,PGAM4,PGK1, PKM,PSMB2,RAN,SLC16A3,TPI1,TUBA1C,USMG5	ANXA2,ANXA2P1,ANXA2P2,ATP1B3,ATP6V0E1,EMC7,SLC35F6, CD63,CRYL1,DOLK,DYNLL1,FUCA2,IFNGR2,MSRA, NUDT5,PGAM1,PRDX4,RHOA,SNX11,UBE2L3,VKORC1

ALDOA,ATP5A1,ATP5B,TIMM21,MCU,EIF4A1,EIF5A, EIF5AL1,ENO1,GAPDH,LDHA,P4HA1,PFKP,PGAM1, PKM,PLEK2,SFXN1,SLC16A3,TPI1,TUBA1B,TYMS	ATP6V1E1,SLIRP,DYNLT1,LSM3,MRPL20,NEDD8,PGAM1, POMP,PSMA1,PSMA2,PSMA3,PSMA6,PSMA7,PSMB1, PSMB5,PSMB6,PSMC2,PSMC3,PSMC4,PSMD13,RHOA

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

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

Top

Pharmacological Information for PGAM1

There's no related Drug.

Top

Cross referenced IDs for PGAM1

* 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