Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 PHGDH
Basic gene info.Gene symbolPHGDH
Gene namephosphoglycerate dehydrogenase
Synonyms3-PGDH|3PGDH|HEL-S-113|NLS|NLS1|PDG|PGAD|PGD|PGDH|PHGDHD|SERA
CytomapUCSC genome browser: 1p12
Genomic locationchr1 :120254418-120286849
Type of geneprotein-coding
RefGenesNM_006623.3,
Ensembl idENSG00000092621
Description3-phosphoglycerate dehydrogenaseD-3-phosphoglycerate dehydrogenaseepididymis secretory protein Li 113
Modification date20141211
dbXrefs MIM : 606879
HGNC : HGNC
Ensembl : ENSG00000092621
HPRD : 06047
Vega : OTTHUMG00000012100
ProteinUniProt: O43175
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PHGDH
BioGPS: 26227
Gene Expression Atlas: ENSG00000092621
The Human Protein Atlas: ENSG00000092621
PathwayNCI Pathway Interaction Database: PHGDH
KEGG: PHGDH
REACTOME: PHGDH
ConsensusPathDB
Pathway Commons: PHGDH
MetabolismMetaCyc: PHGDH
HUMANCyc: PHGDH
RegulationEnsembl's Regulation: ENSG00000092621
miRBase: chr1 :120,254,418-120,286,849
TargetScan: NM_006623
cisRED: ENSG00000092621
ContextiHOP: PHGDH
cancer metabolism search in PubMed: PHGDH
UCL Cancer Institute: PHGDH
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PHGDH in cancer cell metabolism1. Mullarky E, Mattaini KR, Vander Heiden MG, Cantley LC, Locasale JW (2011) PHGDH amplification and altered glucose metabolism in human melanoma. Pigment cell & melanoma research 24: 1112-1115. go to article
2. Kim HM, Jung WH, Koo JS (2014) Site-specific metabolic phenotypes in metastatic breast cancer. Journal of translational medicine 12: 1-17. go to article
3. Mattaini KR, Brignole EJ, Kini M, Davidson SM, Fiske BP, et al. (2015) An epitope tag alters phosphoglycerate dehydrogenase structure and impairs ability to support cell proliferation. Cancer Metab 3: 5. doi: 10.1186/s40170-015-0131-7. pmid: 4414297. go to article
4. Ou Y, Wang SJ, Jiang L, Zheng B, Gu W (2015) p53 Protein-mediated regulation of phosphoglycerate dehydrogenase (PHGDH) is crucial for the apoptotic response upon serine starvation. J Biol Chem 290: 457-466. doi: 10.1074/jbc.M114.616359. pmid: 4281747. go to article
5. Kim SK, Jung WH, Koo JS (2014) Differential expression of enzymes associated with serine/glycine metabolism in different breast cancer subtypes. PLoS One 9: e101004. doi: 10.1371/journal.pone.0101004. pmid: 4076239. go to article
6. Chen J, Chung F, Yang G, Pu M, Gao H, et al. (2013) Phosphoglycerate dehydrogenase is dispensable for breast tumor maintenance and growth. Oncotarget 4: 2502-2511. pmid: 3926844. go to article
7. Ma L, Tao Y, Duran A, Llado V, Galvez A, et al. (2013) Control of nutrient stress-induced metabolic reprogramming by PKCzeta in tumorigenesis. Cell 152: 599-611. doi: 10.1016/j.cell.2012.12.028. pmid: 3963830. go to article

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Phenotypic Information for PHGDH(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PHGDH
Familial Cancer Database: PHGDH
* 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_GLYCINE_SERINE_AND_THREONINE_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM 256520; phenotype.
601815; phenotype.
606879; gene.
Orphanet 2671; Neu-Laxova syndrome.
79351; 3-phosphoglycerate dehydrogenase deficiency.
DiseaseKEGG Disease: PHGDH
MedGen: PHGDH (Human Medical Genetics with Condition)
ClinVar: PHGDH
PhenotypeMGI: PHGDH (International Mouse Phenotyping Consortium)
PhenomicDB: PHGDH

Mutations for PHGDH
* 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 PHGDH related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF804555PHGDH111471120284422120285464PHGDH1372141120285552120285630
BE844016HLA-DRA15189637590983759271PHGDH1842391120286659120286714
AW261826PHGDH194001120285616120286838EPHX13955531226016559226019583
BC004528PHGDH498891120254576120278045UBAC288727341399896770100038682

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  22  
GAIN (# sample)        1 1  22  
LOSS (# sample)                 
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=35)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr1:120263849-120263849p.N65N4
chr1:120285546-120285546p.T442T3
chr1:120284428-120284428p.A373T3
chr1:120283043-120283043p.P327L2
chr1:120278013-120278013p.R247W2
chr1:120285558-120285558p.Q446Q2
chr1:120279735-120279735p.?2
chr1:120277917-120277917p.?2
chr1:120269623-120269623p.?2
chr1:120263923-120263923p.R90K2

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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
# sample1  51   2  821  42111
# mutation1  51   2  821  42111
nonsynonymous SNV   31   2  62   2215
synonymous SNV1  2       2 1  2  6
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
chr1:120279853p.F303F2
chr1:120277271p.R230H1
chr1:120279825p.I511I1
chr1:120286533p.R75S1
chr1:120263834p.P282L1
chr1:120277283p.G79G1
chr1:120279828p.A286V1
chr1:120286594p.L85M1
chr1:120263879p.A291T1
chr1:120277300p.A87A1

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 PHGDH 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 PHGDH

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

AMBN,ATP1A1,BPI,CMC2,CNTN6,FRZB,FTMT,
KCNJ16,MDGA2,NCALD,NECAB2,NOTCH2,PHGDH,PLSCR5,
ROPN1B,SEC22B,SLC39A12,SLC43A3,SPON1,WARS2,ZNF697
ACAD9,FAHD2A,HOOK2,HYI,KLHL22,LPHN1,LRP5,
MDFI,MESP1,PHGDH,PPP1R1B,SCRN2,SELENBP1,SF3B2,
SLC19A1,SLC25A10,SLC25A6,THRA,TYSND1,VPS26B,WIPI2

AARS,ASNS,ATF4,CARS,CBS,GARS,GPT2,
MARS,MTHFD2,PHGDH,PSAT1,SARS,SHMT2,SLC3A2,
SLC4A5,SLC7A5,STC2,TARS,ULBP1,XPOT,YARS
ABCC9,ACTA2,ANXA6,AOC3,ATP1A2,CLIP3,CNGA3,
CPXM2,FBXL22,FHL3,HRASLS5,LOXL4,MAGEE1,NIPAL4,
NLGN1,NPTXR,PDE2A,PHGDH,SLIT2,TGFB1I1,TMEM200B
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 PHGDH
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL2311243; -.
Organism-specific databasesPharmGKB PA33264; -.
Organism-specific databasesCTD 26227; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00157phosphoglycerate dehydrogenaseapproved; nutraceuticalNADH
DB01907phosphoglycerate dehydrogenaseexperimentalNicotinamide-Adenine-Dinucleotide
DB01694phosphoglycerate dehydrogenaseexperimentalD-tartaric acid


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Cross referenced IDs for PHGDH
* 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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