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 GAPDH
Basic gene info.Gene symbolGAPDH
Gene nameglyceraldehyde-3-phosphate dehydrogenase
SynonymsG3PD|GAPD|HEL-S-162eP
CytomapUCSC genome browser: 12p13
Genomic locationchr12 :6644408-6647537
Type of geneprotein-coding
RefGenesNM_001256799.2,
NM_001289745.1,NM_001289746.1,NM_002046.5,
Ensembl idENSG00000111640
Descriptionaging-associated gene 9 proteinepididymis secretory sperm binding protein Li 162ePpeptidyl-cysteine S-nitrosylase GAPDH
Modification date20141222
dbXrefs MIM : 138400
HGNC : HGNC
Ensembl : ENSG00000111640
HPRD : 00713
Vega : OTTHUMG00000137379
ProteinUniProt: P04406
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GAPDH
BioGPS: 2597
Gene Expression Atlas: ENSG00000111640
The Human Protein Atlas: ENSG00000111640
PathwayNCI Pathway Interaction Database: GAPDH
KEGG: GAPDH
REACTOME: GAPDH
ConsensusPathDB
Pathway Commons: GAPDH
MetabolismMetaCyc: GAPDH
HUMANCyc: GAPDH
RegulationEnsembl's Regulation: ENSG00000111640
miRBase: chr12 :6,644,408-6,647,537
TargetScan: NM_001256799
cisRED: ENSG00000111640
ContextiHOP: GAPDH
cancer metabolism search in PubMed: GAPDH
UCL Cancer Institute: GAPDH
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GAPDH in cancer cell metabolism1. Zhang JY, Zhang F, Hong CQ, Giuliano AE, Cui XJ, et al. (2015) Critical protein GAPDH and its regulatory mechanisms in cancer cells. Cancer Biol Med 12: 10-22. doi: 10.7497/j.issn.2095-3941.2014.0019. pmid: 4383849. go to article
2. Jing Z, Heng W, Xia L, Ning W, Yafei Q, et al. (2015) Downregulation of phosphoglycerate dehydrogenase inhibits proliferation and enhances cisplatin sensitivity in cervical adenocarcinoma cells by regulating Bcl-2 and caspase-3. Cancer Biol Ther 16: 541-548. doi: 10.1080/15384047.2015.1017690. go to article
3. Hjerpe E, Brage SE, Frostvik Stolt M, Johansson H, Shoshan M, et al. (2014) Metabolic markers and HSP60 in chemonaive serous solid ovarian cancer versus ascites. Int J Gynecol Cancer 24: 1389-1394. doi: 10.1097/IGC.0000000000000246. go to article

Top
Phenotypic Information for GAPDH(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GAPDH
Familial Cancer Database: GAPDH
* 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
BIOCARTA_GLYCOLYSIS_PATHWAY
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM 138400; gene.
Orphanet
DiseaseKEGG Disease: GAPDH
MedGen: GAPDH (Human Medical Genetics with Condition)
ClinVar: GAPDH
PhenotypeMGI: GAPDH (International Mouse Phenotyping Consortium)
PhenomicDB: GAPDH

Mutations for GAPDH
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 GAPDH related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a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BG391044GAPDH22841266461256646277GAPDH826001266461546647044
BC044944ZNF6381161227160107171603450GAPDH160416591266474826647537
BF820683SRRT172217100483975100484540GAPDH2114201266473226647532

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=2

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=20)
Stat. for Synonymous SNVs
(# total SNVs=3)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr12:6647098-6647098p.S292A2
chr12:6646853-6646853p.S210F2
chr12:6646152-6646152p.V101V2
chr12:6646153-6646153p.F102I1
chr12:6646882-6646882p.V220L1
chr12:6644014-6644014p.V6I1
chr12:6647313-6647313p.A329T1
chr12:6646278-6646278p.G115fs*211
chr12:6646941-6646941p.N239K1
chr12:6645733-6645733p.D35Y1

Top
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
# sample 1111 2    321  11 3
# mutation 1111 2    221  11 3
nonsynonymous SNV 1111      221  11 2
synonymous SNV      2            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
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
chr12:6646512p.A119S,GAPDH2
chr12:6646845p.D35Y,GAPDH1
chr12:6645733p.E21K,GAPDH1
chr12:6646882p.D47G,GAPDH1
chr12:6645907p.V53I,GAPDH1
chr12:6647006p.G73E,GAPDH1
chr12:6646115p.P117P,GAPDH1
chr12:6647098p.V129L,GAPDH1
chr12:6646132p.Q143H,GAPDH1
chr12:6647106p.R158L,GAPDH1

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 GAPDH 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 GAPDH

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.
Top
check002.gifProtein Expression Plot (RPPA)
*RPPA protein expression data were extracted from TCPA (The Cancer Proteome Atlas). Normalized data based on replicated based normalization (RBN) was used to draw following figures.

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

ASPRV1,C1orf68,CCL27,FLG2,GAPDHS,KPRP,KRT1,
KRT2,LCE1A,LCE1B,LCE1C,LCE1D,LCE1E,LCE1F,
LCE2B,LCE2C,LCE2D,LCE5A,LCE6A,LOR,MLANA
ARID1A,CCDC57,CRAMP1L,ERN1,GAPDHS,ITPR3,CLUHP3,
LDB1,LOC100131193,LOC646471,MAML1,NCKAP5,NEK8,PRDM15,
SLC26A1,SPATA13,TUBGCP6,URB1,ZNF335,ZNF500,ZNF710

AHSA2,SNHG20,GAPDHS,KLHL31,LENG8,LOC100129387,LOC100130557,
LOC256880,LOC440944,NSUN5P2,OGT,PMS2P3,TRMT10B,SEPT7P2,
SNORA71E,STAG3L3,TCTE3,TRIM52,WDR27,DPH7,ZNF767P
AHI1,ALG1L2,ASPH,SYNE4,TDRP,COG5,COG6,
FIBCD1,GAPDHS,GPRIN3,KCTD12,KIR2DL1,PRPS1L1,RARRES1,
RGS17,SEC24D,SLC16A7,SLC26A4,SLC6A12,SULT1C2,TBC1D8B
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 GAPDH
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P04406; -.
ChemistryChEMBL CHEMBL2284; -.
Organism-specific databasesPharmGKB PA28554; -.
Organism-specific databasesCTD 2597; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00157glyceraldehyde-3-phosphate dehydrogenaseapproved; nutraceuticalNADH
DB01907glyceraldehyde-3-phosphate dehydrogenaseexperimentalNicotinamide-Adenine-Dinucleotide
DB02059glyceraldehyde-3-phosphate dehydrogenaseexperimentalAdenosine-5-Diphosphoribose
DB03893glyceraldehyde-3-phosphate dehydrogenaseexperimentalThionicotinamide-Adenine-Dinucleotide
DB07347glyceraldehyde-3-phosphate dehydrogenaseexperimental4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
DB02263glyceraldehyde-3-phosphate dehydrogenaseexperimentalGlyceraldehyde-3-Phosphate
DB00269glyceraldehyde-3-phosphate dehydrogenaseapprovedChlorotrianisene
DB00286glyceraldehyde-3-phosphate dehydrogenaseapprovedConjugated Estrogens
DB00890glyceraldehyde-3-phosphate dehydrogenaseapprovedDienestrol
DB00255glyceraldehyde-3-phosphate dehydrogenaseapprovedDiethylstilbestrol
DB00783glyceraldehyde-3-phosphate dehydrogenaseapproved; investigationalEstradiol
DB00655glyceraldehyde-3-phosphate dehydrogenaseapprovedEstrone
DB00977glyceraldehyde-3-phosphate dehydrogenaseapprovedEthinyl Estradiol


Top
Cross referenced IDs for GAPDH
* 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