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 GAD1
Basic gene info.Gene symbolGAD1
Gene nameglutamate decarboxylase 1 (brain, 67kDa)
SynonymsCPSQ1|GAD|SCP
CytomapUCSC genome browser: 2q31
Genomic locationchr2 :171673199-171699269
Type of geneprotein-coding
RefGenesNM_000817.2,
NM_013445.3,
Ensembl idENSG00000128683
Description67 kDa glutamic acid decarboxylaseGAD-67glutamate decarboxylase 1glutamate decarboxylase 67 kDa isoform
Modification date20141222
dbXrefs MIM : 605363
HGNC : HGNC
Ensembl : ENSG00000128683
HPRD : 12011
Vega : OTTHUMG00000044175
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GAD1
BioGPS: 2571
Gene Expression Atlas: ENSG00000128683
The Human Protein Atlas: ENSG00000128683
PathwayNCI Pathway Interaction Database: GAD1
KEGG: GAD1
REACTOME: GAD1
ConsensusPathDB
Pathway Commons: GAD1
MetabolismMetaCyc: GAD1
HUMANCyc: GAD1
RegulationEnsembl's Regulation: ENSG00000128683
miRBase: chr2 :171,673,199-171,699,269
TargetScan: NM_000817
cisRED: ENSG00000128683
ContextiHOP: GAD1
cancer metabolism search in PubMed: GAD1
UCL Cancer Institute: GAD1
Assigned class in ccmGDBC

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Phenotypic Information for GAD1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GAD1
Familial Cancer Database: GAD1
* 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_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM
KEGG_BETA_ALANINE_METABOLISM
KEGG_TAURINE_AND_HYPOTAURINE_METABOLISM
KEGG_BUTANOATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GAD1
MedGen: GAD1 (Human Medical Genetics with Condition)
ClinVar: GAD1
PhenotypeMGI: GAD1 (International Mouse Phenotyping Consortium)
PhenomicDB: GAD1

Mutations for GAD1
* 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 GAD1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW162120SGSM281481722842082284348GAD11446702171705814171716272
DA078791GAD112742171673400171675153ALDOC274581172690197226902481
AW609892GAD14242171690266171690286PARD322470103460603534620262
M85674GAD112682171715328171716410RUNX1T126838289303073193030844

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
There's no copy number variation information in COSMIC data for this gene.

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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=59)
Stat. for Synonymous SNVs
(# total SNVs=13)
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
chr2:171686107-171686107p.R90C4
chr2:171693312-171693312p.R186L3
chr2:171687555-171687555p.R134C3
chr2:171678659-171678659p.G49S2
chr2:171687621-171687621p.L156L2
chr2:171686061-171686061p.K74N2
chr2:171678609-171678609p.W32*2
chr2:171705817-171705817p.L381F2
chr2:171702536-171702536p.A322D2
chr2:171705836-171705836p.R387H2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample42 141 1111 851  1410 8
# mutation42 151 1111 961  1610 9
nonsynonymous SNV42 131 1 1  751  126 6
synonymous SNV   2   1 1 21   44 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])

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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
chr2:171702556p.K74N,GAD13
chr2:171686061p.L329I3
chr2:171686107p.A253T2
chr2:171702021p.A544G2
chr2:171716238p.R90C,GAD12
chr2:171687555p.A219A2
chr2:171700573p.R134C,GAD12
chr2:171702538p.S8S,GAD11
chr2:171687691p.N155T,GAD11
chr2:171709254p.M233I1

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 GAD1 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 GAD1

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

ANKRD20A4,ANKRD20A8P,FAM215A,DENND1B,EVL,FMO5,GAD1,
IQCF1,FAM214A,LOC440925,LOC728606,LRRC6,MAP2K4,MYO3B,
NEK10,PKIB,SCGB1D2,SP5,TNK1,TPRG1,ULK4
LINC00314,CDH7,ELAVL2,GAD1,GUCY1B2,HAO2,IGFL1,
KCNU1,KRT26,MAGEC2,MYO3A,MYO3B,RLN2,ROBO2,
SLC22A1,SNORA4,SOX14,STXBP5L,SYT1,TEX14,ZPLD1

AGR2,ALOXE3,MYRF,CABLES1,CASP4,CCK,DPP4,
ETV5,FOXD1,GAD1,KCNJ3,MTCL1,LHB,LMF2,
LOC440925,LRRC16A,SOX13,SP5,TCIRG1,TRNP1,ZFPM1
CYP4F30P,CEACAM3,DEFA1B,RIPPLY3,EPB41L4A,GAD1,GJB4,
GNRHR,GPR12,HPVC1,KRTAP13-2,MORF4,MSMB,OR2S2,
OTX1,PAPPA2,TAPT1,TMEM105,SYNDIG1L,UNC5C,ZNF720
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 GAD1
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
DB00114glutamate decarboxylase 1 (brain, 67kDa)nutraceuticalPyridoxal Phosphate
DB00142glutamate decarboxylase 1 (brain, 67kDa)approved; nutraceuticalL-Glutamic Acid


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Cross referenced IDs for GAD1
* 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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