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 ABAT
Basic gene info.Gene symbolABAT
Gene name4-aminobutyrate aminotransferase
SynonymsGABA-AT|GABAT|NPD009
CytomapUCSC genome browser: 16p13.2
Genomic locationchr16 :8768443-8878432
Type of geneprotein-coding
RefGenesNM_000663.4,
NM_001127448.1,NM_020686.5,
Ensembl idENSG00000183044
Description(S)-3-amino-2-methylpropionate transaminase4-aminobutyrate aminotransferase, mitochondrial4-aminobutyrate transaminaseGABA aminotransferaseGABA transaminaseGABA transferasegamma-amino-N-butyrate transaminase
Modification date20141207
dbXrefs MIM : 137150
HGNC : HGNC
Ensembl : ENSG00000183044
HPRD : 00661
Vega : OTTHUMG00000048201
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ABAT
BioGPS: 18
Gene Expression Atlas: ENSG00000183044
The Human Protein Atlas: ENSG00000183044
PathwayNCI Pathway Interaction Database: ABAT
KEGG: ABAT
REACTOME: ABAT
ConsensusPathDB
Pathway Commons: ABAT
MetabolismMetaCyc: ABAT
HUMANCyc: ABAT
RegulationEnsembl's Regulation: ENSG00000183044
miRBase: chr16 :8,768,443-8,878,432
TargetScan: NM_000663
cisRED: ENSG00000183044
ContextiHOP: ABAT
cancer metabolism search in PubMed: ABAT
UCL Cancer Institute: ABAT
Assigned class in ccmGDBC

Top
Phenotypic Information for ABAT(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ABAT
Familial Cancer Database: ABAT
* 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_PROPANOATE_METABOLISM
KEGG_BUTANOATE_METABOLISM

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

Mutations for ABAT
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
central_nervous_systemABATchr1687954288795428PMM2chr1688978158897815
ovaryABATchr1687844468784466ABATchr1687851828785202
ovaryABATchr1687904568790476ABATchr1687908828790902
ovaryABATchr1687907878790987SHISA6chr171143806511438265
ovaryABATchr1688473448847364ABATchr1688237548823774
pancreasABATchr1687891358789155ABATchr1687892288789248
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 ABAT related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA002171LDLR1183191124430911244491ABAT1844931688776658877972
BF923967AKNAD1621471109465085109465171ABAT1424441688397118840013
BF064196ABAT3543921688658848865922PSMD12389490176535151065351611
BF944944EDIL3828058344884383449119ABAT2624391688351738835350

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample12   1           
GAIN (# sample)11   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)

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=4

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=41)
Stat. for Synonymous SNVs
(# total SNVs=8)
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
chr16:8858658-8858658p.A171T4
chr16:8844389-8844389p.V103V3
chr16:8862065-8862065p.D207N2
chr16:8868846-8868846p.V352M2
chr16:8873425-8873425p.L453L2
chr16:8844355-8844355p.R92Q2
chr16:8862733-8862733p.S240F2
chr16:8858686-8858686p.R180Q2
chr16:8851628-8851628p.A111T1
chr16:8866761-8866761p.D314G1

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 5 8  5 1  63   126 9
# mutation 5 8  6 1  73   126 9
nonsynonymous SNV 3 7  4 1  52   84 8
synonymous SNV 2 1  2    21   42 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
chr16:8866730p.R92Q,ABAT2
chr16:8858658p.V352L,ABAT2
chr16:8858686p.A171T,ABAT2
chr16:8844355p.R180Q,ABAT2
chr16:8868846p.A304T,ABAT2
chr16:8862065p.M4V,ABAT1
chr16:8873425p.E195K,ABAT1
chr16:8862816p.D306N,ABAT1
chr16:8851634p.P445P,ABAT1
chr16:8868910p.L45L,ABAT1

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 ABAT 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 ABAT

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))
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

ABAT,ACOT4,ADAMTSL5,SAMD15,C16orf62,C16orf71,COG7,
COQ7,FANK1,GLUL,GLYR1,IQCK,NEK11,POLR3E,
RABEP1,THUMPD1,TNRC6A,TTC8,ZNF174,ZSCAN32,ZNF720
ABAT,ARSD,SAMD15,CELSR1,CELSR2,CORO2A,CT62,
DNAJC22,FOXA1,GALNT7,GOLM1,C5AR2,GREB1,HN1L,
ITIH6,MLPH,PKIB,SEC16A,SPATA17,TPBG,XBP1

ABAT,ARFGEF2,ATP9A,C11orf95,FAM217B,ESPN,FITM2,
GGT7,LOC647979,NAALADL2,PIGU,PLAGL2,POFUT1,QPRT,
SLC5A6,STAU1,TAF4,TLE2,TM9SF4,VAV3,ZSWIM3
ABAT,ACO2,ACSL5,AGPAT3,ANKS4B,CNTFR,DHRS11,
ERBB2,FAM73B,FMO4,GDPD2,HADHA,KCNK5,LPCAT3,
MAN1A1,MARCH8,NGEF,PBLD,PNPLA1,SCAMP5,SNX24
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 ABAT
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
DB001144-aminobutyrate aminotransferasenutraceuticalPyridoxal Phosphate
DB001194-aminobutyrate aminotransferaseapproved; nutraceuticalPyruvic acid
DB001424-aminobutyrate aminotransferaseapproved; nutraceuticalL-Glutamic Acid
DB001604-aminobutyrate aminotransferaseapproved; nutraceuticalL-Alanine
DB003134-aminobutyrate aminotransferaseapproved; investigationalValproic Acid
DB007804-aminobutyrate aminotransferaseapprovedPhenelzine
DB010804-aminobutyrate aminotransferaseapprovedVigabatrin
DB016994-aminobutyrate aminotransferaseexperimental(4e)-4-Aminohex-4-Enoic Acid
DB042354-aminobutyrate aminotransferaseexperimental4-Amino Hexanoic Acid


Top
Cross referenced IDs for ABAT
* 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