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 ABAT

Basic gene info.	Gene symbol	ABAT
	Gene name	4-aminobutyrate aminotransferase
	Synonyms	GABA-AT\|GABAT\|NPD009
	Cytomap	UCSC genome browser: 16p13.2
	Genomic location	chr16 :8768443-8878432
	Type of gene	protein-coding
	RefGenes	NM_000663.4, NM_001127448.1,NM_020686.5,
	Ensembl id	ENSG00000183044
	Description	(S)-3-amino-2-methylpropionate transaminase4-aminobutyrate aminotransferase, mitochondrial4-aminobutyrate transaminaseGABA aminotransferaseGABA transaminaseGABA transferasegamma-amino-N-butyrate transaminase
	Modification date	20141207
dbXrefs	MIM : 137150
	HGNC : HGNC
	Ensembl : ENSG00000183044
	HPRD : 00661
	Vega : OTTHUMG00000048201
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ABAT
	BioGPS: 18
	Gene Expression Atlas: ENSG00000183044
	The Human Protein Atlas: ENSG00000183044
Pathway	NCI Pathway Interaction Database: ABAT
	KEGG: ABAT
	REACTOME: ABAT
	ConsensusPathDB
	Pathway Commons: ABAT
Metabolism	MetaCyc: ABAT
	HUMANCyc: ABAT
Regulation	Ensembl's Regulation: ENSG00000183044
	miRBase: chr16 :8,768,443-8,878,432
	TargetScan: NM_000663
	cisRED: ENSG00000183044
Context	iHOP: ABAT
	cancer metabolism search in PubMed: ABAT
	UCL Cancer Institute: ABAT
Assigned class in ccmGDB	C

Top

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

Cancer 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/

Metabolic Pathway Description
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM KEGG_BETA_ALANINE_METABOLISM KEGG_PROPANOATE_METABOLISM KEGG_BUTANOATE_METABOLISM

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

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

Top

- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
central_nervous_system	ABAT	chr16	8795428	8795428	PMM2	chr16	8897815	8897815
ovary	ABAT	chr16	8784446	8784466	ABAT	chr16	8785182	8785202
ovary	ABAT	chr16	8790456	8790476	ABAT	chr16	8790882	8790902
ovary	ABAT	chr16	8790787	8790987	SHISA6	chr17	11438065	11438265
ovary	ABAT	chr16	8847344	8847364	ABAT	chr16	8823754	8823774
pancreas	ABAT	chr16	8789135	8789155	ABAT	chr16	8789228	8789248

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ABAT 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
AA002171	LDLR	1	183	19	11244309	11244491	ABAT	184	493	16	8877665	8877972
BF923967	AKNAD1	62	147	1	109465085	109465171	ABAT	142	444	16	8839711	8840013
BF064196	ABAT	354	392	16	8865884	8865922	PSMD12	389	490	17	65351510	65351611
BF944944	EDIL3	8	280	5	83448843	83449119	ABAT	262	439	16	8835173	8835350

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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)

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=4

Top

Somatic 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

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
chr16:8858658-8858658	p.A171T	4
chr16:8844389-8844389	p.V103V	3
chr16:8862065-8862065	p.D207N	2
chr16:8868846-8868846	p.V352M	2
chr16:8873425-8873425	p.L453L	2
chr16:8844355-8844355	p.R92Q	2
chr16:8862733-8862733	p.S240F	2
chr16:8858686-8858686	p.R180Q	2
chr16:8851628-8851628	p.A111T	1
chr16:8866761-8866761	p.D314G	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		5		8			5		1			6	3				12	6		9
# mutation		5		8			6		1			7	3				12	6		9
nonsynonymous SNV		3		7			4		1			5	2				8	4		8
synonymous SNV		2		1			2					2	1				4	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

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
chr16:8866730	p.A171T,ABAT	2
chr16:8858658	p.R180Q,ABAT	2
chr16:8858686	p.A304T,ABAT	2
chr16:8844355	p.R92Q,ABAT	2
chr16:8868846	p.V352L,ABAT	2
chr16:8862065	p.E141E,ABAT	1
chr16:8873425	p.P254L,ABAT	1
chr16:8862816	p.D385N,ABAT	1
chr16:8851634	p.R401R,ABAT	1
chr16:8868910	p.P152L,ABAT	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 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

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


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

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 ABAT

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00114	4-aminobutyrate aminotransferase	nutraceutical	Pyridoxal Phosphate
DB00119	4-aminobutyrate aminotransferase	approved; nutraceutical	Pyruvic acid
DB00142	4-aminobutyrate aminotransferase	approved; nutraceutical	L-Glutamic Acid
DB00160	4-aminobutyrate aminotransferase	approved; nutraceutical	L-Alanine
DB00313	4-aminobutyrate aminotransferase	approved; investigational	Valproic Acid
DB00780	4-aminobutyrate aminotransferase	approved	Phenelzine
DB01080	4-aminobutyrate aminotransferase	approved	Vigabatrin
DB01699	4-aminobutyrate aminotransferase	experimental	(4e)-4-Aminohex-4-Enoic Acid
DB04235	4-aminobutyrate aminotransferase	experimental	4-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