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 CCBL1
Basic gene info.Gene symbolCCBL1
Gene namecysteine conjugate-beta lyase, cytoplasmic
SynonymsGTK|KAT1|KATI
CytomapUCSC genome browser: 9q34.11
Genomic locationchr9 :131595391-131644354
Type of geneprotein-coding
RefGenesNM_001122671.1,
NM_001122672.1,NM_001287390.1,NM_004059.4,NR_109829.1,
Ensembl idENSG00000171097
Descriptionbeta-lysase, kidneycysteine conjugate-beta lyase; cytoplasmic (glutamine transaminase K, kyneurenine aminotransferase)cysteine-S-conjugate beta-lyaseglutamine transaminase Kglutamine--phenylpyruvate transaminaseglutamine-phenylpyruvate aminotransfera
Modification date20141211
dbXrefs MIM : 600547
HGNC : HGNC
Ensembl : ENSG00000171097
HPRD : 02769
Vega : OTTHUMG00000020767
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CCBL1
BioGPS: 883
Gene Expression Atlas: ENSG00000171097
The Human Protein Atlas: ENSG00000171097
PathwayNCI Pathway Interaction Database: CCBL1
KEGG: CCBL1
REACTOME: CCBL1
ConsensusPathDB
Pathway Commons: CCBL1
MetabolismMetaCyc: CCBL1
HUMANCyc: CCBL1
RegulationEnsembl's Regulation: ENSG00000171097
miRBase: chr9 :131,595,391-131,644,354
TargetScan: NM_001122671
cisRED: ENSG00000171097
ContextiHOP: CCBL1
cancer metabolism search in PubMed: CCBL1
UCL Cancer Institute: CCBL1
Assigned class in ccmGDBC

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Phenotypic Information for CCBL1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CCBL1
Familial Cancer Database: CCBL1
* 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
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CCBL1
MedGen: CCBL1 (Human Medical Genetics with Condition)
ClinVar: CCBL1
PhenotypeMGI: CCBL1 (International Mouse Phenotyping Consortium)
PhenomicDB: CCBL1

Mutations for CCBL1
* 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
* 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
ovaryCCBL1chr9131601227131601247CCBL1chr9131612088131612108
ovaryCCBL1chr9131609831131609851CCBL1chr9131621628131621648
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 CCBL1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF891052CCBL1282129131643217131643402CCBL12085269131640998131641316
BF890958CCBL1152009131643215131643402CCBL11965149131640998131641316
BF743879CCBL161219131596051131597662CCBL11085449131595480131595915

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  
GAIN (# sample)              1  
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=37)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr9:131599985-131599985p.T182T3
chr9:131597853-131597853p.R317C3
chr9:131605043-131605043p.V31M2
chr9:131600026-131600026p.G169S2
chr9:131600088-131600088p.P148L2
chr9:131598075-131598075p.C280R2
chr9:131597782-131597782p.L340L2
chr9:131599152-131599152p.H206R1
chr9:131600355-131600355p.R138H1
chr9:131597818-131597818p.G328G1

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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 16     2 631  82 2
# mutation1 16     2 731  82 2
nonsynonymous SNV1 15     1 621  62 2
synonymous SNV   1     1 11   2   
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
chr9:131600026p.R267C,CCBL12
chr9:131597853p.G119S,CCBL12
chr9:131600339p.V327V,CCBL11
chr9:131605043p.P98T,CCBL11
chr9:131597888p.T292I,CCBL11
chr9:131600340p.S93S,CCBL11
chr9:131607633p.I283I,CCBL11
chr9:131597919p.S93F,CCBL11
chr9:131600353p.K280N,CCBL11
chr9:131607654p.P89S,CCBL11

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 CCBL1 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 CCBL1

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

AKR1D1,CLPSL1,C6orf223,ARMC12,CCBL1,CTNNA2,FCN2,
GGTLC1,GGTLC2,HAAO,HPD,LOC285847,NANOG,RLN3,
RNASE12,RRP7B,SERHL2,SERHL,SLCO1B1,SPINT3,SULT1C3
APOD,B4GALNT2,CCBL1,ENPP3,F9,GSTM2P1,GUSB,
HAAO,HIST1H2AD,HIST1H2AE,HIST1H2BG,HIST1H4H,ISX,NANOG,
NAT2,PON3,PPEF1,SERHL,SPINK8,SULT1C3,UGT2B11

BEAN,CA6,CACNG6,CCBL1,CCK,DGCR5,EPHB6,
FBXO2,FGF19,GAS6-AS2,HGFAC,KLK8,PAK7,PAPL,
PLCH2,SLC1A5,SLIT1,SOHLH1,TCHH,TEX19,ZNF735
ACD,ANKRD29,ARL3,BEND5,METTL22,CA11,CADM1,
CCBL1,CHN1,CRELD1,CYB5R1,FAHD2B,CERS4,MAGED2,
RAMP1,RNF215,SEC22C,STX1A,TOX,TRNP1,ZNF346
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 CCBL1
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
DB00114cysteine conjugate-beta lyase, cytoplasmicnutraceuticalPyridoxal Phosphate
DB02142cysteine conjugate-beta lyase, cytoplasmicexperimentalPyridoxamine-5'-Phosphate
DB02556cysteine conjugate-beta lyase, cytoplasmicexperimentalD-Phenylalanine
DB04083cysteine conjugate-beta lyase, cytoplasmicexperimentalN'-Pyridoxyl-Lysine-5'-Monophosphate
DB07950cysteine conjugate-beta lyase, cytoplasmicexperimental1H-INDOL-3-YLACETIC ACID


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Cross referenced IDs for CCBL1
* 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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