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 CCBL2
Basic gene info.Gene symbolCCBL2
Gene namecysteine conjugate-beta lyase 2
SynonymsKAT3|KATIII
CytomapUCSC genome browser: 1p22.2
Genomic locationchr1 :89401455-89458643
Type of geneprotein-coding
RefGenesNM_001008661.2,
NM_001008662.2,
Ensembl idENSG00000137944
DescriptionRP11-82K18.3cysteine-S-conjugate beta-lyase 2kynurenine aminotransferase IIIkynurenine--glyoxylate transaminasekynurenine--oxoglutarate transaminase 3kynurenine--oxoglutarate transaminase IIIkynurenine-oxoglutarate transaminase 3
Modification date20141207
dbXrefs MIM : 610656
HGNC : HGNC
Ensembl : ENSG00000137944
HPRD : 13752
Vega : OTTHUMG00000010617
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CCBL2
BioGPS: 56267
Gene Expression Atlas: ENSG00000137944
The Human Protein Atlas: ENSG00000137944
PathwayNCI Pathway Interaction Database: CCBL2
KEGG: CCBL2
REACTOME: CCBL2
ConsensusPathDB
Pathway Commons: CCBL2
MetabolismMetaCyc: CCBL2
HUMANCyc: CCBL2
RegulationEnsembl's Regulation: ENSG00000137944
miRBase: chr1 :89,401,455-89,458,643
TargetScan: NM_001008661
cisRED: ENSG00000137944
ContextiHOP: CCBL2
cancer metabolism search in PubMed: CCBL2
UCL Cancer Institute: CCBL2
Assigned class in ccmGDBC

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Phenotypic Information for CCBL2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CCBL2
Familial Cancer Database: CCBL2
* 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: CCBL2
MedGen: CCBL2 (Human Medical Genetics with Condition)
ClinVar: CCBL2
PhenotypeMGI: CCBL2 (International Mouse Phenotyping Consortium)
PhenomicDB: CCBL2

Mutations for CCBL2
* 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
ovaryCCBL2chr18945346689453486CCBL2chr18944714089447160
pancreasCCBL2chr18940345789403477MGMTchr10131348988131349008
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 CCBL2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=60)
Stat. for Synonymous SNVs
(# total SNVs=12)
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
chr1:89449434-89449434p.T26A5
chr1:89449298-89449298p.G71A4
chr1:89449390-89449390p.I40M4
chr1:89449278-89449278p.A78S3
chr1:89449483-89449483p.K9N3
chr1:89448812-89448812p.D233A3
chr1:89448769-89448769p.G247G2
chr1:89449399-89449399p.V37V2
chr1:89448518-89448518p.R331Q2
chr1:89449037-89449037p.G158V2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2219  4 3   4   25 7
# mutation2219  4 3   4   25 8
nonsynonymous SNV2218  3 3   2   23 8
synonymous SNV   1  1     2    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
chr1:89408756p.V378I,CCBL23
chr1:89414893p.S307Y,CCBL22
chr1:89414899p.A280A,CCBL21
chr1:89427770p.N61D,CCBL21
chr1:89454019p.W415L,CCBL21
chr1:89408751p.L268V,CCBL21
chr1:89418758p.K53N,CCBL21
chr1:89427824p.I411N,CCBL21
chr1:89408752p.G256G,CCBL21
chr1:89418796p.G37S,CCBL21

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 CCBL2 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 CCBL2

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

AHCYL1,BCL10,CCBL2,CTBS,DDAH1,DNTTIP2,DPH5,
FNBP1L,GLMN,GTF2B,KBTBD3,ODF2L,PKN2,RBMXL1,
RPAP2,RPF1,RWDD3,SEP15,SH3GLB1,USP33,ZFP2
ACTR6,ARV1,C11orf1,METTL25,TMA16,FAM206A,CCBL2,
DUS4L,DYNC2LI1,EAPP,EEF1E1,GABPB1,KHDRBS1,MBIP,
NUP54,ORC5,PPP1R8,RSL24D1,TMEM128,ZCCHC7,ZNF22

ABCD3,ATP5F1,BCAS2,PLGRKT,CCBL2,GLMN,GNG5,
GTF2B,LAMTOR5,ITGB3BP,MDH1,MRPL1,MRPL50,PPA2,
RPAP2,RPL5,RTCA,RWDD4,SEP15,UQCRH,WARS2
ALG6,APOO,ATP5A1,ATP5B,ATP5G3,CAMKMT,C2orf43,
CCBL2,CCT8,CPSF3,EIF3M,FARSB,FH,MYCBP,
NDUFA9,PPIA,PPP2R2A,PPP6C,PRPF38A,SUGT1,UQCRHL
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 CCBL2
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 2nutraceuticalPyridoxal Phosphate
DB00142cysteine conjugate-beta lyase 2approved; nutraceuticalL-Glutamic Acid


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Cross referenced IDs for CCBL2
* 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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