Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	CCBL1
	Gene name	cysteine conjugate-beta lyase, cytoplasmic
	Synonyms	GTK\|KAT1\|KATI
	Cytomap	UCSC genome browser: 9q34.11
	Genomic location	chr9 :131595391-131644354
	Type of gene	protein-coding
	RefGenes	NM_001122671.1, NM_001122672.1,NM_001287390.1,NM_004059.4,NR_109829.1,
	Ensembl id	ENSG00000171097
	Description	beta-lysase, kidneycysteine conjugate-beta lyase; cytoplasmic (glutamine transaminase K, kyneurenine aminotransferase)cysteine-S-conjugate beta-lyaseglutamine transaminase Kglutamine--phenylpyruvate transaminaseglutamine-phenylpyruvate aminotransfera
	Modification date	20141211
dbXrefs	MIM : 600547
	HGNC : HGNC
	Ensembl : ENSG00000171097
	HPRD : 02769
	Vega : OTTHUMG00000020767
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CCBL1
	BioGPS: 883
	Gene Expression Atlas: ENSG00000171097
	The Human Protein Atlas: ENSG00000171097
Pathway	NCI Pathway Interaction Database: CCBL1
	KEGG: CCBL1
	REACTOME: CCBL1
	ConsensusPathDB
	Pathway Commons: CCBL1
Metabolism	MetaCyc: CCBL1
	HUMANCyc: CCBL1
Regulation	Ensembl's Regulation: ENSG00000171097
	miRBase: chr9 :131,595,391-131,644,354
	TargetScan: NM_001122671
	cisRED: ENSG00000171097
Context	iHOP: CCBL1
	cancer metabolism search in PubMed: CCBL1
	UCL Cancer Institute: CCBL1
Assigned class in ccmGDB	C

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Phenotypic Information for CCBL1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

Others
OMIM
Orphanet
Disease	KEGG Disease: CCBL1
	MedGen: CCBL1 (Human Medical Genetics with Condition)
	ClinVar: CCBL1
Phenotype	MGI: CCBL1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	CCBL1	chr9	131601227	131601247	CCBL1	chr9	131612088	131612108
ovary	CCBL1	chr9	131609831	131609851	CCBL1	chr9	131621628	131621648

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 CCBL1 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
BF891052	CCBL1	28	212	9	131643217	131643402	CCBL1	208	526	9	131640998	131641316
BF890958	CCBL1	15	200	9	131643215	131643402	CCBL1	196	514	9	131640998	131641316
BF743879	CCBL1	6	121	9	131596051	131597662	CCBL1	108	544	9	131595480	131595915

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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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)

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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=3

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Somatic 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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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
chr9:131599985-131599985	p.T182T	3
chr9:131597853-131597853	p.R317C	3
chr9:131597782-131597782	p.L340L	2
chr9:131605043-131605043	p.V31M	2
chr9:131600026-131600026	p.G169S	2
chr9:131600088-131600088	p.P148L	2
chr9:131598075-131598075	p.C280R	2
chr9:131600646-131600646	p.G68S	1
chr9:131598112-131598112	p.K267K	1
chr9:131605019-131605019	p.D39H	1

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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	1		1	6						2		6	3	1			8	2		2
# mutation	1		1	6						2		7	3	1			8	2		2
nonsynonymous SNV	1		1	5						1		6	2	1			6	2		2
synonymous SNV				1						1		1	1				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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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
chr9:131600026	p.R267C,CCBL1	2
chr9:131597853	p.G119S,CCBL1	2
chr9:131597812	p.G86V,CCBL1	1
chr9:131604965	p.L91P,CCBL1	1
chr9:131597818	p.R265H,CCBL1	1
chr9:131600067	p.P90S,CCBL1	1
chr9:131605002	p.Y255Y,CCBL1	1
chr9:131600089	p.G68S,CCBL1	1
chr9:131605022	p.E245K,CCBL1	1
chr9:131597858	p.K217K,CCBL1	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 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

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))

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CNV 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

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


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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

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	cysteine conjugate-beta lyase, cytoplasmic	nutraceutical	Pyridoxal Phosphate
DB02142	cysteine conjugate-beta lyase, cytoplasmic	experimental	Pyridoxamine-5'-Phosphate
DB02556	cysteine conjugate-beta lyase, cytoplasmic	experimental	D-Phenylalanine
DB04083	cysteine conjugate-beta lyase, cytoplasmic	experimental	N'-Pyridoxyl-Lysine-5'-Monophosphate
DB07950	cysteine conjugate-beta lyase, cytoplasmic	experimental	1H-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