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 KYNU

Basic gene info.	Gene symbol	KYNU
	Gene name	kynureninase
	Synonyms	KYNUU
	Cytomap	UCSC genome browser: 2q22.2
	Genomic location	chr2 :143635194-143747106
	Type of gene	protein-coding
	RefGenes	NM_001032998.1, NM_001199241.1,NM_003937.2,
	Ensembl id	ENSG00000115919
	Description	L-kynurenine hydrolase
	Modification date	20141207
dbXrefs	MIM : 605197
	HGNC : HGNC
	Ensembl : ENSG00000115919
	HPRD : 08940
	Vega : OTTHUMG00000131829
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_KYNU
	BioGPS: 8942
	Gene Expression Atlas: ENSG00000115919
	The Human Protein Atlas: ENSG00000115919
Pathway	NCI Pathway Interaction Database: KYNU
	KEGG: KYNU
	REACTOME: KYNU
	ConsensusPathDB
	Pathway Commons: KYNU
Metabolism	MetaCyc: KYNU
	HUMANCyc: KYNU
Regulation	Ensembl's Regulation: ENSG00000115919
	miRBase: chr2 :143,635,194-143,747,106
	TargetScan: NM_001032998
	cisRED: ENSG00000115919
Context	iHOP: KYNU
	cancer metabolism search in PubMed: KYNU
	UCL Cancer Institute: KYNU
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: KYNU
	Familial Cancer Database: KYNU

* 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_TRYPTOPHAN_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

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

Mutations for KYNU

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	KYNU	chr2	143642601	143642621	KYNU	chr2	143651108	143651128
pancreas	KYNU	chr2	143642540	143642560	KYNU	chr2	143642713	143642733
prostate	KYNU	chr2	143744304	143744304		chr12	71796900	71796900

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 KYNU 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
BP333200	HTN1	1	359	4	70916155	70924377	KYNU	353	374	2	143795116	143795138
BF997792	TGOLN2	1	181	2	85547966	85548146	KYNU	174	316	2	143725826	143725968
BF907726	KYNU	14	90	2	143743515	143743591	KYNU	90	327	2	143712379	143718221
CB851853	KYNU	13	289	2	143746830	143747106	KYNU	286	377	2	143746729	143746820

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=60)	Stat. for Synonymous SNVs (# total SNVs=14)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	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
chr2:143643019-143643019	p.R28K	4
chr2:143643073-143643073	p.F46Y	3
chr2:143743579-143743579	p.T297T	3
chr2:143713800-143713800	p.R155Q	3
chr2:143712381-143712381	p.A126T	2
chr2:143713833-143713833	p.P166H	2
chr2:143676226-143676226	p.G73E	2
chr2:143718341-143718341	p.?	2
chr2:143676232-143676232	p.S75Y	2
chr2:143742717-143742717	p.W265*	2

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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=3

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		10	1		6	1		1		16	4	1		1	14	7		7
# mutation		1		12	1		6	1		1		18	4	1		1	13	7		7
nonsynonymous SNV		1		8	1		4	1		1		11	3	1		1	9	4		6
synonymous SNV				4			2					7	1				4	3		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])

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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
chr2:143743579	p.T297T,KYNU	3
chr2:143676226	p.G77G,KYNU	2
chr2:143676239	p.F305L	2
chr2:143718222	p.I204M,KYNU	2
chr2:143746426	p.G73E,KYNU	2
chr2:143643069	p.K157N,KYNU	1
chr2:143718272	p.C271S,KYNU	1
chr2:143685295	p.P393P,KYNU	1
chr2:143787241	p.E89K,KYNU	1
chr2:143713833	p.P166S,KYNU	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 KYNU 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 KYNU

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


ACSM1,ALOX15B,CLDN8,FCN2,FKBP5,G6PD,GGT1, GGT3P,GRAMD2,ISX,KMO,KYNU,MPV17L,OXER1, PNLIPRP3,SERHL2,SLCO1B1,SPINK8,SRD5A1,SULT1C2,SULT1C3	ABCC11,ADAM2,AFMID,ALOX15B,C15orf43,DHRS2,GGT1, GGTLC2,HMGCS2,HPGD,IDI1,KYNU,LST-3TM12,MPV17L, PNLIPRP3,SERHL2,SERHL,SPINK8,SRD5A1,TARP,UGT2B10

ARL4C,BEAN,C20orf197,CD274,GBP1,HAPLN3,HLA-DRB6, IL17C,IL23A,IL31RA,KYNU,LCE1F,LETM2,LOC153910, LOC285735,PLAU,PMAIP1,SERPINB9,TNFAIP2,TYMP,UBASH3B	AIF1,C1orf162,CCR1,CD40,CD86,CYBB,DOK2, FCER1G,GIMAP4,GNA15,INSL4,KYNU,LILRB2,LILRB4, NCF2,PDCD1LG2,PLEK,SIGLEC9,SPI1,TMEM106A,TNFSF13B

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 KYNU

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	kynureninase	nutraceutical	Pyridoxal Phosphate
DB00160	kynureninase	approved; nutraceutical	L-Alanine
DB07069	kynureninase	experimental	3-Hydroxyhippuric acid
DB02343	kynureninase	experimental	3,6,9,12,15-Pentaoxaheptadecane
DB00130	kynureninase	approved; nutraceutical; investigational	L-Glutamine
DB00150	kynureninase	approved; nutraceutical	L-Tryptophan

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Cross referenced IDs for KYNU

* 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