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 YWHAZ

Basic gene info.	Gene symbol	YWHAZ
	Gene name	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta
	Synonyms	14-3-3-zeta\|HEL-S-3\|HEL4\|KCIP-1\|YWHAD
	Cytomap	UCSC genome browser: 8q23.1
	Genomic location	chr8 :101930803-101962799
	Type of gene	protein-coding
	RefGenes	NM_001135699.1, NM_001135700.1,NM_001135701.1,NM_001135702.1,NM_003406.3, NM_145690.2,
	Ensembl id	ENSG00000164924
	Description	14-3-3 delta14-3-3 protein zeta/delta14-3-3 protein/cytosolic phospholipase A214-3-3 zetaepididymis luminal protein 4epididymis secretory protein Li 3phospholipase A2protein kinase C inhibitor protein 1protein kinase C inhibitor protein-1tyrosine
	Modification date	20141222
dbXrefs	MIM : 601288
	HGNC : HGNC
	Ensembl : ENSG00000164924
	HPRD : 03183
	Vega : OTTHUMG00000134291
Protein	UniProt: P63104 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_YWHAZ
	BioGPS: 7534
	Gene Expression Atlas: ENSG00000164924
	The Human Protein Atlas: ENSG00000164924
Pathway	NCI Pathway Interaction Database: YWHAZ
	KEGG: YWHAZ
	REACTOME: YWHAZ
	ConsensusPathDB
	Pathway Commons: YWHAZ
Metabolism	MetaCyc: YWHAZ
	HUMANCyc: YWHAZ
Regulation	Ensembl's Regulation: ENSG00000164924
	miRBase: chr8 :101,930,803-101,962,799
	TargetScan: NM_001135699
	cisRED: ENSG00000164924
Context	iHOP: YWHAZ
	cancer metabolism search in PubMed: YWHAZ
	UCL Cancer Institute: YWHAZ
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: YWHAZ
	Familial Cancer Database: YWHAZ

* 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_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	601288; gene. 601288; gene.
Orphanet
Disease	KEGG Disease: YWHAZ
	MedGen: YWHAZ (Human Medical Genetics with Condition)
	ClinVar: YWHAZ
Phenotype	MGI: YWHAZ (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: YWHAZ

Mutations for YWHAZ

* 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	YWHAZ	chr8	101936730	101936930		chr8	101757242	101757442
ovary	YWHAZ	chr8	101951124	101951144	YWHAZ	chr8	101951174	101951194

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 YWHAZ 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
AA307240	SRCAP	9	116	16	30748537	30748642	YWHAZ	109	415	8	101960844	101964177
BG284443	YWHAZ	1	337	8	101936487	101960996	NDUFB9	330	501	8	125562047	125562218
DB135580	YWHAZ	1	121	8	101965496	101965616	AZIN1	119	549	8	103851958	103870380
BF754131	YWHAZ	21	74	8	101947415	101947468	ACTL6A	72	334	3	179304363	179305922
BG985122	YWHAZ	22	137	8	101943586	101943701	CAMTA2	129	242	17	4875587	4875700
AI761355	YWHAZ	1	190	8	101951468	101951657	ABCC3	188	273	17	48721338	48721423
BF910449	YWHAZ	3	205	8	101942751	101942953	YWHAZ	203	413	8	101942158	101942368
BF329619	KIF7	19	281	15	90175272	90175540	YWHAZ	277	350	8	101935311	101935384
AW860114	YWHAZ	7	250	8	101961160	101961402	DYRK1A	247	309	21	38741268	38741331

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=17)	Stat. for Synonymous SNVs (# total SNVs=9)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=2)
There's no deleted 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
chr8:101960848-101960848	p.L90L	2
chr8:101960863-101960863	p.K85N	2
chr8:101932928-101932929	p.E244fs*>3	2
chr8:101960878-101960878	p.R80R	2
chr8:101932962-101932962	p.Q233E	1
chr8:101937250-101937250	p.F104L	1
chr8:101960887-101960887	p.Q77H	1
chr8:101932970-101932970	p.S230L	1
chr8:101960825-101960825	p.L98P	1
chr8:101960935-101960935	p.V61V	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=1

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		2			2					1						3		1
# mutation	1	1		2			2					1						3		1
nonsynonymous SNV	1	1		1			2											2		1
synonymous SNV				1								1						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
chr8:101936216	p.S230L,YWHAZ	1
chr8:101936232	p.L220V,YWHAZ	1
chr8:101936241	p.I217T,YWHAZ	1
chr8:101937190	p.T215T,YWHAZ	1
chr8:101937250	p.S210L,YWHAZ	1
chr8:101960911	p.S207I,YWHAZ	1
chr8:101961019	p.D124E,YWHAZ	1
chr8:101932959	p.F104L,YWHAZ	1
chr8:101961020	p.T69T,YWHAZ	1
chr8:101932970	p.G33G,YWHAZ	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 YWHAZ 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 YWHAZ

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


ANKRD46,ATP6V1C1,AZIN1,DCAF13,DERL1,EBAG9,ESRP1, INTS8,MTDH,MTERF3,NUDCD1,OTUD6B,POLR2K,PTDSS1, RAD21,RAD54B,SLC25A32,STK3,EMC2,YWHAZ,ZNF706	CALM2,CHMP2B,DYNLT3,FAM49B,GOLT1B,BBIP1,NDFIP1, PLEKHA3,POLR2K,LRR1,RAB28,RAP1B,RNF139,SLC25A32, STK3,TCEA1,TRAM1,VPS26A,YPEL5,YWHAZ,ZNF706

ATP6V1C1,AZIN1,CHRAC1,CPNE3,DCAF13,DERL1,EBAG9, ENY2,RMDN1,FAM91A1,NUDCD1,POLR2K,RAB2A,RAD21, RNF139,SLC25A32,TCEB1,EMC2,UBE2V2,YWHAZ,ZNF706	AAGAB,ATG4A,C12orf49,CAP1,CHMP2B,MICU2,GMFB, HDAC1,NIPA2,PEX13,PPP6C,RAB11A,RALA,SLC25A24, STX19,TMEM167A,TPMT,UBE2K,VPS26A,YWHAB,YWHAZ

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 YWHAZ

There's no related Drug.

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Cross referenced IDs for YWHAZ

* 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