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

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 YWHAB

Basic gene info.	Gene symbol	YWHAB
	Gene name	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta
	Synonyms	GW128\|HEL-S-1\|HS1\|KCIP-1\|YWHAA
	Cytomap	UCSC genome browser: 20q13.1
	Genomic location	chr20 :43514343-43537161
	Type of gene	protein-coding
	RefGenes	NM_003404.4, NM_139323.3,
	Ensembl id	ENSG00000166913
	Description	14-3-3 alpha14-3-3 protein beta/alphabrain protein 14-3-3, beta isoformepididymis secretory protein Li 1protein 1054protein kinase C inhibitor protein 1protein kinase C inhibitor protein-1tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activati
	Modification date	20141207
dbXrefs	MIM : 601289
	HGNC : HGNC
	Ensembl : ENSG00000166913
	HPRD : 03184
	Vega : OTTHUMG00000032549
Protein	UniProt: P31946 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_YWHAB
	BioGPS: 7529
	Gene Expression Atlas: ENSG00000166913
	The Human Protein Atlas: ENSG00000166913
Pathway	NCI Pathway Interaction Database: YWHAB
	KEGG: YWHAB
	REACTOME: YWHAB
	ConsensusPathDB
	Pathway Commons: YWHAB
Metabolism	MetaCyc: YWHAB
	HUMANCyc: YWHAB
Regulation	Ensembl's Regulation: ENSG00000166913
	miRBase: chr20 :43,514,343-43,537,161
	TargetScan: NM_003404
	cisRED: ENSG00000166913
Context	iHOP: YWHAB
	cancer metabolism search in PubMed: YWHAB
	UCL Cancer Institute: YWHAB
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of YWHAB in cancer cell metabolism	1. Zhao J, Wen G, Ding M, Pan J-Y, Yu M-L, et al. (2012) Comparative Proteomic Analysis of Colon Cancer Cell HCT-15 in Response to All-Trans Retinoic Acid Treatment. Protein and peptide letters 19: 1272-1280. go to article

Top

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

Cancer Description
Cancer	CGAP: YWHAB
	Familial Cancer Database: YWHAB

* 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	601289; gene.
Orphanet
Disease	KEGG Disease: YWHAB
	MedGen: YWHAB (Human Medical Genetics with Condition)
	ClinVar: YWHAB
Phenotype	MGI: YWHAB (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: YWHAB

Mutations for YWHAB

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows YWHAB 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
BQ302015	YWHAB	1	97	20	43530306	43530402	YWHAB	91	368	20	43530376	43533663
BM975208	COL3A1	15	528	2	189875531	189876781	YWHAB	525	747	20	43514415	43530285
BQ961579	TSG101	1	47	11	18512062	18512108	YWHAB	44	832	20	43530206	43535158
DB142934	YWHAB	1	479	20	43532679	43535161	GJA1	479	565	6	121756829	121756915
BU626199	YWHAB	2	118	20	43536698	43536814	SLC29A3	112	642	10	73115874	73122114
CB242961	YWHAB	1	203	20	43534674	43535161	YWHAB	200	318	20	43533671	43534658
BU675977	YWHAB	1	149	20	43536936	43537082	DZIP1	130	260	13	96271828	96271958
BF898629	YWHAB	1	103	20	43536396	43536499	YWHAB	98	260	20	43536501	43536663
BE547046	YWHAB	9	177	20	43535622	43535789	YWHAB	173	700	20	43535783	43536318
CN276496	YWHAB	1	104	20	43534683	43535071	YWHAB	100	329	20	43530285	43532673
BC000883	YWHAB	28	195	20	43535622	43535789	YWHAB	191	1221	20	43535783	43536814

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

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)

Top

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

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=18)	Stat. for Synonymous SNVs (# total SNVs=8)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

Top

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
chr20:43533712-43533712	p.F176L	2
chr20:43530295-43530295	p.E41K	2
chr20:43532645-43532645	p.D104E	2
chr20:43530347-43530347	p.R58L	2
chr20:43530229-43530229	p.E19K	1
chr20:43530358-43530358	p.R62C	1
chr20:43530233-43530233	p.R20Q	1
chr20:43530375-43530375	p.I67I	1
chr20:43533725-43533725	p.Y181D	1
chr20:43530234-43530234	p.R20R	1

Top

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	2	1		4			2		2			1	1	1			3	4		2
# mutation	2	1		4			2		2			1	1	1			3	4		2
nonsynonymous SNV	2	1		4			1						1	1			1	1
synonymous SNV							1		2			1					2	3		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])

Top

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
chr20:43532645	p.E41K,YWHAB	2
chr20:43530295	p.D104E,YWHAB	2
chr20:43530261	p.S232S,YWHAB	1
chr20:43532644	p.K29K,YWHAB	1
chr20:43530282	p.D240D,YWHAB	1
chr20:43532690	p.H36H,YWHAB	1
chr20:43530312	p.G242R,YWHAB	1
chr20:43533619	p.L46L,YWHAB	1
chr20:43530314	p.S47F,YWHAB	1
chr20:43533772	p.A49V,YWHAB	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 YWHAB 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]

Top

Gene Expression for YWHAB

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


ADNP,OSER1,ELMO2,FITM2,IFT52,ITCH,NCOA3, RAB22A,RALGAPB,SERINC3,SLMO2,STAU1,STK4,SYS1, TMED2,TOMM34,TOP1,TP53RK,TTPAL,YWHAB,ZSWIM1	ARF4,ARL2BP,ATP6AP2,C4orf3,CAP1,CAPZA1,CDC42, DYNLT3,FKBP1A,KDELR2,LEPROTL1,MAPRE1,MGAT2,NDFIP1, RAB1A,RALB,RAP1B,SEPT7,TMEM126B,UBE2A,YWHAB

OSER1,AAR2,RTFDC1,CTNNBL1,DPM1,HNF4A,IFT52, MAPRE1,MOCS3,RPRD1B,SERINC3,STAU1,STK4,SYS1, NELFCD,TP53RK,TTPAL,UBE2V1,VAPB,YWHAB,ZSWIM3	ACTR2,ALAS1,CAB39,CCDC68,CEACAM1,DLG3,DSC2, ABHD17C,GCNT3,GPD2,KIF16B,KRT20,NIPA2,NT5C2, PPP2R1B,RAB14,RAC1,RALA,STX3,VDAC1,YWHAB

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

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for YWHAB

There's no related Drug.

Top

Cross referenced IDs for YWHAB

* 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