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 YWHAB
Basic gene info.Gene symbolYWHAB
Gene nametyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta
SynonymsGW128|HEL-S-1|HS1|KCIP-1|YWHAA
CytomapUCSC genome browser: 20q13.1
Genomic locationchr20 :43514343-43537161
Type of geneprotein-coding
RefGenesNM_003404.4,
NM_139323.3,
Ensembl idENSG00000166913
Description14-3-3 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 date20141207
dbXrefs MIM : 601289
HGNC : HGNC
Ensembl : ENSG00000166913
HPRD : 03184
Vega : OTTHUMG00000032549
ProteinUniProt: P31946
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_YWHAB
BioGPS: 7529
Gene Expression Atlas: ENSG00000166913
The Human Protein Atlas: ENSG00000166913
PathwayNCI Pathway Interaction Database: YWHAB
KEGG: YWHAB
REACTOME: YWHAB
ConsensusPathDB
Pathway Commons: YWHAB
MetabolismMetaCyc: YWHAB
HUMANCyc: YWHAB
RegulationEnsembl's Regulation: ENSG00000166913
miRBase: chr20 :43,514,343-43,537,161
TargetScan: NM_003404
cisRED: ENSG00000166913
ContextiHOP: YWHAB
cancer metabolism search in PubMed: YWHAB
UCL Cancer Institute: YWHAB
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of YWHAB in cancer cell metabolism1. 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

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Phenotypic Information for YWHAB(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM 601289; gene.
Orphanet
DiseaseKEGG Disease: YWHAB
MedGen: YWHAB (Human Medical Genetics with Condition)
ClinVar: YWHAB
PhenotypeMGI: YWHAB (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows YWHAB related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ302015YWHAB197204353030643530402YWHAB91368204353037643533663
BM975208COL3A1155282189875531189876781YWHAB525747204351441543530285
BQ961579TSG101147111851206218512108YWHAB44832204353020643535158
DB142934YWHAB1479204353267943535161GJA14795656121756829121756915
BU626199YWHAB2118204353669843536814SLC29A3112642107311587473122114
CB242961YWHAB1203204353467443535161YWHAB200318204353367143534658
BU675977YWHAB1149204353693643537082DZIP1130260139627182896271958
BF898629YWHAB1103204353639643536499YWHAB98260204353650143536663
BE547046YWHAB9177204353562243535789YWHAB173700204353578343536318
CN276496YWHAB1104204353468343535071YWHAB100329204353028543532673
BC000883YWHAB28195204353562243535789YWHAB1911221204353578343536814

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample      1          
GAIN (# sample)      1          
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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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=3

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check002.gifSomatic 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.

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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
chr20:43530347-43530347p.R58L2
chr20:43533712-43533712p.F176L2
chr20:43530295-43530295p.E41K2
chr20:43532645-43532645p.D104E2
chr20:43530214-43530214p.L14F1
chr20:43530343-43530343p.R57C1
chr20:43533619-43533619p.S145S1
chr20:43530216-43530216p.L14L1
chr20:43533689-43533689p.R169C1
chr20:43530229-43530229p.E19K1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample21 4  2 2  111  34 2
# mutation21 4  2 2  111  34 2
nonsynonymous SNV21 4  1     11  11  
synonymous SNV      1 2  1    23 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
chr20:43532645p.E41K,YWHAB2
chr20:43530295p.D104E,YWHAB2
chr20:43530177p.M1I,YWHAB1
chr20:43530358p.S145S,YWHAB1
chr20:43530229p.E19K,YWHAB1
chr20:43530375p.T196T,YWHAB1
chr20:43530261p.K29K,YWHAB1
chr20:43532644p.S232S,YWHAB1
chr20:43530282p.H36H,YWHAB1
chr20:43532690p.D240D,YWHAB1

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 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]

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Gene Expression for YWHAB

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

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
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 YWHAB


There's no related Drug.
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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



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