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 TUBB4A
Basic gene info.Gene symbolTUBB4A
Gene nametubulin, beta 4A class IVa
SynonymsDYT4|TUBB4|beta-5
CytomapUCSC genome browser: 19p13.3
Genomic locationchr19 :6494329-6502330
Type of geneprotein-coding
RefGenesNM_001289123.1,
NM_001289127.1,NM_001289129.1,NM_001289130.1,NM_001289131.1,
NM_006087.3,
Ensembl idENSG00000104833
Descriptiondystonia 4, torsion (autosomal dominant)tubulin beta-4 chaintubulin beta-4A chaintubulin, beta 4tubulin, beta, 5
Modification date20141209
dbXrefs MIM : 602662
HGNC : HGNC
Ensembl : ENSG00000104833
HPRD : 04045
Vega : OTTHUMG00000181829
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TUBB4A
BioGPS: 10382
Gene Expression Atlas: ENSG00000104833
The Human Protein Atlas: ENSG00000104833
PathwayNCI Pathway Interaction Database: TUBB4A
KEGG: TUBB4A
REACTOME: TUBB4A
ConsensusPathDB
Pathway Commons: TUBB4A
MetabolismMetaCyc: TUBB4A
HUMANCyc: TUBB4A
RegulationEnsembl's Regulation: ENSG00000104833
miRBase: chr19 :6,494,329-6,502,330
TargetScan: NM_001289123
cisRED: ENSG00000104833
ContextiHOP: TUBB4A
cancer metabolism search in PubMed: TUBB4A
UCL Cancer Institute: TUBB4A
Assigned class in ccmGDBC

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Phenotypic Information for TUBB4A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TUBB4A
Familial Cancer Database: TUBB4A
* 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_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: TUBB4A
MedGen: TUBB4A (Human Medical Genetics with Condition)
ClinVar: TUBB4A
PhenotypeMGI: TUBB4A (International Mouse Phenotyping Consortium)
PhenomicDB: TUBB4A

Mutations for TUBB4A
* 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

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
haematopoietic_and_lymphoid_tissueTUBB4Achr1964972496497249TUBB4Achr1964972496497249
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TUBB4A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CB146214KDM5A2127712402041402297TUBB4A2734461964947266494899
AW953448TUBG211485174081820140818876TUBB4A4846521964945536494721
DA073851MALAT11245116526651665266760TUBB4A2465891965013316502323
AA683237TUBB4A13691964945656494933RBM2036644510112494468112494549
BF945627RILPL11229712123968777123969063TUBB4A2934081964945596494674
T06068TUBB4A1531964943316494383TCF454300185289628852901841
BF946266LDB35201108845825988458454TUBB4A1884251964951546495391
BF933096PPT21288633976863397973TUBB4A2863571964950656495139
BI035864PBX21266635047873505293TUBB4A2603291964944646494533

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

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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=0

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=0)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no ns-snv.There's no s-snv.
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

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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
# sample221106 4 21 14421 68 7
# mutation22196 4 21 16521 68 12
nonsynonymous SNV2 143 3 11 1042  35 8
synonymous SNV 2 53 1 1  61 1 33 4
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
chr19:6495313p.R318Q,TUBB4A2
chr19:6495341p.V183I,TUBB4A2
chr19:6495747p.A339A,TUBB4A2
chr19:6495277p.A182G,TUBB4A2
chr19:6495749p.T327T,TUBB4A2
chr19:6495585p.R237C,TUBB4A2
chr19:6495587p.G236A,TUBB4A1
chr19:6501323p.I138I,TUBB4A1
chr19:6495820p.I12I,TUBB4A1
chr19:6502176p.R319C,TUBB4A1

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 TUBB4A 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 TUBB4A

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

AMHR2,AQP2,CYP11A1,CYP17A1,CYP19A1,FDX1,FSHR,
HOXA11-AS,HPCAL4,INSL3,LHCGR,LOC286467,MBOAT4,QRICH2,
SCARB1,STAR,TAC4,TMEM14E,TREML5P,TUBB4A,ZDHHC19
ARHGDIA,C6orf226,CFL1,CRIP2,DRAP1,FAM58A,GIPC1,
GUK1,JMJD8,PFN1,RABAC1,RHOC,RNH1,LAMTOR2,
TBCB,TMSB10,TUBB2A,TUBB4B,TUBB4A,YIF1A,ZNHIT1

ASTN1,ATCAY,ATP2B3,C1QL1,CHRNB4,CLVS2,DPYSL5,
GABRA1,GABRG2,GPR123,HPCAL4,IGSF11,JPH4,NRXN1,
SLC7A14,SYT4,TAGLN3,TCEAL5,TMEM59L,TUBB4A,UNC80
ATCAY,ATP1A3,CNTN2,CTNNA2,DNER,DPYSL5,EEF1A2,
INA,KIF1A,NEFH,NEFL,NEFM,PHOX2B,SLC7A14,
SNAP91,ST8SIA3,SYN1,TMEM130,TMEM59L,TUBB3,TUBB4A
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 TUBB4A
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01873tubulin, beta 4A class IVaexperimental; investigationalEpothilone D
DB03010tubulin, beta 4A class IVaexperimental; investigationalEpothilone B


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Cross referenced IDs for TUBB4A
* 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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