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 TUBA4A
Basic gene info.Gene symbolTUBA4A
Gene nametubulin, alpha 4a
SynonymsH2-ALPHA|TUBA1
CytomapUCSC genome browser: 2q35
Genomic locationchr2 :220115000-220118638
Type of geneprotein-coding
RefGenesNM_001278552.1,
NM_006000.2,
Ensembl idENSG00000127824
Descriptiontubulin H2-alphatubulin alpha-1 chaintubulin alpha-4A chaintubulin, alpha 1 (testis specific)
Modification date20141207
dbXrefs MIM : 191110
HGNC : HGNC
Ensembl : ENSG00000127824
HPRD : 01851
Vega : OTTHUMG00000133126
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TUBA4A
BioGPS: 7277
Gene Expression Atlas: ENSG00000127824
The Human Protein Atlas: ENSG00000127824
PathwayNCI Pathway Interaction Database: TUBA4A
KEGG: TUBA4A
REACTOME: TUBA4A
ConsensusPathDB
Pathway Commons: TUBA4A
MetabolismMetaCyc: TUBA4A
HUMANCyc: TUBA4A
RegulationEnsembl's Regulation: ENSG00000127824
miRBase: chr2 :220,115,000-220,118,638
TargetScan: NM_001278552
cisRED: ENSG00000127824
ContextiHOP: TUBA4A
cancer metabolism search in PubMed: TUBA4A
UCL Cancer Institute: TUBA4A
Assigned class in ccmGDBC

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Phenotypic Information for TUBA4A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TUBA4A
Familial Cancer Database: TUBA4A
* 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: TUBA4A
MedGen: TUBA4A (Human Medical Genetics with Condition)
ClinVar: TUBA4A
PhenotypeMGI: TUBA4A (International Mouse Phenotyping Consortium)
PhenomicDB: TUBA4A

Mutations for TUBA4A
* 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 TUBA4A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA812020TM9SF41402203069753330729350TUBA4A3957882220116326220118638

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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=36)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
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
chr2:220115768-220115768p.D218G3
chr2:220116426-220116426p.R79Q3
chr2:220115877-220115877p.V182I2
chr2:220115880-220115880p.V181M2
chr2:220115938-220115938p.Y161Y2
chr2:220115764-220115764p.I219I2
chr2:220115939-220115939p.Y161F2
chr2:220115714-220115714p.S236F1
chr2:220116737-220116737p.T73T1
chr2:220116329-220116329p.G111G1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 121 3 21 313 151 10
# mutation 1 81 3 21 313 161 15
nonsynonymous SNV 1 71 1 21 3 3  41 10
synonymous SNV   1  2     1  12  5
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
chr2:220116426p.D203G,TUBA4A3
chr2:220115768p.R64Q,TUBA4A3
chr2:220116737p.T58T,TUBA4A2
chr2:220115938p.Y146Y,TUBA4A2
chr2:220115939p.Y146F,TUBA4A2
chr2:220116417p.R293R,TUBA4A1
chr2:220115325p.V167A,TUBA4A1
chr2:220115736p.F52L,TUBA4A1
chr2:220115948p.V288V,TUBA4A1
chr2:220115406p.T35P,TUBA4A1

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 TUBA4A 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 TUBA4A

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

ARHGEF4,BNC1,CA9,ENO1,FERMT1,FGFBP1,FSCN1,
GJB3,GJB5,GPR87,KRT5,KRT6B,MYO7B,PCSK9,
PLEK2,RPSAP52,S100A2,SFN,SOX15,TNFSF9,TUBA4A
PERM1,CACNB1,CHRNA10,YBX3,FEM1A,FHL3,GAMT,
GAPDH,GMPR,GOT2,IDI2,MYL6B,PDLIM3,RBM38,
RTN2,SH2B2,SHISA4,TCEA3,TPM1,TPM2,TUBA4A

ATPIF1,UQCC3,CD320,DTYMK,EXOSC7,MZT2B,HNRNPAB,
ILKAP,LSM4,LSM7,MRPS34,MXD3,NOP16,PPIH,
PRELID1,STARD10,TIMM13,TUBA1C,TUBA4A,TUBB4B,UQCRQ
AGR2,ARF4,CCT7,CDC37,CGB,GALE,GARS,
GORASP2,KCTD14,KDELR3,NABP2,PPP5C,RGS8,S100P,
SLC16A14,SYNGR2,TFF1,TMED9,TTC39A,TUBA4A,TUBG1
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 TUBA4A
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
DB00541tubulin, alpha 4aapproved; investigationalVincristine
DB01179tubulin, alpha 4aapprovedPodofilox
DB01873tubulin, alpha 4aexperimental; investigationalEpothilone D
DB03010tubulin, alpha 4aexperimental; investigationalEpothilone B
DB06772tubulin, alpha 4aapprovedCabazitaxel
DB01033tubulin, alpha 4aapprovedMercaptopurine
DB00563tubulin, alpha 4aapprovedMethotrexate


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Cross referenced IDs for TUBA4A
* 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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