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 TUBB2A
Basic gene info.Gene symbolTUBB2A
Gene nametubulin, beta 2A class IIa
SynonymsCDCBM5|TUBB|TUBB2|dJ40E16.7
CytomapUCSC genome browser: 6p25
Genomic locationchr6 :3153901-3157783
Type of geneprotein-coding
RefGenesNM_001069.2,
Ensembl idENSG00000137267
Descriptionclass IIa beta-tubulintubulin beta class IIatubulin beta-2A chaintubulin, beta polypeptide 2
Modification date20141207
dbXrefs MIM : 615101
HGNC : HGNC
Ensembl : ENSG00000137267
HPRD : 01852
Vega : OTTHUMG00000014135
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TUBB2A
BioGPS: 7280
Gene Expression Atlas: ENSG00000137267
The Human Protein Atlas: ENSG00000137267
PathwayNCI Pathway Interaction Database: TUBB2A
KEGG: TUBB2A
REACTOME: TUBB2A
ConsensusPathDB
Pathway Commons: TUBB2A
MetabolismMetaCyc: TUBB2A
HUMANCyc: TUBB2A
RegulationEnsembl's Regulation: ENSG00000137267
miRBase: chr6 :3,153,901-3,157,783
TargetScan: NM_001069
cisRED: ENSG00000137267
ContextiHOP: TUBB2A
cancer metabolism search in PubMed: TUBB2A
UCL Cancer Institute: TUBB2A
Assigned class in ccmGDBC

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Phenotypic Information for TUBB2A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TUBB2A
Familial Cancer Database: TUBB2A
* 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: TUBB2A
MedGen: TUBB2A (Human Medical Genetics with Condition)
ClinVar: TUBB2A
PhenotypeMGI: TUBB2A (International Mouse Phenotyping Consortium)
PhenomicDB: TUBB2A

Mutations for TUBB2A
* 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 TUBB2A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF525947CSNK1A113215148930404148930724TUBB2A315531631539023154114
BQ277692YY1269514100728650100744074TUBB2A6961036631558603157761
AW956098TUBB2A1222631539053154126SRSF421936012947990829737679

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=15)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=1)
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
chr6:3154871-3154871p.S188S4
chr6:3154127-3154127p.F436F2
chr6:3154153-3154153p.A428T2
chr6:3154115-3154115p.E440D1
chr6:3155906-3155906p.R77T1
chr6:3154249-3154249p.H396Y1
chr6:3154832-3154832p.S201S1
chr6:3155921-3155921p.T72I1
chr6:3154378-3154378p.V353M1
chr6:3154851-3154851p.N195fs*211

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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
# sample11 5       32   44 7
# mutation11 5       32   44 7
nonsynonymous SNV 1 4       32   22 2
synonymous SNV1  1            22 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
chr6:3154115p.E432G1
chr6:3154797p.Q94H1
chr6:3155921p.D431D1
chr6:3154116p.F90F1
chr6:3154798p.A428T1
chr6:3155931p.T72I1
chr6:3154127p.S420S1
chr6:3154816p.E69K1
chr6:3155958p.D417N1
chr6:3154135p.V60L1

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 TUBB2A 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 TUBB2A

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

LINC01551,PXDC1,CCKBR,DBN1,FAM127A,GJC2,GPSM1,
KIF1C,LMNA,NPM3,NSMCE4A,NXN,PCBP4,PDLIM7,
PFN1,PLSCR3,PRKCDBP,SMTN,TP53I3,TUBB2A,TUBB2B
ANXA11,AP2M1,ARHGDIA,ARL8A,B3GALT4,KXD1,SMIM12,
CCDC107,CCM2,CD151,DDAH2,EFEMP2,GPX1,MYL6,
NUCB1,PPP2R5B,PSMD9,RNH1,TUBB2A,TUBB4B,TUBB4A

ANTXR2,C10orf54,MIR22HG,CIDEC,ISG20,LRP10,MALL,
POLD4,QSOX1,RAB3B,RELL1,RIPK1,RNF152,SDCBP2,
SGMS2,SMPD1,TNIP1,TSPAN1,TUBB2A,TUBB4A,VILL
ACTG2,BVES,CDC42EP3,CTXN1,DACT3,DES,DGKG,
DMPK,DNAJB5,LDB3,MAP7D1,NPTXR,PCYT1B,PDLIM7,
PDZD4,PTRF,PYGM,REEP2,SLC2A4,TUBB2A,TUBB2B
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 TUBB2A


There's no related Drug.
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Cross referenced IDs for TUBB2A
* 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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