Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 TUBB4B
Basic gene info.Gene symbolTUBB4B
Gene nametubulin, beta 4B class IVb
SynonymsBeta2|TUBB2|TUBB2C
CytomapUCSC genome browser: 9q34
Genomic locationchr9 :140135710-140138159
Type of geneprotein-coding
RefGenesNM_006088.5,
Ensembl idENSG00000188229
Descriptionclass IVb beta tubulinclass IVb beta-tubulintubulin beta-2 chaintubulin beta-2C chaintubulin beta-4B chaintubulin, beta 2Ctubulin, beta, 2
Modification date20141207
dbXrefs MIM : 602660
HGNC : HGNC
Ensembl : ENSG00000188229
HPRD : 04043
Vega : OTTHUMG00000131783
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TUBB4B
BioGPS: 10383
Gene Expression Atlas: ENSG00000188229
The Human Protein Atlas: ENSG00000188229
PathwayNCI Pathway Interaction Database: TUBB4B
KEGG: TUBB4B
REACTOME: TUBB4B
ConsensusPathDB
Pathway Commons: TUBB4B
MetabolismMetaCyc: TUBB4B
HUMANCyc: TUBB4B
RegulationEnsembl's Regulation: ENSG00000188229
miRBase: chr9 :140,135,710-140,138,159
TargetScan: NM_006088
cisRED: ENSG00000188229
ContextiHOP: TUBB4B
cancer metabolism search in PubMed: TUBB4B
UCL Cancer Institute: TUBB4B
Assigned class in ccmGDBC

Top
Phenotypic Information for TUBB4B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TUBB4B
Familial Cancer Database: TUBB4B
* 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: TUBB4B
MedGen: TUBB4B (Human Medical Genetics with Condition)
ClinVar: TUBB4B
PhenotypeMGI: TUBB4B (International Mouse Phenotyping Consortium)
PhenomicDB: TUBB4B

Mutations for TUBB4B
* 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 TUBB4B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a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check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
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.

Top
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

Top
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.

Top
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

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample13 81 3 21 4 1   212
# mutation13 71 3 21 5 1   212
nonsynonymous SNV13 4  1  1 4 1   212
synonymous SNV   31 2 2  1        
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
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
chr9:140137892p.F408L3
chr9:140137041p.A124V2
chr9:140137871p.V49V1
chr9:140136262p.M293V1
chr9:140137408p.Y51C1
chr9:140137873p.T312T1
chr9:140136267p.I84N1
chr9:140137441p.R359L1
chr9:140137888p.F378L1
chr9:140136447p.D128D1

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 TUBB4B 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 TUBB4B

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))
Top
check002.gifCNV 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
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

C9orf142,C9orf69,RABL6,NELFB,DPM2,EDF1,NTMT1,
NDOR1,NDUFA8,PMPCA,PTGES2,SIVA1,SSNA1,SURF2,
TMEM203,TUBB4B,UBAC1,UCK1,WDR34,ZDHHC12,ZMYND19
ARHGDIA,CFL1,COPE,CRELD2,GIPC1,GNB2,GUK1,
MBD3,MRPL28,PPP4C,PSMC4,RBM42,RHOC,SCO2,
SLC39A3,TBCB,ALYREF,TSSC4,TUBB4B,UBE2J2,YIF1B

AURKAIP1,C14orf80,C9orf142,CDC20,COQ4,EDF1,MZT2B,
EMC9,FPGS,MRPL41,MXD3,PMPCA,PTGES2,PTTG1,
SSNA1,TACC3,TUBA1B,TUBA1C,TUBB4B,WDR34,ZDHHC12
ACTG1,ARHGDIA,ATP2A2,B3GNT3,BAIAP2L1,BCL10,DPP9,
IPPK,KCTD5,NPLOC4,PHLDA2,PLAUR,PSME3,RAB35,
RDH13,RPS6KA4,SFN,TRIM15,TUBA1C,TUBB4B,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

Top
check002.gifInteracting Genes (from Pathway Commons)

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

Top
Pharmacological Information for TUBB4B
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
DB00518tubulin, beta 4B class IVbapprovedAlbendazole
DB00643tubulin, beta 4B class IVbapprovedMebendazole
DB01873tubulin, beta 4B class IVbexperimental; investigationalEpothilone D
DB03010tubulin, beta 4B class IVbexperimental; investigationalEpothilone B


Top
Cross referenced IDs for TUBB4B
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas