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 TUBB3
Basic gene info.Gene symbolTUBB3
Gene nametubulin, beta 3 class III
SynonymsCDCBM|CDCBM1|CFEOM3|CFEOM3A|FEOM3|TUBB4|beta-4
CytomapUCSC genome browser: 16q24.3
Genomic locationchr16 :89989686-90002505
Type of geneprotein-coding
RefGenesNM_001197181.1,
NM_006086.3,
Ensembl idENSG00000198211
Descriptionclass III beta-tubulintubulin beta-3 chaintubulin beta-4 chaintubulin beta-III
Modification date20141222
dbXrefs MIM : 602661
HGNC : HGNC
Ensembl : ENSG00000258947
HPRD : 04044
Vega : OTTHUMG00000138985
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TUBB3
BioGPS: 10381
Gene Expression Atlas: ENSG00000198211
The Human Protein Atlas: ENSG00000198211
PathwayNCI Pathway Interaction Database: TUBB3
KEGG: TUBB3
REACTOME: TUBB3
ConsensusPathDB
Pathway Commons: TUBB3
MetabolismMetaCyc: TUBB3
HUMANCyc: TUBB3
RegulationEnsembl's Regulation: ENSG00000198211
miRBase: chr16 :89,989,686-90,002,505
TargetScan: NM_001197181
cisRED: ENSG00000198211
ContextiHOP: TUBB3
cancer metabolism search in PubMed: TUBB3
UCL Cancer Institute: TUBB3
Assigned class in ccmGDBC

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Phenotypic Information for TUBB3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TUBB3
Familial Cancer Database: TUBB3
* 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: TUBB3
MedGen: TUBB3 (Human Medical Genetics with Condition)
ClinVar: TUBB3
PhenotypeMGI: TUBB3 (International Mouse Phenotyping Consortium)
PhenomicDB: TUBB3

Mutations for TUBB3
* 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 TUBB3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI148209TUBB35293169000221090002498IGFBP729444245789868957899479

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=3

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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=17)
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
chr16:89999920-89999920p.G71R3
chr16:90001817-90001817p.R320C3
chr16:90001646-90001646p.L263M2
chr16:89999962-89999962p.F85L2
chr16:90001339-90001339p.P160P2
chr16:90001562-90001562p.G235R2
chr16:90001364-90001364p.V169I2
chr16:90002086-90002086p.T409T2
chr16:90001203-90001203p.S115L2
chr16:90001971-90001971p.S371N1

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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
# sample51111  2 2  424  613 8
# mutation51110  2 2  424  613 8
nonsynonymous SNV51 8  1 2  113  28 5
synonymous SNV  12  1    311  45 3
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
chr16:89999962p.F13L,TUBB32
chr16:90002028p.P171L,TUBB32
chr16:90001393p.S43L,TUBB32
chr16:90001203p.R318Q,TUBB32
chr16:90001587p.T106T,TUBB32
chr16:90001817p.R248C,TUBB32
chr16:90001986p.A356A,TUBB31
chr16:90001360p.P274L,TUBB31
chr16:90001642p.E359D,TUBB31
chr16:89999920p.F13S,TUBB31

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 TUBB3 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 TUBB3

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

ACOT7,BNC1,C11orf87,USB1,CDH4,EMC8,DBNDD1,
ENO1,FSCN1,HAS3,HSD17B3,KRT75,MC1R,MYO7B,
NUP93,OR2J3,PCSK9,PLEK2,RPSAP52,S100A2,TUBB3
ACOT7,AGTRAP,C9orf89,CAPS,CFL1,COPE,CTXN1,
MIF,PHLDA2,PPP1CA,PPP4C,PSMC4,PTRH1,RHOC,
S100A9,SDCBP2,TSPAN17,TSTA3,TUBB4B,TUBB3,YIF1B

BEAN,ADIRF,CA6,CACNG6,EPHB6,FGF19,GAS6-AS2,
HGFAC,KLK6,KLK8,MC1R,MSX2,MSX2P1,PAK7,
PAPL,SLC2A1,SLIT1,SOHLH1,TCHH,TUBB3,ZNF735
APLP1,ATCAY,ATP1A3,CALY,CELF4,CHRNB4,CNTN2,
CTNNA2,ELAVL3,HMP19,KIF5A,MYT1L,NDRG4,NEFL,
PHOX2B,PIRT,PRPH,PTPRN,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 TUBB3
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 3 class IIIexperimental; investigationalEpothilone D
DB03010tubulin, beta 3 class IIIexperimental; investigationalEpothilone B
DB04845tubulin, beta 3 class IIIapproved; investigationalIxabepilone


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Cross referenced IDs for TUBB3
* 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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