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 TUBB2B
Basic gene info.Gene symbolTUBB2B
Gene nametubulin, beta 2B class IIb
SynonymsPMGYSA|bA506K6.1
CytomapUCSC genome browser: 6p25
Genomic locationchr6 :3224494-3227968
Type of geneprotein-coding
RefGenesNM_178012.4,
Ensembl idENSG00000137285
Descriptionclass II beta-tubulin isotypeclass IIb beta-tubulintubulin beta-2B chaintubulin, beta polypeptide paralog
Modification date20141207
dbXrefs MIM : 612850
HGNC : HGNC
Ensembl : ENSG00000137285
HPRD : 14707
Vega : OTTHUMG00000014143
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TUBB2B
BioGPS: 347733
Gene Expression Atlas: ENSG00000137285
The Human Protein Atlas: ENSG00000137285
PathwayNCI Pathway Interaction Database: TUBB2B
KEGG: TUBB2B
REACTOME: TUBB2B
ConsensusPathDB
Pathway Commons: TUBB2B
MetabolismMetaCyc: TUBB2B
HUMANCyc: TUBB2B
RegulationEnsembl's Regulation: ENSG00000137285
miRBase: chr6 :3,224,494-3,227,968
TargetScan: NM_178012
cisRED: ENSG00000137285
ContextiHOP: TUBB2B
cancer metabolism search in PubMed: TUBB2B
UCL Cancer Institute: TUBB2B
Assigned class in ccmGDBC

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Phenotypic Information for TUBB2B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TUBB2B
Familial Cancer Database: TUBB2B
* 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: TUBB2B
MedGen: TUBB2B (Human Medical Genetics with Condition)
ClinVar: TUBB2B
PhenotypeMGI: TUBB2B (International Mouse Phenotyping Consortium)
PhenomicDB: TUBB2B

Mutations for TUBB2B
* 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 TUBB2B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW498865NACA160125711265857112717TUBB2B61352632259383226861
DA506064TUBB2B1484632259493227887DYRK2484572126805230768052395

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=16)
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
chr6:3226446-3226446p.S75L3
chr6:3225015-3225015p.F436F3
chr6:3225000-3225000p.G441G2
chr6:3226486-3226486p.R62R2
chr6:3225881-3225881p.G148S1
chr6:3227744-3227744p.C12G1
chr6:3225151-3225151p.R391H1
chr6:3226033-3226033p.A97V1
chr6:3225266-3225266p.V353M1
chr6:3226399-3226399p.V91M1

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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 8    2  2   1 315
# mutation 1 6    2  2   1 315
nonsynonymous SNV 1 3    2  2   1 112
synonymous SNV   3             2 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
chr6:3225015p.F436F3
chr6:3225820p.G441G2
chr6:3225000p.S168N2
chr6:3226446p.S75L2
chr6:3227744p.R62R1
chr6:3225881p.P61T1
chr6:3226399p.A445A1
chr6:3224988p.V23F1
chr6:3226415p.N14S1
chr6:3225005p.E440K1

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 TUBB2B 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 TUBB2B

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

ATE1,COLCA2,LINC01551,KHDC3L,CCKBR,DCAF8L1,HSPB2,
MAMLD1,NPM3,NSMCE4A,PCBP4,PGPEP1L,PRDM9,RSPO4,
TRIM51,TBC1D21,TUBB2A,TUBB2B,UNC93A,ZCCHC18,ZNF232
ACTG2,CA11,CADM4,CNN1,CSRP1,FBXO2,IGFBP2,
IL34,KRT14,KRT17,KRT5,PDLIM4,PLEKHA4,RAB34,
SFN,TAGLN,TCEAL3,TGFB1I1,TUBB2B,VASP,ZYX

ASTN1,ATCAY,BSX,CLVS2,CNIH2,FERD3L,JPH4,
KCNN1,LRRC4B,RGAG4,SLC17A7,SLC7A14,SYT4,SYT5,
TAGLN3,TECRL,TMEM59L,TUBB2B,VWA5B2,ZCCHC12,ZDHHC22
ACTA2,ACTG2,AOC3,CNN1,COL22A1,DACT3,DGKG,
RBFOX3,ILDR2,KIF26B,MAPT,NPTXR,PCP4L1,PCYT1B,
PDLIM7,PYGM,REEP2,TAGLN,TUBA1A,TUBB2B,ZFHX4
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 TUBB2B
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
DB07574tubulin, beta 2B class IIbexperimental2-MERCAPTO-N-[1,2,3,10-TETRAMETHOXY-9-OXO-5,6,7,9-TETRAHYDRO-BENZO[A]HEPTALEN-7-YL]ACETAMIDE


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Cross referenced IDs for TUBB2B
* 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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