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 TUBA1B
Basic gene info.Gene symbolTUBA1B
Gene nametubulin, alpha 1b
SynonymsK-ALPHA-1
CytomapUCSC genome browser: 12q13.12
Genomic locationchr12 :49521566-49525304
Type of geneprotein-coding
RefGenesNM_006082.2,
Ensembl idENSG00000123416
Descriptionalpha tubulinalpha-tubulin ubiquitoustubulin K-alpha-1tubulin alpha-1B chaintubulin alpha-ubiquitous chaintubulin, alpha, ubiquitous
Modification date20141207
dbXrefs MIM : 602530
HGNC : HGNC
Ensembl : ENSG00000123416
HPRD : 03960
Vega : OTTHUMG00000170410
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TUBA1B
BioGPS: 10376
Gene Expression Atlas: ENSG00000123416
The Human Protein Atlas: ENSG00000123416
PathwayNCI Pathway Interaction Database: TUBA1B
KEGG: TUBA1B
REACTOME: TUBA1B
ConsensusPathDB
Pathway Commons: TUBA1B
MetabolismMetaCyc: TUBA1B
HUMANCyc: TUBA1B
RegulationEnsembl's Regulation: ENSG00000123416
miRBase: chr12 :49,521,566-49,525,304
TargetScan: NM_006082
cisRED: ENSG00000123416
ContextiHOP: TUBA1B
cancer metabolism search in PubMed: TUBA1B
UCL Cancer Institute: TUBA1B
Assigned class in ccmGDBC

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Phenotypic Information for TUBA1B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TUBA1B
Familial Cancer Database: TUBA1B
* 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: TUBA1B
MedGen: TUBA1B (Human Medical Genetics with Condition)
ClinVar: TUBA1B
PhenotypeMGI: TUBA1B (International Mouse Phenotyping Consortium)
PhenomicDB: TUBA1B

Mutations for TUBA1B
* 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 TUBA1B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a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-1711551220160714220161983
BC001209TMEM2464419859104237608104249328TUBA1B19863598124952156549525164
DB368876TUBA1B1131124952156949521699CNOT713252381708728217087676

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=11

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=32)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr12:49523173-49523173p.D76A11
chr12:49522719-49522719p.A126A3
chr12:49523353-49523353p.F52F2
chr12:49522578-49522578p.P173P2
chr12:49522602-49522602p.S165S2
chr12:49522057-49522057p.C347F2
chr12:49521785-49521785p.D438Y2
chr12:49523033-49523033p.R123C2
chr12:49521833-49521833p.R422C1
chr12:49522238-49522238p.S287T1

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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 2161 3    22   73 5
# mutation 2151 3    22   63 5
nonsynonymous SNV 2151 2    12   41 5
synonymous SNV      1    1    22  
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
chr12:49522057p.G29D2
chr12:49523423p.R123C2
chr12:49523033p.C347F2
chr12:49523492p.G43W1
chr12:49523058p.I335M1
chr12:49522081p.R308C1
chr12:49523061p.G29R1
chr12:49522092p.A278V1
chr12:49523074p.S6F1
chr12:49522175p.P175P1

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 TUBA1B 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 TUBA1B

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

AURKB,CDC20,CDC25C,CDC45,CDT1,E2F1,FEN1,
H2AFZ,LMNB1,PKMYT1,PLK1,PTTG1,RAD54L,RNASEH2A,
TACC3,ALYREF,TROAP,TUBA1B,TUBA1C,UBE2C,UBE2S
AP2M1,ARPC1B,ARPC4,CFL1,EFHD2,FAM109B,IFI27L2,
NECAP2,PFN1,PLOD3,PLSCR3,RGS19,RHOG,SHISA5,
SHKBP1,TAGLN2,TAX1BP3,TIMP1,TMSB10,TUBA1B,TUBA1C

AURKB,CDC20,CDC45,CDCA8,CENPM,H2AFZ,HMGN2,
ORC1,PSMD9,RACGAP1,RAD51,RAN,RCC1,RFC5,
SRSF9,SKA1,TK1,TPI1,TUBA1B,TUBA1C,TYMS
ATXN10,CMSS1,CCT7,CENPW,CSE1L,GSTCD,HAUS7,
IARS,LDHB,MLH1,NUP93,PA2G4,POLA2,PSMC3,
RANBP1,RUVBL1,S100A11,TCF19,TIPIN,TUBA1B,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 TUBA1B
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, alpha 1bexperimental; investigationalEpothilone D
DB03010tubulin, alpha 1bexperimental; investigationalEpothilone B
DB07574tubulin, alpha 1bexperimental2-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 TUBA1B
* 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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