Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 TUBB6
Basic gene info.Gene symbolTUBB6
Gene nametubulin, beta 6 class V
SynonymsHsT1601|TUBB-5
CytomapUCSC genome browser: 18p11.21
Genomic locationchr18 :12308256-12326568
Type of geneprotein-coding
RefGenesNM_032525.1,
Ensembl idENSG00000176014
Descriptionclass V beta-tubulintubulin beta MGC4083tubulin beta class Vtubulin beta-6 chain
Modification date20141207
dbXrefs MIM : 615103
HGNC : HGNC
Ensembl : ENSG00000176014
HPRD : 11349
Vega : OTTHUMG00000131692
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TUBB6
BioGPS: 84617
Gene Expression Atlas: ENSG00000176014
The Human Protein Atlas: ENSG00000176014
PathwayNCI Pathway Interaction Database: TUBB6
KEGG: TUBB6
REACTOME: TUBB6
ConsensusPathDB
Pathway Commons: TUBB6
MetabolismMetaCyc: TUBB6
HUMANCyc: TUBB6
RegulationEnsembl's Regulation: ENSG00000176014
miRBase: chr18 :12,308,256-12,326,568
TargetScan: NM_032525
cisRED: ENSG00000176014
ContextiHOP: TUBB6
cancer metabolism search in PubMed: TUBB6
UCL Cancer Institute: TUBB6
Assigned class in ccmGDBC

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Phenotypic Information for TUBB6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TUBB6
Familial Cancer Database: TUBB6
* 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: TUBB6
MedGen: TUBB6 (Human Medical Genetics with Condition)
ClinVar: TUBB6
PhenotypeMGI: TUBB6 (International Mouse Phenotyping Consortium)
PhenomicDB: TUBB6

Mutations for TUBB6
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasTUBB6chr181231524012315260TUBB6chr181231595212315972
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TUBB6 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU927907IL4I13229195041077950411007TUBB6224429181232634512326549
BF095880ADI11432235025013504659TUBB6429487181232607612326134
AA416878RYR21341551237787094237787116TUBB6152496181232489812325242

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=22)
Stat. for Synonymous SNVs
(# total SNVs=16)
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
chr18:12326001-12326001p.E405K2
chr18:12325590-12325590p.P268S2
chr18:12326037-12326037p.D417N2
chr18:12308793-12308793p.S55S2
chr18:12325685-12325685p.M299I2
chr18:12311054-12311054p.?1
chr18:12325723-12325723p.T312I1
chr18:12325368-12325368p.E194*1
chr18:12308711-12308711p.H28R1
chr18:12325072-12325072p.T95M1

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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
# sample21 7  4 1  31   710 9
# mutation21 8  4 1  31   811 9
nonsynonymous SNV21 4  3 1       77 5
synonymous SNV   4  1    31   14 4
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
chr18:12326037p.P268S2
chr18:12325590p.D417N2
chr18:12325183p.S172L1
chr18:12325927p.T285T1
chr18:12325517p.H28R1
chr18:12325656p.P173L1
chr18:12308734p.T290A1
chr18:12325201p.Y36H1
chr18:12325960p.E205K1
chr18:12325518p.D295N1

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 TUBB6 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 TUBB6

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

ARHGAP22,B4GALT2,BATF3,BRI3,PXDC1,CDC42EP1,FHL3,
KIFC3,LMNA,MICALL1,NXN,PDLIM7,PIM1,PLAUR,
PLSCR3,PRKCDBP,PTRF,S100A10,TPM2,TUBB6,VIM
AP1M1,ADIRF,CCDC107,CD81,EHD2,FNDC4,HABP4,
LGALS1,NUMBL,PALM,PNMA1,PRR5,PTRF,RRAS,
SURF4,TESK1,TFE3,TPD52L2,TUBB6,VEGFB,VIM

AMOTL1,BNC2,CNRIP1,COPZ2,DPYSL3,EFEMP2,EFS,
EHD2,EMILIN1,FBXL7,FERMT2,FEZ1,GLI3,GYPC,
LAYN,MRAS,PDLIM7,PLEKHO1,PTRF,RAB34,TUBB6
BVES,CALD1,CSRP1,DNAJB5,DPYSL3,FERMT2,ITGB1BP2,
LOC401093,MSRB3,MYLK,NCS1,PDLIM3,PDLIM4,PDLIM7,
PTRF,SYNPO2,TPM1,TPM2,TSPAN2,TUBA1A,TUBB6
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 TUBB6


There's no related Drug.
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Cross referenced IDs for TUBB6
* 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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