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 TUBA1C
Basic gene info.Gene symbolTUBA1C
Gene nametubulin, alpha 1c
SynonymsTUBA6|bcm948
CytomapUCSC genome browser: 12q13.12
Genomic locationchr12 :49658864-49667113
Type of geneprotein-coding
RefGenesNM_001303114.1,
NM_001303115.1,NM_001303116.1,NM_001303117.1,NM_032704.4,
Ensembl idENSG00000167553
Descriptionalpha-tubulin 6tubulin alpha-1C chaintubulin alpha-6 chaintubulin, alpha 6
Modification date20141218
dbXrefs HGNC : HGNC
Ensembl : ENSG00000167553
HPRD : 06747
Vega : OTTHUMG00000169497
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TUBA1C
BioGPS: 84790
Gene Expression Atlas: ENSG00000167553
The Human Protein Atlas: ENSG00000167553
PathwayNCI Pathway Interaction Database: TUBA1C
KEGG: TUBA1C
REACTOME: TUBA1C
ConsensusPathDB
Pathway Commons: TUBA1C
MetabolismMetaCyc: TUBA1C
HUMANCyc: TUBA1C
RegulationEnsembl's Regulation: ENSG00000167553
miRBase: chr12 :49,658,864-49,667,113
TargetScan: NM_001303114
cisRED: ENSG00000167553
ContextiHOP: TUBA1C
cancer metabolism search in PubMed: TUBA1C
UCL Cancer Institute: TUBA1C
Assigned class in ccmGDBC

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Phenotypic Information for TUBA1C(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TUBA1C
Familial Cancer Database: TUBA1C
* 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: TUBA1C
MedGen: TUBA1C (Human Medical Genetics with Condition)
ClinVar: TUBA1C
PhenotypeMGI: TUBA1C (International Mouse Phenotyping Consortium)
PhenomicDB: TUBA1C

Mutations for TUBA1C
* 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 TUBA1C related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM785206TUBA1C4389124965886749663672RPS2338345558157188381571955
CD368754NCF2183351183524697183525014TUBA1C330634124966609549666398
CD367941TUBA1C16581124966655249667117UBB577698171628567616285798
BE907310TUBA1C1539124966656049667098VPS39539742154245124742451456

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=30)
Stat. for Synonymous SNVs
(# total SNVs=11)
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
chr12:49663397-49663397p.T51T2
chr12:49666563-49666563p.Q301H2
chr12:49666312-49666312p.D218N2
chr12:49663751-49663751p.R123C2
chr12:49666490-49666490p.S277C1
chr12:49666787-49666787p.C376F1
chr12:49663340-49663340p.P32P1
chr12:49666042-49666042p.Q128*1
chr12:49666509-49666509p.H283H1
chr12:49666823-49666823p.W388*1

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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
# sample1215    2  33   23 5
# mutation1215    2  33   23 5
nonsynonymous SNV1214       21   13 5
synonymous SNV   1    2  12   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])

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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
chr12:49666312p.D218N2
chr12:49666924p.T349A1
chr12:49663619p.R79C1
chr12:49666252p.N356S1
chr12:49666957p.G81D1
chr12:49663626p.P364T1
chr12:49663698p.R105Q1
chr12:49666490p.A374A1
chr12:49663746p.R121Q1
chr12:49666534p.L397L1

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 TUBA1C 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 TUBA1C

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,AUNIP,CCNB1,CCNB2,CDC20,CDCA3,CDCA8,
CENPA,CENPN,CKS1B,KIF20A,KIF2C,PLK1,PSMB2,
PTTG1,RAN,TPX2,TROAP,TUBA1B,TUBA1C,UBE2C
ACOT7,ACTB,ATP6V0B,R3HDM4,CFL1,CLIC1,DNAJB11,
GNA15,HM13,HNRNPAB,MANF,PFN1,PPP4C,PRELID1,
RHOC,TAGLN2,TUBA1A,TUBA1B,TUBA1C,TUBB4B,VASP

CCT2,COX6A1,DIABLO,EMG1,EPR1,HN1,MCRS1,
MRPS12,NDUFA12,NME1,NUP37,PGAM5,PSMA5,PSMD9,
PTGES3,RAN,SRSF9,SNRPF,TUBA1B,TUBA1C,UBE2N
AAGAB,AMD1,ANXA2,ANXA2P2,ARPC4,ATG4A,BZW1,
C12orf49,C20orf24,CSTF2,F2RL1,NMNAT1,ORMDL2,RABIF,
SERPINB1,SLMO2,TAGLN2,TPMT,TUBA1C,TUBB4B,UPP1
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 TUBA1C
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 1cexperimental; investigationalEpothilone D
DB03010tubulin, alpha 1cexperimental; investigationalEpothilone B
DB07574tubulin, alpha 1cexperimental2-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 TUBA1C
* 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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