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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for TUBB2A |
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Phenotypic Information for TUBB2A(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: TUBB2A |
Familial Cancer Database: TUBB2A |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_PROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: TUBB2A |
MedGen: TUBB2A (Human Medical Genetics with Condition) | |
ClinVar: TUBB2A | |
Phenotype | MGI: TUBB2A (International Mouse Phenotyping Consortium) |
PhenomicDB: TUBB2A |
Mutations for TUBB2A |
* 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TUBB2A related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
BF525947 | CSNK1A1 | 1 | 321 | 5 | 148930404 | 148930724 | TUBB2A | 315 | 531 | 6 | 3153902 | 3154114 | |
BQ277692 | YY1 | 2 | 695 | 14 | 100728650 | 100744074 | TUBB2A | 696 | 1036 | 6 | 3155860 | 3157761 | |
AW956098 | TUBB2A | 1 | 222 | 6 | 3153905 | 3154126 | SRSF4 | 219 | 360 | 1 | 29479908 | 29737679 |
Other DBs for Structural Variants |
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Copy 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=15) | (# total SNVs=9) |
(# total SNVs=1) | (# total SNVs=0) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr6:3154871-3154871 | p.S188S | 4 |
chr6:3154153-3154153 | p.A428T | 2 |
chr6:3154127-3154127 | p.F436F | 2 |
chr6:3154140-3154140 | p.E432G | 1 |
chr6:3156300-3156300 | p.N48N | 1 |
chr6:3154784-3154784 | p.L217L | 1 |
chr6:3154934-3154934 | p.F167F | 1 |
chr6:3154142-3154142 | p.D431D | 1 |
chr6:3156348-3156348 | p.P32P | 1 |
chr6:3154797-3154797 | p.R213H | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 1 | 1 |   | 5 |   |   |   |   |   |   |   | 3 | 2 |   |   |   | 4 | 4 |   | 7 |
# mutation | 1 | 1 |   | 5 |   |   |   |   |   |   |   | 3 | 2 |   |   |   | 4 | 4 |   | 7 |
nonsynonymous SNV |   | 1 |   | 4 |   |   |   |   |   |   |   | 3 | 2 |   |   |   | 2 | 2 |   | 2 |
synonymous SNV | 1 |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   | 2 | 2 |   | 5 |
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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr6:3154140 | p.T143T | 1 |
chr6:3154823 | p.F436F | 1 |
chr6:3156348 | p.S95N | 1 |
chr6:3154142 | p.G434R | 1 |
chr6:3154832 | p.Q94H | 1 |
chr6:3154153 | p.E432G | 1 |
chr6:3154882 | p.F90F | 1 |
chr6:3154175 | p.D431D | 1 |
chr6:3155006 | p.T72I | 1 |
chr6:3154186 | p.A428T | 1 |
Other DBs for Point Mutations |
Copy Number for TUBB2A 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 TUBB2A |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
LINC01551,PXDC1,CCKBR,DBN1,FAM127A,GJC2,GPSM1, KIF1C,LMNA,NPM3,NSMCE4A,NXN,PCBP4,PDLIM7, PFN1,PLSCR3,PRKCDBP,SMTN,TP53I3,TUBB2A,TUBB2B | ANXA11,AP2M1,ARHGDIA,ARL8A,B3GALT4,KXD1,SMIM12, CCDC107,CCM2,CD151,DDAH2,EFEMP2,GPX1,MYL6, NUCB1,PPP2R5B,PSMD9,RNH1,TUBB2A,TUBB4B,TUBB4A |
ANTXR2,C10orf54,MIR22HG,CIDEC,ISG20,LRP10,MALL, POLD4,QSOX1,RAB3B,RELL1,RIPK1,RNF152,SDCBP2, SGMS2,SMPD1,TNIP1,TSPAN1,TUBB2A,TUBB4A,VILL | ACTG2,BVES,CDC42EP3,CTXN1,DACT3,DES,DGKG, DMPK,DNAJB5,LDB3,MAP7D1,NPTXR,PCYT1B,PDLIM7, PDZD4,PTRF,PYGM,REEP2,SLC2A4,TUBB2A,TUBB2B |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for TUBB2A |
There's no related Drug. |
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Cross referenced IDs for TUBB2A |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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