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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for TUBA1A |
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Phenotypic Information for TUBA1A(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: TUBA1A |
Familial Cancer Database: TUBA1A |
* 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 | 602529; gene. 611603; phenotype. |
Orphanet | 171680; Lissencephaly due to TUBA1A mutation. |
Disease | KEGG Disease: TUBA1A |
MedGen: TUBA1A (Human Medical Genetics with Condition) | |
ClinVar: TUBA1A | |
Phenotype | MGI: TUBA1A (International Mouse Phenotyping Consortium) |
PhenomicDB: TUBA1A |
Mutations for TUBA1A |
* 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 TUBA1A 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 |
AI198453 | TUBA1A | 8 | 242 | 12 | 49578582 | 49578816 | SNRNP27 | 234 | 452 | 2 | 70122273 | 70124540 | |
AU099292 | PTPN13 | 9 | 90 | 4 | 87622394 | 87622475 | TUBA1A | 90 | 300 | 12 | 49580508 | 49582861 | |
AI199092 | TUBA1A | 1 | 232 | 12 | 49578585 | 49578816 | SNRNP27 | 224 | 401 | 2 | 70122314 | 70124540 |
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=0) | (# total SNVs=0) |
(# total SNVs=0) | (# 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 |
chr12:49579743-49579743 | p.L136L | 1 |
chr12:49580453-49580453 | p.T56M | 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 | 2 | 1 |   | 2 | 1 |   | 1 |   | 1 |   | 1 | 4 | 1 |   | 1 |   | 3 | 3 | 1 | 10 |
# mutation | 2 | 1 |   | 2 | 1 |   | 1 |   | 1 |   | 1 | 5 | 1 |   | 1 |   | 3 | 3 | 1 | 10 |
nonsynonymous SNV | 2 | 1 |   | 1 | 1 |   |   |   | 1 |   | 1 | 4 | 1 |   | 1 |   | 3 | 2 |   | 9 |
synonymous SNV |   |   |   | 1 |   |   | 1 |   |   |   |   | 1 |   |   |   |   |   | 1 | 1 | 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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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 |
chr12:49580453 | p.T56M,TUBA1A | 2 |
chr12:49579071 | p.R308C,TUBA1A | 1 |
chr12:49579509 | p.A65V,TUBA1A | 1 |
chr12:49580443 | p.H266Q,TUBA1A | 1 |
chr12:49579083 | p.R64L,TUBA1A | 1 |
chr12:49579554 | p.P263S,TUBA1A | 1 |
chr12:49580452 | p.G59G,TUBA1A | 1 |
chr12:49579153 | p.E254K,TUBA1A | 1 |
chr12:49579664 | p.T56T,TUBA1A | 1 |
chr12:49579170 | p.L252M,TUBA1A | 1 |
Other DBs for Point Mutations |
Copy Number for TUBA1A 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 TUBA1A |
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 |
NREP,CCDC23,CLIP2,DBN1,DIRAS1,GPR161,H2BFXP, HDAC2,KDM1A,KIF3C,MAD2L2,MEX3A,MEX3B,NCS1, NXN,SOX4,STMN1,TMEFF1,TMSB15B,TUBA1A,TUBA1B | ACTB,ACTG1,CFL1,CRIP2,FXYD5,JUND,KIF9, MED27,NXT1,OVCA2,PDLIM1,RAB34,S100A16,SERTAD1, SF3B4,SLC10A3,TAGLN2,TNFRSF12A,TUBA1A,TUBA1C,ZYX | ||||
BNC2,CNRIP1,COX7A1,DZIP1,EFEMP2,FERMT2,FEZ1, ARHGEF25,GYPC,HSPB2,JAM3,LAYN,MSRB3,NAP1L3, PRKD1,RAB34,SYT11,TCEAL7,TGFB1I1,TUBA1A,TUBB6 | CASQ2,CSRP1,DACT3,DES,ILK,KCNMB1,LGALS1, LMO3,MYL9,MYLK,PDLIM3,PDLIM7,PNCK,SMTN, TAGLN,TMEM35,TPM1,TPM2,TSPAN2,TUBA1A,TUBB6 |
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 TUBA1A |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Chemistry | BindingDB | Q71U36; -. |
Chemistry | ChEMBL | CHEMBL2095182; -. |
Organism-specific databases | PharmGKB | PA162407319; -. |
Organism-specific databases | CTD | 7846; -. |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00518 | tubulin, alpha 1a | approved | Albendazole | ||
DB00570 | tubulin, alpha 1a | approved | Vinblastine | ||
DB00643 | tubulin, alpha 1a | approved | Mebendazole | ||
DB01873 | tubulin, alpha 1a | experimental; investigational | Epothilone D | ||
DB03010 | tubulin, alpha 1a | experimental; investigational | Epothilone B | ||
DB07574 | tubulin, alpha 1a | experimental | 2-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 TUBA1A |
* 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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