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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for TUBA4A |
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Phenotypic Information for TUBA4A(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: TUBA4A |
Familial Cancer Database: TUBA4A |
* 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: TUBA4A |
MedGen: TUBA4A (Human Medical Genetics with Condition) | |
ClinVar: TUBA4A | |
Phenotype | MGI: TUBA4A (International Mouse Phenotyping Consortium) |
PhenomicDB: TUBA4A |
Mutations for TUBA4A |
* 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 TUBA4A 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 |
DA812020 | TM9SF4 | 1 | 402 | 20 | 30697533 | 30729350 | TUBA4A | 395 | 788 | 2 | 220116326 | 220118638 |
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=36) | (# total SNVs=10) |
(# total SNVs=2) | (# 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 |
chr2:220115768-220115768 | p.D218G | 3 |
chr2:220116426-220116426 | p.R79Q | 3 |
chr2:220115938-220115938 | p.Y161Y | 2 |
chr2:220115764-220115764 | p.I219I | 2 |
chr2:220115939-220115939 | p.Y161F | 2 |
chr2:220115877-220115877 | p.V182I | 2 |
chr2:220115880-220115880 | p.V181M | 2 |
chr2:220115406-220115406 | p.R339C | 1 |
chr2:220116371-220116371 | p.E97E | 1 |
chr2:220116931-220116931 | p.V9M | 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 |   | 12 | 1 |   | 3 |   | 2 | 1 |   | 3 | 1 | 3 |   | 1 | 5 | 1 |   | 10 |
# mutation |   | 1 |   | 8 | 1 |   | 3 |   | 2 | 1 |   | 3 | 1 | 3 |   | 1 | 6 | 1 |   | 15 |
nonsynonymous SNV |   | 1 |   | 7 | 1 |   | 1 |   | 2 | 1 |   | 3 |   | 3 |   |   | 4 | 1 |   | 10 |
synonymous SNV |   |   |   | 1 |   |   | 2 |   |   |   |   |   | 1 |   |   | 1 | 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 |
chr2:220116426 | p.D203G,TUBA4A | 3 |
chr2:220115768 | p.R64Q,TUBA4A | 3 |
chr2:220115938 | p.T58T,TUBA4A | 2 |
chr2:220115939 | p.Y146Y,TUBA4A | 2 |
chr2:220116737 | p.Y146F,TUBA4A | 2 |
chr2:220116329 | p.R249L,TUBA4A | 1 |
chr2:220115525 | p.R108C,TUBA4A | 1 |
chr2:220116808 | p.V9M | 1 |
chr2:220115780 | p.P246S,TUBA4A | 1 |
chr2:220116339 | p.L104L,TUBA4A | 1 |
Other DBs for Point Mutations |
Copy Number for TUBA4A 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 TUBA4A |
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 |
ARHGEF4,BNC1,CA9,ENO1,FERMT1,FGFBP1,FSCN1, GJB3,GJB5,GPR87,KRT5,KRT6B,MYO7B,PCSK9, PLEK2,RPSAP52,S100A2,SFN,SOX15,TNFSF9,TUBA4A | PERM1,CACNB1,CHRNA10,YBX3,FEM1A,FHL3,GAMT, GAPDH,GMPR,GOT2,IDI2,MYL6B,PDLIM3,RBM38, RTN2,SH2B2,SHISA4,TCEA3,TPM1,TPM2,TUBA4A | ||||
ATPIF1,UQCC3,CD320,DTYMK,EXOSC7,MZT2B,HNRNPAB, ILKAP,LSM4,LSM7,MRPS34,MXD3,NOP16,PPIH, PRELID1,STARD10,TIMM13,TUBA1C,TUBA4A,TUBB4B,UQCRQ | AGR2,ARF4,CCT7,CDC37,CGB,GALE,GARS, GORASP2,KCTD14,KDELR3,NABP2,PPP5C,RGS8,S100P, SLC16A14,SYNGR2,TFF1,TMED9,TTC39A,TUBA4A,TUBG1 |
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 TUBA4A |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
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 |
DB00541 | tubulin, alpha 4a | approved; investigational | Vincristine | ||
DB01179 | tubulin, alpha 4a | approved | Podofilox | ||
DB01873 | tubulin, alpha 4a | experimental; investigational | Epothilone D | ||
DB03010 | tubulin, alpha 4a | experimental; investigational | Epothilone B | ||
DB06772 | tubulin, alpha 4a | approved | Cabazitaxel | ||
DB01033 | tubulin, alpha 4a | approved | Mercaptopurine | ||
DB00563 | tubulin, alpha 4a | approved | Methotrexate |
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Cross referenced IDs for TUBA4A |
* 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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