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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for OAT |
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Phenotypic Information for OAT(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: OAT |
Familial Cancer Database: OAT |
* 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 | |
KEGG_ARGININE_AND_PROLINE_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: OAT |
MedGen: OAT (Human Medical Genetics with Condition) | |
ClinVar: OAT | |
Phenotype | MGI: OAT (International Mouse Phenotyping Consortium) |
PhenomicDB: OAT |
Mutations for OAT |
* 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 OAT 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 |
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=21) | (# total SNVs=6) |
(# 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 |
chr10:126086581-126086581 | p.P417Q | 2 |
chr10:126086638-126086638 | p.R398Q | 2 |
chr10:126089434-126089434 | p.N378N | 2 |
chr10:126094027-126094027 | p.Y209C | 2 |
chr10:126100568-126100568 | p.L58S | 2 |
chr10:126090297-126090297 | p.E338K | 1 |
chr10:126097201-126097201 | p.E144* | 1 |
chr10:126100674-126100674 | p.A23S | 1 |
chr10:126090306-126090306 | p.A335T | 1 |
chr10:126097379-126097379 | p.V119I | 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 |   |   |   | 3 |   |   | 1 |   | 1 |   |   | 2 |   |   |   |   | 3 | 1 |   | 7 |
# mutation |   |   |   | 3 |   |   | 1 |   | 1 |   |   | 2 |   |   |   |   | 3 | 1 |   | 7 |
nonsynonymous SNV |   |   |   | 2 |   |   |   |   | 1 |   |   | 2 |   |   |   |   | 3 | 1 |   | 6 |
synonymous SNV |   |   |   | 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 |
chr10:126086638 | p.R260Q,OAT | 2 |
chr10:126094005 | p.C115G,OAT | 1 |
chr10:126086581 | p.E78D,OAT | 1 |
chr10:126097148 | p.K23N,OAT | 1 |
chr10:126097379 | p.V119I | 1 |
chr10:126086643 | p.A114V | 1 |
chr10:126097393 | p.K96N | 1 |
chr10:126086651 | p.L70L | 1 |
chr10:126097446 | p.P279Q,OAT | 1 |
chr10:126089546 | p.K66K | 1 |
Other DBs for Point Mutations |
Copy Number for OAT 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 OAT |
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 |
ALDH18A1,BCCIP,MCMBP,CACUL1,CEACAM1,DHX32,DLAT, EHF,EIF3A,FAM175B,FAM45A,FAM45B,OAT,PLEKHA1, PRDX3,SEC23IP,SLC5A1,SMNDC1,SOX9,TIAL1,TM9SF3 | CTBP2,DSC2,FAM60A,GRHL1,LRRC8D,NKRF,OAT, PAICS,PPAT,PRKCI,PRMT3,RFC3,RHPN2,SLC12A2, SRPK1,SUDS3,TDP1,TMEM123,TRIM2,TTC19,ZNF146 | ||||
ACADSB,ACSL4,APOO,ATF1,ATP6AP2,BAG3,MCMBP, FAM216A,CLCN4,DGKG,EIF2S3,FAM175B,FTSJ1,HCCS, ISCU,MORF4L2,NXT2,OAT,PLEKHA1,PRPS1,UHRF1BP1L | ABCG5,APOA1,APOA4,APOB,APOC3,C17orf78,CPO, CPS1,CUBN,DPEP1,FABP6,FMO1,GSTA2,KCNJ13, KHK,MTTP,OAT,SOAT2,SPANXN3,TMPR |
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 OAT |
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 |
DB00114 | ornithine aminotransferase | nutraceutical | Pyridoxal Phosphate | ||
DB00129 | ornithine aminotransferase | approved; nutraceutical | L-Ornithine | ||
DB02054 | ornithine aminotransferase | experimental | Gabaculine | ||
DB02821 | ornithine aminotransferase | experimental | Canaline | ||
DB00125 | ornithine aminotransferase | approved; nutraceutical | L-Arginine | ||
DB03904 | ornithine aminotransferase | experimental | Urea | ||
DB00172 | ornithine aminotransferase | approved; nutraceutical | L-Proline |
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Cross referenced IDs for OAT |
* 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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