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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for CRAT |
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Phenotypic Information for CRAT(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: CRAT |
Familial Cancer Database: CRAT |
* 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_PEROXISOMAL_LIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: CRAT |
MedGen: CRAT (Human Medical Genetics with Condition) | |
ClinVar: CRAT | |
Phenotype | MGI: CRAT (International Mouse Phenotyping Consortium) |
PhenomicDB: CRAT |
Mutations for CRAT |
* 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 |
- Statistics for Tissue and Mutation type | Top |
- For Inter-chromosomal Variations |
There's no inter-chromosomal structural variation. |
- For Intra-chromosomal Variations |
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
pancreas | CRAT | chr9 | 131862986 | 131863006 | chr9 | 131835683 | 131835703 |
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CRAT 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 |
AW843407 | SPTAN1 | 16 | 162 | 9 | 131395632 | 131395779 | CRAT | 157 | 304 | 9 | 131860855 | 131862217 | |
T12603 | CRAT | 1 | 241 | 9 | 131860133 | 131862545 | DOLPP1 | 238 | 341 | 9 | 131847201 | 131847304 |
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=3) | (# total SNVs=2) |
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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 |
chr9:131865314-131865314 | p.D148N | 2 |
chr9:131860614-131860614 | p.F414F | 2 |
chr9:131857840-131857840 | p.G573S | 2 |
chr9:131860304-131860304 | p.D484D | 2 |
chr9:131857859-131857859 | p.F566F | 2 |
chr9:131860315-131860315 | p.A481P | 2 |
chr9:131864813-131864814 | p.K166fs*48 | 2 |
chr9:131857756-131857756 | p.A601T | 2 |
chr9:131857787-131857787 | p.S590S | 1 |
chr9:131862207-131862207 | p.Y341Y | 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 | 5 | 4 | 1 | 7 | 1 |   | 1 |   |   | 1 |   | 1 | 2 | 1 |   |   | 7 | 5 | 1 | 4 |
# mutation | 5 | 4 | 1 | 7 | 1 |   | 1 |   |   | 1 |   | 1 | 2 | 1 |   |   | 7 | 5 | 1 | 4 |
nonsynonymous SNV | 5 | 3 | 1 | 6 | 1 |   |   |   |   | 1 |   | 1 |   | 1 |   |   | 4 | 2 |   | 2 |
synonymous SNV |   | 1 |   | 1 |   |   | 1 |   |   |   |   |   | 2 |   |   |   | 3 | 3 | 1 | 2 |
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 |
chr9:131860614 | p.A601T,CRAT | 2 |
chr9:131857756 | p.F414F,CRAT | 2 |
chr9:131857852 | p.R82H,CRAT | 1 |
chr9:131870096 | p.F566F,CRAT | 1 |
chr9:131860528 | p.Y300Y,CRAT | 1 |
chr9:131864290 | p.D71N,CRAT | 1 |
chr9:131857859 | p.M564V,CRAT | 1 |
chr9:131870139 | p.S275F,CRAT | 1 |
chr9:131860611 | p.S26S,CRAT | 1 |
chr9:131864310 | p.A558V,CRAT | 1 |
Other DBs for Point Mutations |
Copy Number for CRAT 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 CRAT |
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 |
ABCC11,ACAA1,ALDH4A1,ALOX15B,ARRDC1,CRAT,CYB561D2, DALRD3,FAH,GGT1,GGT3P,GGTLC1,MPV17L,PPP2R4, REEP6,SERHL2,SPDEF,SPINK8,TMEM141,TMEM62,TMEM63C | ACADM,ACO2,ATP1A2,IDI2-AS1,CCDC141,CECR2,CRAT, DNAJA4,FHOD1,IDH2,MFN2,NDUFAF1,NDUFS2,OGDH, ECI2,POLDIP2,RNF10,SAR1B,SDHA,SIX1,UQCRC1 | ||||
CD5,CRAT,DEGS2,EPHB3,EPHX1,FAM63A,FPGS, GJC2,LOC729467,MKNK2,PI4KB,PLA2G4F,PPP2R4,PROM2, RAB25,RILP,RPLP0P2,SDC1,SYK,TMEM150C,TMEM2 | ACO2,SOWAHA,C1orf115,CDHR5,CES2,CRAT,GDPD2, INPP5J,KIAA2013,LOC151534,MSRA,NCK2,PNPLA6,POR, RAB17,RARA,SLC25A1,SLC9A3R1,TMEM120A,TPRG1L,TTBK1 |
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 CRAT |
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 |
DB00583 | carnitine O-acetyltransferase | approved | L-Carnitine | ||
DB01992 | carnitine O-acetyltransferase | experimental | Coenzyme A | ||
DB02648 | carnitine O-acetyltransferase | experimental | (3-Carboxy-2-(R)-Hydroxy-Propyl)-Trimethyl-Ammonium |
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Cross referenced IDs for CRAT |
* 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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