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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for CROT |
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Phenotypic Information for CROT(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: CROT |
Familial Cancer Database: CROT |
* 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: CROT |
MedGen: CROT (Human Medical Genetics with Condition) | |
ClinVar: CROT | |
Phenotype | MGI: CROT (International Mouse Phenotyping Consortium) |
PhenomicDB: CROT |
Mutations for CROT |
* 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 CROT 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=66) | (# total SNVs=13) |
(# total SNVs=1) | (# total SNVs=1) |
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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 |
chr7:87006749-87006749 | p.F321L | 4 |
chr7:87011450-87011450 | p.K375E | 4 |
chr7:86990850-86990850 | p.L129I | 3 |
chr7:87022269-87022269 | p.G535V | 2 |
chr7:87011492-87011492 | p.R389G | 2 |
chr7:87011494-87011494 | p.R389S | 2 |
chr7:86990745-86990745 | p.R94C | 2 |
chr7:87011495-87011495 | p.E390K | 2 |
chr7:87022321-87022321 | p.Q552H | 2 |
chr7:87011811-87011811 | p.T418K | 2 |
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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 | 5 |   | 12 | 1 |   | 1 | 1 | 2 |   |   | 12 | 5 | 2 |   | 1 | 3 | 6 |   | 9 |
# mutation | 3 | 5 |   | 11 | 1 |   | 1 | 1 | 3 |   |   | 11 | 5 | 2 |   | 1 | 3 | 7 |   | 10 |
nonsynonymous SNV | 3 | 3 |   | 7 |   |   | 1 | 1 | 2 |   |   | 10 | 5 | 2 |   | 1 | 3 | 7 |   | 7 |
synonymous SNV |   | 2 |   | 4 | 1 |   |   |   | 1 |   |   | 1 |   |   |   |   |   |   |   | 3 |
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 |
chr7:87011450 | p.K375E,CROT | 4 |
chr7:86990850 | p.L129F,CROT | 3 |
chr7:87022269 | p.Q270Q,CROT | 2 |
chr7:87022321 | p.Q552H,CROT | 2 |
chr7:87005203 | p.G535V,CROT | 2 |
chr7:87021891 | p.S392S,CROT | 1 |
chr7:86998763 | p.N134D,CROT | 1 |
chr7:87006753 | p.E288D,CROT | 1 |
chr7:87011494 | p.T418K,CROT | 1 |
chr7:87021902 | p.P585P,CROT | 1 |
Other DBs for Point Mutations |
Copy Number for CROT 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 CROT |
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 |
ANKRA2,APPL2,AR,SMIM14,CROT,HNMT,INPP4B, FAM214A,MEGF9,MPV17L,NEDD4,RETSAT,RHOB,RNF103, SC5D,SEC14L2,SEMA3C,TMEM62,TP53TG1,TRIM6,USP40 | ACPP,ALCAM,ARSD,ATG16L1,HEXA-AS1,CROT,FAM174B, FOXA1,GALNT3,MBOAT2,PTPLAD1,PXMP4,SLC38A1,STYK1, TFAP2B,TMEM63C,TMEM87B,TRIM36,ZNF613,ZNF626,ZNF649 | ||||
ANKIB1,TMEM243,TMEM248,CCDC132,COG5,CRCP,CROT, FAM185A,FAM200A,GALNT11,GATAD1,KRIT1,NAPEPLD,PEX1, RPS6KA6,SEMA3C,TP53TG1,TRIM4,TYW1,VKORC1L1,ZSCAN25 | ACVR2A,AKR1B10,ANO10,AP1AR,BMF,SUGCT,CROT, ETFDH,FAM73B,FMO4,HADHA,HADHB,KALRN,LPCAT3, PBLD,RBKS,SEPSECS,SLC27A4,SLC41A2,TMEM82,UGT1A9 |
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 CROT |
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-octanoyltransferase | approved | L-Carnitine | ||
DB02648 | carnitine O-octanoyltransferase | experimental | (3-Carboxy-2-(R)-Hydroxy-Propyl)-Trimethyl-Ammonium | ||
DB03832 | carnitine O-octanoyltransferase | experimental | 3-Carboxy-N,N,N-Trimethyl-2-(Octanoyloxy)Propan-1-Aminium |
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Cross referenced IDs for CROT |
* 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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