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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for RETSAT |
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Phenotypic Information for RETSAT(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: RETSAT |
Familial Cancer Database: RETSAT |
* 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_RETINOL_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: RETSAT |
MedGen: RETSAT (Human Medical Genetics with Condition) | |
ClinVar: RETSAT | |
Phenotype | MGI: RETSAT (International Mouse Phenotyping Consortium) |
PhenomicDB: RETSAT |
Mutations for RETSAT |
* 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 RETSAT 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 |
AW847517 | TMEM151B | 1 | 184 | 6 | 44272402 | 44272822 | RETSAT | 177 | 329 | 2 | 85570959 | 85571111 | |
CA312858 | RETSAT | 17 | 130 | 2 | 85569220 | 85569333 | HLA-DRB5 | 126 | 323 | 6 | 32485146 | 32485343 |
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=46) | (# total SNVs=14) |
(# 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 |
chr2:85570849-85570849 | p.G536R | 5 |
chr2:85571228-85571228 | p.A476G | 5 |
chr2:85570857-85570857 | p.A533V | 4 |
chr2:85578126-85578126 | p.R125H | 4 |
chr2:85577263-85577263 | p.P233P | 3 |
chr2:85571180-85571180 | p.S492F | 3 |
chr2:85571210-85571210 | p.R482L | 2 |
chr2:85581487-85581487 | p.K48K | 2 |
chr2:85571225-85571225 | p.E477G | 2 |
chr2:85570442-85570442 | p.A586T | 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 | 2 | 2 |   | 5 |   |   | 1 | 1 | 1 | 2 |   | 11 | 1 | 1 |   | 1 | 9 | 7 |   | 9 |
# mutation | 2 | 2 |   | 5 |   |   | 1 | 1 | 1 | 1 |   | 12 | 1 | 1 |   | 1 | 9 | 8 |   | 9 |
nonsynonymous SNV | 2 | 2 |   | 4 |   |   |   |   | 1 | 1 |   | 8 | 1 | 1 |   | 1 | 7 | 7 |   | 7 |
synonymous SNV |   |   |   | 1 |   |   | 1 | 1 |   |   |   | 4 |   |   |   |   | 2 | 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 |
chr2:85578126 | p.R369C | 2 |
chr2:85573110 | p.S492F | 2 |
chr2:85576630 | p.R125L | 2 |
chr2:85571180 | p.P292S | 2 |
chr2:85571194 | p.S253F | 1 |
chr2:85573154 | p.L12L | 1 |
chr2:85577189 | p.R543C | 1 |
chr2:85570768 | p.L364L | 1 |
chr2:85571218 | p.H207N | 1 |
chr2:85578130 | p.L9L | 1 |
Other DBs for Point Mutations |
Copy Number for RETSAT 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 RETSAT |
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 |
ALCAM,AR,ARHGEF38,ATP13A4,APMAP,RHOV___CHP1,CROT, ELMOD3,FZD4,GGCX,IQGAP2,MAN2B2,MPV17L,PCYOX1, RETSAT,RNF103,SCP2,SLC9A1,TMEM62,TMEM63C,TMEM86A | ACO1,AIFM2,AOC2,AOC3,BTD,DHDDS,EHD2, GPD1,HEPN1,MGLL,MRAS,MYO1C,PLIN1,PLXNA4, PYGL,RDH5,RETSAT,TFE3,TK2,TLN2,VKORC1L1 | ||||
ABHD3,B3GALT5,BTNL3,BTNL8,CDHR5,DHRS9,GDPD3, GPA33,GPT,LIMA1,MALL,MMP28,P2RX4,PTPRH, RETSAT,SDCBP2,SLC41A2,STYK1,TMPRSS2,TSPAN1,VILL | ACOX1,ALDH18A1,APPL2,C1orf106,CDKN2B,RHOV___CHP1,ERBB3, TMEM236,HNF4A,KALRN,MARVELD3,MAST2,MGAT4A,MYO1D, PRKCD,PSEN1,RETSAT,RNF103,SLC22A5,SLC41A2,SPINT1 |
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 RETSAT |
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 |
DB00162 | retinol saturase (all-trans-retinol 13,14-reductase) | approved; nutraceutical | Vitamin A |
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Cross referenced IDs for RETSAT |
* 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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