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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SCARB1 |
Basic gene info. | Gene symbol | SCARB1 |
Gene name | scavenger receptor class B, member 1 | |
Synonyms | CD36L1|CLA-1|CLA1|HDLQTL6|SR-BI|SRB1 | |
Cytomap | UCSC genome browser: 12q24.31 | |
Genomic location | chr12 :125262173-125348519 | |
Type of gene | protein-coding | |
RefGenes | NM_001082959.1, NM_005505.4, | |
Ensembl id | ENSG00000073060 | |
Description | CD36 and LIMPII analogous 1CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 1scavenger receptor class B member 1scavenger receptor class B type III | |
Modification date | 20141207 | |
dbXrefs | MIM : 601040 | |
HGNC : HGNC | ||
Ensembl : ENSG00000073060 | ||
HPRD : 03024 | ||
Vega : OTTHUMG00000168544 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_SCARB1 | |
BioGPS: 949 | ||
Gene Expression Atlas: ENSG00000073060 | ||
The Human Protein Atlas: ENSG00000073060 | ||
Pathway | NCI Pathway Interaction Database: SCARB1 | |
KEGG: SCARB1 | ||
REACTOME: SCARB1 | ||
ConsensusPathDB | ||
Pathway Commons: SCARB1 | ||
Metabolism | MetaCyc: SCARB1 | |
HUMANCyc: SCARB1 | ||
Regulation | Ensembl's Regulation: ENSG00000073060 | |
miRBase: chr12 :125,262,173-125,348,519 | ||
TargetScan: NM_001082959 | ||
cisRED: ENSG00000073060 | ||
Context | iHOP: SCARB1 | |
cancer metabolism search in PubMed: SCARB1 | ||
UCL Cancer Institute: SCARB1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for SCARB1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: SCARB1 |
Familial Cancer Database: SCARB1 |
* 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_LIPIDS_AND_LIPOPROTEINS REACTOME_LIPOPROTEIN_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: SCARB1 |
MedGen: SCARB1 (Human Medical Genetics with Condition) | |
ClinVar: SCARB1 | |
Phenotype | MGI: SCARB1 (International Mouse Phenotyping Consortium) |
PhenomicDB: SCARB1 |
Mutations for SCARB1 |
* 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 |
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'. |
- 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 |
ovary | SCARB1 | chr12 | 125337464 | 125337484 | chr12 | 126225424 | 126225444 |
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 SCARB1 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 |
AI123607 | ROBO3 | 27 | 152 | 11 | 124751231 | 124751356 | SCARB1 | 149 | 266 | 12 | 125262885 | 125263002 | |
CB115292 | SCARB1 | 2 | 363 | 12 | 125262716 | 125263077 | UBC | 364 | 490 | 12 | 125396192 | 125396318 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   | 1 |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   | |||
GAIN (# sample) |   | 1 |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract) |
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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=42) | (# total SNVs=12) |
(# 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 |
chr12:125294788-125294788 | p.S258S | 2 |
chr12:125294816-125294816 | p.D249G | 2 |
chr12:125348263-125348263 | p.G2S | 2 |
chr12:125298827-125298827 | p.K184R | 2 |
chr12:125292364-125292364 | p.E318K | 2 |
chr12:125298921-125298921 | p.M153V | 2 |
chr12:125284671-125284671 | p.P376L | 2 |
chr12:125302181-125302181 | p.V67I | 2 |
chr12:125284748-125284748 | p.A350A | 2 |
chr12:125284769-125284769 | p.S343S | 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 | 1 | 2 | 1 | 10 | 2 |   |   |   | 2 |   | 1 | 3 | 4 |   | 1 | 1 | 2 | 5 |   | 4 |
# mutation | 1 | 2 | 1 | 10 | 2 |   |   |   | 2 |   | 1 | 3 | 4 |   | 1 | 1 | 2 | 5 |   | 6 |
nonsynonymous SNV |   | 2 |   | 5 |   |   |   |   | 2 |   | 1 | 3 | 3 |   |   | 1 | 2 | 4 |   | 6 |
synonymous SNV | 1 |   | 1 | 5 | 2 |   |   |   |   |   |   |   | 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 |
chr12:125302250 | p.S343S,SCARB1 | 2 |
chr12:125284769 | p.E318K,SCARB1 | 2 |
chr12:125292364 | p.Y446Y,SCARB1 | 2 |
chr12:125270966 | p.V44M,SCARB1 | 2 |
chr12:125298947 | p.G399V,SCARB1 | 1 |
chr12:125271972 | p.K202E,SCARB1 | 1 |
chr12:125294743 | p.P33R,SCARB1 | 1 |
chr12:125299563 | p.L390L,SCARB1 | 1 |
chr12:125279747 | p.F201F,SCARB1 | 1 |
chr12:125348169 | p.P376L,SCARB1 | 1 |
Other DBs for Point Mutations |
Copy Number for SCARB1 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 SCARB1 |
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 |
AADAC,C1orf141,FOXL2NB,MGARP,CELA2A,CYP11A1,CYP17A1, CYP19A1,FSHR,HSD3B1,INHA,INSL3,KLHL4,LHCGR, MBOAT4,MRO,REG3G,SCARB1,STAR,TCF21,TREML5P | ACVRL1,AVPR2,C10orf54,CCM2L,CCL14,CLDN15,ENG, HLX,ICAM2,MFNG,MFRP,NDUFA4L2,NOVA2,PLAC9, PLVAP,RASIP1,SCARB1,SEMA6B,SH2D3C,TNFRSF1B,TTLL10 | ||||
ACE2,AIFM1,CEBPA,DDX54,DHCR7,DHX37,HNF1A, MMAB,MVK,NSDHL,PPM1H,PPP1R14D,PRDM4,PUS1, PVR,SCARB1,SLC11A2,SLC39A5,SLC5A6,SPPL3,VIL1 | ATP6AP1,CACFD1,CES3,DGCR2,FOXD2,GRAMD4,GRN, KIAA0195,LOC283070,LRP4,MUC20,MYO1D,PADI2,PHKA2, PIGZ,PTPRF,RIN1,SCARB1,SLC8B1,SLC26A6,TSPAN7 |
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 SCARB1 |
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 |
DB00144 | scavenger receptor class B, member 1 | approved; nutraceutical | Phosphatidylserine | ||
DB01039 | scavenger receptor class B, member 1 | approved | Fenofibrate | ||
DB00334 | scavenger receptor class B, member 1 | approved; investigational | Olanzapine |
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Cross referenced IDs for SCARB1 |
* 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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