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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for HMGCR |
Basic gene info. | Gene symbol | HMGCR |
Gene name | 3-hydroxy-3-methylglutaryl-CoA reductase | |
Synonyms | LDLCQ3 | |
Cytomap | UCSC genome browser: 5q13.3-q14 | |
Genomic location | chr5 :74632992-74657926 | |
Type of gene | protein-coding | |
RefGenes | NM_000859.2, NM_001130996.1, | |
Ensembl id | ENSG00000113161 | |
Description | 3-hydroxy-3-methylglutaryl CoA reductase (NADPH)3-hydroxy-3-methylglutaryl-Coenzyme A reductaseHMG-CoA reductasehydroxymethylglutaryl-CoA reductase | |
Modification date | 20141207 | |
dbXrefs | MIM : 142910 | |
HGNC : HGNC | ||
Ensembl : ENSG00000113161 | ||
HPRD : 00836 | ||
Vega : OTTHUMG00000102069 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_HMGCR | |
BioGPS: 3156 | ||
Gene Expression Atlas: ENSG00000113161 | ||
The Human Protein Atlas: ENSG00000113161 | ||
Pathway | NCI Pathway Interaction Database: HMGCR | |
KEGG: HMGCR | ||
REACTOME: HMGCR | ||
ConsensusPathDB | ||
Pathway Commons: HMGCR | ||
Metabolism | MetaCyc: HMGCR | |
HUMANCyc: HMGCR | ||
Regulation | Ensembl's Regulation: ENSG00000113161 | |
miRBase: chr5 :74,632,992-74,657,926 | ||
TargetScan: NM_000859 | ||
cisRED: ENSG00000113161 | ||
Context | iHOP: HMGCR | |
cancer metabolism search in PubMed: HMGCR | ||
UCL Cancer Institute: HMGCR | ||
Assigned class in ccmGDB | A - This gene has a literature evidence and it belongs to cancer gene. | |
References showing role of HMGCR in cancer cell metabolism | 1. Sangeetha M, Deepa PR, Rishi P, Khetan V, Krishnakumar S (2015) Global Gene Deregulations in FASN Silenced Retinoblastoma Cancer Cells: Molecular and Clinico-Pathological Correlations. J Cell Biochem. doi: 10.1002/jcb.25217. go to article 2. Zhang H, Feng Z, Huang R, Xia Z, Xiang G, et al. (2014) MicroRNA-449 suppresses proliferation of hepatoma cell lines through blockade lipid metabolic pathway related to SIRT1. Int J Oncol 45: 2143-2152. doi: 10.3892/ijo.2014.2596. go to article 3. Pandyra A, Mullen PJ, Kalkat M, Yu R, Pong JT, et al. (2014) Immediate utility of two approved agents to target both the metabolic mevalonate pathway and its restorative feedback loop. Cancer Res 74: 4772-4782. doi: 10.1158/0008-5472.CAN-14-0130. go to article 4. Yeganeh B, Wiechec E, Ande SR, Sharma P, Moghadam AR, et al. (2014) Targeting the mevalonate cascade as a new therapeutic approach in heart disease, cancer and pulmonary disease. Pharmacol Ther 143: 87-110. doi: 10.1016/j.pharmthera.2014.02.007. pmid: 4005604. go to article |
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Phenotypic Information for HMGCR(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: HMGCR |
Familial Cancer Database: HMGCR |
* 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/ |
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REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: HMGCR |
MedGen: HMGCR (Human Medical Genetics with Condition) | |
ClinVar: HMGCR | |
Phenotype | MGI: HMGCR (International Mouse Phenotyping Consortium) |
PhenomicDB: HMGCR |
Mutations for HMGCR |
* 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. |
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- Statistics for Tissue and Mutation type | Top |
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- 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'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | HMGCR | chr5 | 74639466 | 74639486 | chr5 | 74579729 | 74579749 | |
pancreas | HMGCR | chr5 | 74647500 | 74647520 | HMGCR | chr5 | 74647426 | 74647446 |
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) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HMGCR 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 |
DB238220 | WDR41 | 1 | 348 | 5 | 76758920 | 76788045 | HMGCR | 349 | 584 | 5 | 74647342 | 74650477 | |
BF853983 | HMGCR | 3 | 115 | 5 | 74657009 | 74657122 | TP53INP2 | 113 | 214 | 20 | 33300042 | 33300143 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=49) | (# total SNVs=13) |
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(# total SNVs=2) | (# total SNVs=0) |
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* 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 |
chr5:74654610-74654610 | p.S705S | 2 |
chr5:74638449-74638449 | p.R7G | 2 |
chr5:74645924-74645924 | p.Y205C | 2 |
chr5:74643063-74643063 | p.A162G | 1 |
chr5:74647395-74647395 | p.E446K | 1 |
chr5:74655871-74655871 | p.R840Q | 1 |
chr5:74646122-74646122 | p.L235V | 1 |
chr5:74651240-74651240 | p.G591G | 1 |
chr5:74639763-74639763 | p.R84H | 1 |
chr5:74646732-74646732 | p.R300I | 1 |
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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 |   | 8 |   |   | 3 |   | 3 |   |   | 6 | 2 | 2 |   | 1 | 4 | 10 |   | 12 |
# mutation | 1 | 2 |   | 8 |   |   | 3 |   | 3 |   |   | 5 | 2 | 2 |   | 1 | 7 | 11 |   | 15 |
nonsynonymous SNV | 1 | 1 |   | 7 |   |   | 3 |   | 1 |   |   | 4 | 2 | 2 |   |   | 6 | 7 |   | 11 |
synonymous SNV |   | 1 |   | 1 |   |   |   |   | 2 |   |   | 1 |   |   |   | 1 | 1 | 4 |   | 4 |
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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* 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 |
chr5:74646642 | p.H270L,HMGCR | 2 |
chr5:74646121 | p.V492A,HMGCR | 1 |
chr5:74654542 | p.G610C,HMGCR | 1 |
chr5:74647031 | p.L220F,HMGCR | 1 |
chr5:74655921 | p.R495H,HMGCR | 1 |
chr5:74640131 | p.V630I,HMGCR | 1 |
chr5:74651226 | p.L27L,HMGCR | 1 |
chr5:74646146 | p.Q234Q,HMGCR | 1 |
chr5:74655086 | p.L509L,HMGCR | 1 |
chr5:74647374 | p.N697S,HMGCR | 1 |
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* 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. |
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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 HMGCR |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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AADAC,AMHR2,C1orf141,FOXL2NB,MGARP,CELA2A,CYP11A1, CYP17A1,CYP19A1,FSHR,HMGCR,HSD3B1,HSD3B2,INHA, KLHL4,LHCGR,MBOAT4,MRO,STAR,TCF21,TREML5P | ABCC11,ABCC2,ACSL3,AFMID,AKR1D1,ALOX15B,B3GAT1, C6orf223,CCDC15,GSTT2,HMGCR,HMGCS1,MPV17L,NSUN2, PXMP4,MSMO1,SLC5A11,SLCO1B1,SRD5A1,TARP,ZP2 | ||||
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ACAT2,ACSL3,AP3B1,CYP51A1,DHCR24,DHCR7,ELOVL6, FDFT1,FDPS,HMGCR,HMGCS1,HSD17B7,IDI1,LSS, MVD,MVK,PANK3,PCSK9,MSMO1,SC5D,STARD4 | ACTR2,AP1G1,APAF1,BAZ1A,CCDC186,CLTC,CTTNBP2NL, CYP51A1,DHCR24,FAM199X,FDFT1,FNDC3B,GAN,GPD2, HMGCR,KDM1B,LOC284441,PGGT1B,RRBP1,TOP1,YME1L1 |
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* 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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Pharmacological Information for HMGCR |
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DB Category | DB Name | DB's ID and Url link |
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* Gene Centered Interaction Network. |
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* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00157 | 3-hydroxy-3-methylglutaryl-CoA reductase | approved; nutraceutical | NADH | ![]() | ![]() |
DB00175 | 3-hydroxy-3-methylglutaryl-CoA reductase | approved | Pravastatin | ![]() | ![]() |
DB00227 | 3-hydroxy-3-methylglutaryl-CoA reductase | approved; investigational | Lovastatin | ![]() | ![]() |
DB00439 | 3-hydroxy-3-methylglutaryl-CoA reductase | withdrawn | Cerivastatin | ![]() | ![]() |
DB00641 | 3-hydroxy-3-methylglutaryl-CoA reductase | approved | Simvastatin | ![]() | ![]() |
DB01076 | 3-hydroxy-3-methylglutaryl-CoA reductase | approved | Atorvastatin | ![]() | ![]() |
DB01095 | 3-hydroxy-3-methylglutaryl-CoA reductase | approved | Fluvastatin | ![]() | ![]() |
DB01098 | 3-hydroxy-3-methylglutaryl-CoA reductase | approved | Rosuvastatin | ![]() | ![]() |
DB01992 | 3-hydroxy-3-methylglutaryl-CoA reductase | experimental | Coenzyme A | ![]() | ![]() |
DB03431 | 3-hydroxy-3-methylglutaryl-CoA reductase | experimental | Adenosine-5'-Diphosphate | ![]() | ![]() |
DB03461 | 3-hydroxy-3-methylglutaryl-CoA reductase | experimental | 2'-Monophosphoadenosine 5'-Diphosphoribose | ![]() | ![]() |
DB04377 | 3-hydroxy-3-methylglutaryl-CoA reductase | experimental | 3-Hydroxy-3-Methyl-Glutaric Acid | ![]() | ![]() |
DB04447 | 3-hydroxy-3-methylglutaryl-CoA reductase | experimental | 1,4-Dithiothreitol | ![]() | ![]() |
DB06693 | 3-hydroxy-3-methylglutaryl-CoA reductase | experimental | Mevastatin | ![]() | ![]() |
DB06846 | 3-hydroxy-3-methylglutaryl-CoA reductase | experimental | 7-[3-(4-FLUORO-PHENYL)-1-ISOPROPYL-1H-INDOL-2-YL]-3,5-DIHYDROXY-HEPTANOIC ACID | ![]() | ![]() |
DB01907 | 3-hydroxy-3-methylglutaryl-CoA reductase | experimental | Nicotinamide-Adenine-Dinucleotide | ![]() | ![]() |
DB03518 | 3-hydroxy-3-methylglutaryl-CoA reductase | experimental | (R)-Mevalonate | ![]() | ![]() |
DB03785 | 3-hydroxy-3-methylglutaryl-CoA reductase | experimental | (3r,5r)-7-((1r,2r,6s,8r,8as)-2,6-Dimethyl-8-{[(2r)-2-Methylbutanoyl]Oxy}-1,2,6,7,8,8a-Hexahydronaphthalen-1-Yl)-3,5-Dihydroxyheptanoic Acid | ![]() | ![]() |
DB00363 | 3-hydroxy-3-methylglutaryl-CoA reductase | approved | Clozapine | ![]() | ![]() |
DB00502 | 3-hydroxy-3-methylglutaryl-CoA reductase | approved | Haloperidol | ![]() | ![]() |
DB00264 | 3-hydroxy-3-methylglutaryl-CoA reductase | approved; investigational | Metoprolol | ![]() | ![]() |
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Cross referenced IDs for HMGCR |
* 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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