Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for LDLR
Basic gene info.Gene symbolLDLR
Gene namelow density lipoprotein receptor
SynonymsFH|FHC|LDLCQ2
CytomapUCSC genome browser: 19p13.2
Genomic locationchr19 :11200037-11244505
Type of geneprotein-coding
RefGenesNM_000527.4,
NM_001195798.1,NM_001195799.1,NM_001195800.1,NM_001195803.1,
NM_001195802.1,
Ensembl idENSG00000130164
DescriptionLDL receptorlow-density lipoprotein receptorlow-density lipoprotein receptor class A domain-containing protein 3
Modification date20141222
dbXrefs MIM : 606945
HGNC : HGNC
Ensembl : ENSG00000130164
HPRD : 06091
Vega : OTTHUMG00000171935
ProteinUniProt: P01130
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LDLR
BioGPS: 3949
Gene Expression Atlas: ENSG00000130164
The Human Protein Atlas: ENSG00000130164
PathwayNCI Pathway Interaction Database: LDLR
KEGG: LDLR
REACTOME: LDLR
ConsensusPathDB
Pathway Commons: LDLR
MetabolismMetaCyc: LDLR
HUMANCyc: LDLR
RegulationEnsembl's Regulation: ENSG00000130164
miRBase: chr19 :11,200,037-11,244,505
TargetScan: NM_000527
cisRED: ENSG00000130164
ContextiHOP: LDLR
cancer metabolism search in PubMed: LDLR
UCL Cancer Institute: LDLR
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of LDLR in cancer cell metabolism1. Nagiec MM, Skepner AP, Negri J, Eichhorn M, Kuperwasser N, et al. (2015) Modulators of hepatic lipoprotein metabolism identified in a search for small-molecule inducers of tribbles pseudokinase 1 expression. PLoS One 10: e0120295. doi: 10.1371/journal.pone.0120295. pmid: 4374785. go to article
2. Bissig-Choisat B, Wang L, Legras X, Saha PK, Chen L, et al. (2015) Development and rescue of human familial hypercholesterolaemia in a xenograft mouse model. Nat Commun 6: 7339. doi: 10.1038/ncomms8339. go to article
3. Guillaumond F, Bidaut G, Ouaissi M, Servais S, Gouirand V, et al. (2015) Cholesterol uptake disruption, in association with chemotherapy, is a promising combined metabolic therapy for pancreatic adenocarcinoma. Proc Natl Acad Sci U S A 112: 2473-2478. doi: 10.1073/pnas.1421601112. pmid: 4345573. go to article
4. Rios-Marco P, Martin-Fernandez M, Soria-Bretones I, Rios A, Carrasco MP, et al. (2013) Alkylphospholipids deregulate cholesterol metabolism and induce cell-cycle arrest and autophagy in U-87 MG glioblastoma cells. Biochim Biophys Acta 1831: 1322-1334. doi: 10.1016/j.bbalip.2013.05.004. go to article
5. Daker M, Bhuvanendran S, Ahmad M, Takada K, Khoo AS (2013) Deregulation of lipid metabolism pathway genes in nasopharyngeal carcinoma cells. Mol Med Rep 7: 731-741. doi: 10.3892/mmr.2012.1253. pmid: 3597460. go to article

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Phenotypic Information for LDLR(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LDLR
Familial Cancer Database: LDLR
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS
REACTOME_LIPOPROTEIN_METABOLISM

check002.gifOthers
OMIM 143890; phenotype.
143890; phenotype.
606945; gene.
606945; gene.
Orphanet 391665; Homozygous familial hypercholesterolemia.
391665; Homozygous familial hypercholesterolemia.
406; Heterozygous familial hypercholesterolemia.
406; Heterozygous familial hypercholesterolemia.
DiseaseKEGG Disease: LDLR
MedGen: LDLR (Human Medical Genetics with Condition)
ClinVar: LDLR
PhenotypeMGI: LDLR (International Mouse Phenotyping Consortium)
PhenomicDB: LDLR

Mutations for LDLR
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryLDLRchr191120495211204972GATAD2Achr191953751119537531
pancreasLDLRchr191122943211229452LDLRchr191121242611212446
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LDLR related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU631838EXOSC619181167028413470284296LDLR176688191124195911243622
AA002171LDLR1183191124430911244491ABAT1844931688776658877972
BF753479LDLR6111191123747511237581ANKRD11103190168948129289481379

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1  2      2      
GAIN (# sample)1  2      2      
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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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=63)
Stat. for Synonymous SNVs
(# total SNVs=19)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=1)

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr19:11224014-11224014p.R416Q3
chr19:11218140-11218140p.N297S3
chr19:11241983-11241983p.D858D2
chr19:11224354-11224354p.A501V2
chr19:11240220-11240220p.F807F2
chr19:11210922-11210922p.E31K2
chr19:11231084-11231085p.G676fs*402
chr19:11215910-11215910p.S110P2
chr19:11215918-11215918p.D112E2
chr19:11227680-11227680p.?2

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample13 145 4 21 645 1179 6
# mutation13 145 4 21 645 1249 7
nonsynonymous SNV11 93 3 11 545 1155 4
synonymous SNV 2 52 1 1  1    94 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr19:11218140p.N129S,LDLR3
chr19:11210922p.R248Q,LDLR2
chr19:11224428p.P358S,LDLR2
chr19:11224014p.E31K,LDLR2
chr19:11216248p.S59S,LDLR1
chr19:11224382p.P155L,LDLR1
chr19:11230871p.P193L,LDLR1
chr19:11221353p.K336R,LDLR1
chr19:11238760p.L512L,LDLR1
chr19:11215934p.A692V,LDLR1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for LDLR 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 LDLR

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-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

: Open all plots for all cancer types

AKR1A1,ATPIF1,CNKSR1,CTDSP1,MTFR1L,FAM73B,GPATCH3,
GPN2,JMJD7-PLA2G4B,LDLRAP1,LYPLA2,LYPLA2P1,PEX14,PINK1,
PQLC2,SEPN1,SYF2,TMEM222,TRAPPC12,ZBTB17,ZNF296
APEX2,ARFIP2,C10orf35,SYNE4,CACFD1,CADM4,CLN3,
DAK,DGCR2,DNAL4,ISYNA1,ITGA3,LDLRAP1,LPAR2,
LSR,PAK4,PRKCZ,PRPF19,PRRG2,RAB17,SPINT2

ARHGEF10L,ATP13A2,KDF1,STPG1,CASP9,CASZ1,CLSTN1,
DHDDS,DNAJC16,FUCA1,GALE,KIAA1522,LDLRAP1,LYPLA2,
NBL1,PAFAH2,PQLC2,RPS6KA1,SLC44A4,TMEM57,TRIOBP
BDH1,CCNJL,CDX2,CPT2,DTX4,FUK,GOLPH3L,
IHH,LDLRAP1,LGALS4,MB,NADK,SFXN5,SHD,
SPR,STAP2,TRAF3IP2,TST,VAV3,WDR78,ZBTB7C
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for LDLR
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P01130; -.
ChemistryChEMBL CHEMBL3311; -.
ChemistryBindingDB P01130; -.
ChemistryChEMBL CHEMBL3311; -.
Organism-specific databasesPharmGKB PA227; -.
Organism-specific databasesPharmGKB PA227; -.
Organism-specific databasesCTD 3949; -.
Organism-specific databasesCTD 3949; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00707low density lipoprotein receptorapproved; investigationalPorfimer
DB02944low density lipoprotein receptorexperimentalAlpha-D-Mannose
DB01095low density lipoprotein receptorapprovedFluvastatin
DB00335low density lipoprotein receptorapprovedAtenolol
DB01029low density lipoprotein receptorapproved; investigationalIrbesartan
DB01076low density lipoprotein receptorapprovedAtorvastatin
DB00264low density lipoprotein receptorapproved; investigationalMetoprolol


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Cross referenced IDs for LDLR
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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