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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for LRP2 |
Basic gene info. | Gene symbol | LRP2 |
Gene name | low density lipoprotein receptor-related protein 2 | |
Synonyms | DBS|GP330 | |
Cytomap | UCSC genome browser: 2q31.1 | |
Genomic location | chr2 :169983618-170219122 | |
Type of gene | protein-coding | |
RefGenes | NM_004525.2, | |
Ensembl id | ENSG00000081479 | |
Description | Heymann nephritis antigen homologLRP-2calcium sensor proteinglycoprotein 330low-density lipoprotein receptor-related protein 2megalin | |
Modification date | 20141219 | |
dbXrefs | MIM : 600073 | |
HGNC : HGNC | ||
Ensembl : ENSG00000081479 | ||
HPRD : 02509 | ||
Vega : OTTHUMG00000132179 | ||
Protein | UniProt: P98164 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_LRP2 | |
BioGPS: 4036 | ||
Gene Expression Atlas: ENSG00000081479 | ||
The Human Protein Atlas: ENSG00000081479 | ||
Pathway | NCI Pathway Interaction Database: LRP2 | |
KEGG: LRP2 | ||
REACTOME: LRP2 | ||
ConsensusPathDB | ||
Pathway Commons: LRP2 | ||
Metabolism | MetaCyc: LRP2 | |
HUMANCyc: LRP2 | ||
Regulation | Ensembl's Regulation: ENSG00000081479 | |
miRBase: chr2 :169,983,618-170,219,122 | ||
TargetScan: NM_004525 | ||
cisRED: ENSG00000081479 | ||
Context | iHOP: LRP2 | |
cancer metabolism search in PubMed: LRP2 | ||
UCL Cancer Institute: LRP2 | ||
Assigned class in ccmGDB | B - This gene belongs to cancer gene. |
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Phenotypic Information for LRP2(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: LRP2 |
Familial Cancer Database: LRP2 |
* 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_STEROID_HORMONES_AND_VITAMINS_A_AND_D REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | 222448; phenotype. 600073; gene. |
Orphanet | 2143; Donnai-Barrow syndrome. |
Disease | KEGG Disease: LRP2 |
MedGen: LRP2 (Human Medical Genetics with Condition) | |
ClinVar: LRP2 | |
Phenotype | MGI: LRP2 (International Mouse Phenotyping Consortium) |
PhenomicDB: LRP2 |
Mutations for LRP2 |
* 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 |
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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | LRP2 | chr2 | 170044529 | 170044549 | LRP2 | chr2 | 170038437 | 170038457 |
pancreas | LRP2 | chr2 | 170218399 | 170218419 | chr2 | 170219132 | 170219152 |
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 LRP2 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 |
CV324821 | LRP2 | 1 | 93 | 2 | 169983703 | 169983795 | PAPPA | 75 | 360 | 9 | 118988097 | 118988381 | |
BF992267 | LRP2 | 10 | 114 | 2 | 169983691 | 169983795 | PAPPA | 96 | 381 | 9 | 118988097 | 118988381 | |
BQ369809 | PAPPA | 18 | 301 | 9 | 118988097 | 118988381 | LRP2 | 283 | 387 | 2 | 169983691 | 169983795 | |
BF991744 | LRP2 | 8 | 119 | 2 | 169983684 | 169983795 | PAPPA | 101 | 337 | 9 | 118988097 | 118988332 |
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 |   |   |   |   |   |   |   |   | 2 |   |   |   | 1 |   |   | 1 | 1 | |||
GAIN (# sample) |   |   |   |   |   |   |   |   | 2 |   |   |   |   |   |   |   | 1 | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   | 1 |   |
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=617) | (# total SNVs=184) |
(# total SNVs=10) | (# total SNVs=8) |
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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 |
chr2:170044659-170044659 | p.V3050A | 6 |
chr2:170066148-170066148 | p.R2095Q | 5 |
chr2:170066149-170066149 | p.R2095* | 5 |
chr2:170034511-170034511 | p.R3399* | 5 |
chr2:170063045-170063045 | p.S2395S | 4 |
chr2:170062935-170062935 | p.R2432I | 4 |
chr2:170147488-170147488 | p.V263V | 4 |
chr2:170044660-170044660 | p.V3050I | 4 |
chr2:170014006-170014006 | p.G3965E | 4 |
chr2:170044680-170044680 | p.R3043H | 4 |
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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 | 11 | 26 | 4 | 94 | 16 |   | 35 |   | 19 | 3 |   | 66 | 40 | 17 | 2 | 3 | 60 | 42 | 2 | 44 |
# mutation | 11 | 27 | 4 | 114 | 17 |   | 37 |   | 20 | 3 |   | 90 | 53 | 19 | 2 | 3 | 106 | 56 | 2 | 106 |
nonsynonymous SNV | 8 | 24 | 3 | 84 | 15 |   | 25 |   | 11 | 2 |   | 73 | 36 | 16 | 1 | 2 | 80 | 43 | 1 | 82 |
synonymous SNV | 3 | 3 | 1 | 30 | 2 |   | 12 |   | 9 | 1 |   | 17 | 17 | 3 | 1 | 1 | 26 | 13 | 1 | 24 |
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 |
chr2:170044659 | p.V3050A | 6 |
chr2:170115593 | p.R3086C | 4 |
chr2:170044552 | p.S2395S | 4 |
chr2:170063045 | p.R819C | 4 |
chr2:170025080 | p.V263V | 4 |
chr2:170147488 | p.G3868G | 4 |
chr2:170032999 | p.G4301E | 3 |
chr2:170101368 | p.R1089C | 3 |
chr2:170034509 | p.S2395P | 3 |
chr2:170070306 | p.R3399R | 3 |
Other DBs for Point Mutations |
Copy Number for LRP2 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 LRP2 |
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 |
CACNB2,CARTPT,CCDC158,DACH1,ENTPD5,FGF10,FGF14, GLRA1,GRIK1,IQSEC2,KCND3,UNC79,LRP2,MAST4, NTRK2,PEX5L,SCG2,SLC1A2,SLC5A8,SLCO3A1,TAT | ARHGAP32,SAMD15,C1orf226,C2orf15,CELSR2,CHDH,ERN1, GPR98,IGSF3,KIAA1324,KIAA1549,LRP2,MYO5B,NEO1, NOS1AP,RALGPS1,SHROOM3,THSD4,TOM1L1,TTLL5,ZNF107 | ||||
ARHGEF33,CSH2,CYLC2,DPYS,BRINP2,HMX2,IL12RB2, INA,KCNA4,KLHL14,LINC01105,LOC400696,LRP2,OR5B17, PKHD1L1,POU3F2,PTPRQ,SLC38A8,TMEM121,UCHL1,ZYG11A | AQP12A,BMP10,C3orf22,CCDC83,CDY2B,CSRP3,FAM66E, HTR2C,LAMA3,LAMC2,LOC151658,LOC441601,LRP2,OPN5, OR2F1,OVCH2,PMEPA1,RAB22A,RXFP2,SPINK14,TTLL8, ZN |
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 LRP2 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Organism-specific databases | PharmGKB | PA30452; -. |
Organism-specific databases | CTD | 4036; -. |
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 |
DB00798 | low density lipoprotein receptor-related protein 2 | approved | Gentamicin | ||
DB00136 | low density lipoprotein receptor-related protein 2 | approved; nutraceutical | Calcitriol | ||
DB00515 | low density lipoprotein receptor-related protein 2 | approved | Cisplatin |
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Cross referenced IDs for LRP2 |
* 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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