Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 LDLRAP1
Basic gene info.Gene symbolLDLRAP1
Gene namelow density lipoprotein receptor adaptor protein 1
SynonymsARH|ARH1|ARH2|FHCB1|FHCB2
CytomapUCSC genome browser: 1p36-p35
Genomic locationchr1 :25870075-25895377
Type of geneprotein-coding
RefGenesNM_015627.2,
Ensembl idENSG00000157978
DescriptionLDL receptor adaptor proteinautosomal recessive hypercholesterolemia proteinlow density lipoprotein receptor adapter protein 1
Modification date20141207
dbXrefs MIM : 605747
HGNC : HGNC
Ensembl : ENSG00000157978
HPRD : 05765
Vega : OTTHUMG00000007386
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LDLRAP1
BioGPS: 26119
Gene Expression Atlas: ENSG00000157978
The Human Protein Atlas: ENSG00000157978
PathwayNCI Pathway Interaction Database: LDLRAP1
KEGG: LDLRAP1
REACTOME: LDLRAP1
ConsensusPathDB
Pathway Commons: LDLRAP1
MetabolismMetaCyc: LDLRAP1
HUMANCyc: LDLRAP1
RegulationEnsembl's Regulation: ENSG00000157978
miRBase: chr1 :25,870,075-25,895,377
TargetScan: NM_015627
cisRED: ENSG00000157978
ContextiHOP: LDLRAP1
cancer metabolism search in PubMed: LDLRAP1
UCL Cancer Institute: LDLRAP1
Assigned class in ccmGDBC

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Phenotypic Information for LDLRAP1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LDLRAP1
Familial Cancer Database: LDLRAP1
* 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
Orphanet
DiseaseKEGG Disease: LDLRAP1
MedGen: LDLRAP1 (Human Medical Genetics with Condition)
ClinVar: LDLRAP1
PhenotypeMGI: LDLRAP1 (International Mouse Phenotyping Consortium)
PhenomicDB: LDLRAP1

Mutations for LDLRAP1
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LDLRAP1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 # sample             1   
GAIN (# sample)                 
LOSS (# sample)             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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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=16)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=5)
Stat. for Insertions
(# total SNVs=2)

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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
chr1:25889632-25889632p.S202fs*24
chr1:25880526-25880526p.A68S2
chr1:25893450-25893450p.S298S2
chr1:25889565-25889565p.K179K2
chr1:25889626-25889627p.S202fs*192
chr1:25890153-25890153p.L206F2
chr1:25891695-25891695p.S260L2
chr1:25883675-25883675p.D126N2
chr1:25883750-25883750p.R151G2
chr1:25880433-25880433p.D37Y1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2  3     1 3 1  24 5
# mutation2  3     1 3 1  24 5
nonsynonymous SNV1  2     1 2    22 3
synonymous SNV1  1       1 1   2 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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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
chr1:25891695p.S260L2
chr1:25880532p.R95Q1
chr1:25891685p.D126N1
chr1:25880543p.C143C1
chr1:25891690p.R151G1
chr1:25881403p.F171L1
chr1:25891691p.Q173R1
chr1:25883675p.L203L1
chr1:25883728p.E235K1
chr1:25893369p.P237S1

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 LDLRAP1 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 LDLRAP1

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 LDLRAP1


There's no related Drug.
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Cross referenced IDs for LDLRAP1
* 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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