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 CAV1
Basic gene info.Gene symbolCAV1
Gene namecaveolin 1, caveolae protein, 22kDa
SynonymsBSCL3|CGL3|LCCNS|MSTP085|PPH3|VIP21
CytomapUCSC genome browser: 7q31.1
Genomic locationchr7 :116166411-116201239
Type of geneprotein-coding
RefGenesNM_001172895.1,
NM_001172896.1,NM_001172897.1,NM_001753.4,
Ensembl idENSG00000105974
Descriptioncaveolin-1cell growth-inhibiting protein 32
Modification date20141207
dbXrefs MIM : 601047
HGNC : HGNC
Ensembl : ENSG00000105974
HPRD : 03028
Vega : OTTHUMG00000023413
ProteinUniProt: Q03135
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CAV1
BioGPS: 857
Gene Expression Atlas: ENSG00000105974
The Human Protein Atlas: ENSG00000105974
PathwayNCI Pathway Interaction Database: CAV1
KEGG: CAV1
REACTOME: CAV1
ConsensusPathDB
Pathway Commons: CAV1
MetabolismMetaCyc: CAV1
HUMANCyc: CAV1
RegulationEnsembl's Regulation: ENSG00000105974
miRBase: chr7 :116,166,411-116,201,239
TargetScan: NM_001172895
cisRED: ENSG00000105974
ContextiHOP: CAV1
cancer metabolism search in PubMed: CAV1
UCL Cancer Institute: CAV1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CAV1 in cancer cell metabolism1. Hall DP, Cost NG, Hegde S, Kellner E, Mikhaylova O, et al. (2014) TRPM3 and miR-204 establish a regulatory circuit that controls oncogenic autophagy in clear cell renal cell carcinoma. Cancer Cell 26: 738-753. doi: 10.1016/j.ccell.2014.09.015. pmid: 4269832. go to article

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Phenotypic Information for CAV1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CAV1
Familial Cancer Database: CAV1
* 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

check002.gifOthers
OMIM 601047; gene.
606721; phenotype.
612526; phenotype.
615343; phenotype.
Orphanet 220393; Diffuse cutaneous systemic sclerosis.
220402; Limited cutaneous systemic sclerosis.
275777; Heritable pulmonary arterial hypertension.
528; Berardinelli-Seip congenital lipodystrophy.
DiseaseKEGG Disease: CAV1
MedGen: CAV1 (Human Medical Genetics with Condition)
ClinVar: CAV1
PhenotypeMGI: CAV1 (International Mouse Phenotyping Consortium)
PhenomicDB: CAV1

Mutations for CAV1
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 CAV1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP260187ANKRD11397109267889392680843CAV13985847116165090116166708
BF476043CHCHD41314431415358514153716CAV11354417116200112116200417
BF196928CAV121827116201048116201228MCM91705056119134792119135127
D61924OXR141468107764771107764915CAV11422997116201009116201569
BE930754CAV1141347116184295116184415IQGAP212825157600310776003230

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) 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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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=13)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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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
chr7:116199315-116199315p.R171C2
chr7:116166586-116166586p.L13H1
chr7:116199076-116199076p.T91I1
chr7:116199329-116199329p.Q175Q1
chr7:116166591-116166591p.T15A1
chr7:116199077-116199077p.T91T1
chr7:116199333-116199333p.E177Q1
chr7:116166604-116166604p.R19Q1
chr7:116199088-116199088p.T95M1
chr7:116166610-116166610p.Q21L1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 1     1      34 3
# mutation11 1     1      34 3
nonsynonymous SNV 1 1            24 3
synonymous SNV1        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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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
chr7:116166591p.T15A1
chr7:116199329p.R19Q1
chr7:116166604p.D12D,CAV11
chr7:116199333p.L28L,CAV11
chr7:116166677p.S57T,CAV11
chr7:116166725p.F58S,CAV11
chr7:116199067p.T60I,CAV11
chr7:116199070p.T64M,CAV11
chr7:116199076p.R70C,CAV11
chr7:116199088p.R115C,CAV11

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 CAV1 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 CAV1

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.
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check002.gifProtein Expression Plot (RPPA)
*RPPA protein expression data were extracted from TCPA (The Cancer Proteome Atlas). Normalized data based on replicated based normalization (RBN) was used to draw following figures.

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

AOC3,CAV1,CAV2,CD34,CDH5,CNRIP1,CXorf36,
EBF1,ERG,GNG11,JAM2,LDB2,LHFP,MMRN2,
MYCT1,NPR1,PDE2A,RHOJ,ROBO4,S1PR1,VWF
ASPH,MTURN,CAV1,CAV2,ECM2,EHBP1,FAM69A,
FERMT2,GLYAT,GTDC1,ITGB1BP1,LAMA4,MGST1,MMD,
PALM2-AKAP2,PALMD,PYGL,SAR1A,SORBS1,TSPAN3,VKORC1L1

A4GALT,AXL,CAV1,CAV2,CDK14,FRMD6,IGFBP6,
IL20RB,ITGB1,ITPRIP,LIPK,LOC100126784,LOXL4,LRAT,
MYH16,NTNG1,PDGFC,RPSAP52,SERPINE1,TSC22D3,VASN
ADAMTSL3,AKT3,AMOTL1,ANKS1B,APBB1,ARHGAP10,C16orf45,
CAV1,DMD,EML1,EPM2A,FAM129A,HAND2,ICA1L,
JAM3,LIMS2,MEIS1,NXN,PPP1R12B,PRICKLE2,SMARCA1
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 CAV1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA26107; -.
Organism-specific databasesCTD 857; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00394caveolin 1, caveolae protein, 22kDaapprovedBeclomethasone
DB00443caveolin 1, caveolae protein, 22kDaapprovedBetamethasone
DB01222caveolin 1, caveolae protein, 22kDaapproved; investigationalBudesonide
DB01410caveolin 1, caveolae protein, 22kDaapproved; investigationalCiclesonide
DB01260caveolin 1, caveolae protein, 22kDaapproved; investigationalDesonide
DB01234caveolin 1, caveolae protein, 22kDaapproved; investigationalDexamethasone
DB00180caveolin 1, caveolae protein, 22kDaapproved; investigationalFlunisolide
DB00588caveolin 1, caveolae protein, 22kDaapproved; investigationalFluticasone Propionate
DB00741caveolin 1, caveolae protein, 22kDaapprovedHydrocortisone
DB00959caveolin 1, caveolae protein, 22kDaapprovedMethylprednisolone
DB00764caveolin 1, caveolae protein, 22kDaapprovedMometasone
DB01384caveolin 1, caveolae protein, 22kDaapprovedParamethasone
DB00860caveolin 1, caveolae protein, 22kDaapprovedPrednisolone
DB00635caveolin 1, caveolae protein, 22kDaapprovedPrednisone
DB00896caveolin 1, caveolae protein, 22kDaapprovedRimexolone
DB00620caveolin 1, caveolae protein, 22kDaapprovedTriamcinolone
DB00125caveolin 1, caveolae protein, 22kDaapproved; nutraceuticalL-Arginine
DB00155caveolin 1, caveolae protein, 22kDaapproved; nutraceuticalL-Citrulline
DB00435caveolin 1, caveolae protein, 22kDaapprovedNitric Oxide
DB00131caveolin 1, caveolae protein, 22kDaapproved; nutraceuticalAdenosine monophosphate
DB00171caveolin 1, caveolae protein, 22kDaapproved; nutraceuticalAdenosine triphosphate
DB00360caveolin 1, caveolae protein, 22kDaapproved; investigationalTetrahydrobiopterin


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Cross referenced IDs for CAV1
* 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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