Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 CAV1

Basic gene info.	Gene symbol	CAV1
	Gene name	caveolin 1, caveolae protein, 22kDa
	Synonyms	BSCL3\|CGL3\|LCCNS\|MSTP085\|PPH3\|VIP21
	Cytomap	UCSC genome browser: 7q31.1
	Genomic location	chr7 :116166411-116201239
	Type of gene	protein-coding
	RefGenes	NM_001172895.1, NM_001172896.1,NM_001172897.1,NM_001753.4,
	Ensembl id	ENSG00000105974
	Description	caveolin-1cell growth-inhibiting protein 32
	Modification date	20141207
dbXrefs	MIM : 601047
	HGNC : HGNC
	Ensembl : ENSG00000105974
	HPRD : 03028
	Vega : OTTHUMG00000023413
Protein	UniProt: Q03135 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CAV1
	BioGPS: 857
	Gene Expression Atlas: ENSG00000105974
	The Human Protein Atlas: ENSG00000105974
Pathway	NCI Pathway Interaction Database: CAV1
	KEGG: CAV1
	REACTOME: CAV1
	ConsensusPathDB
	Pathway Commons: CAV1
Metabolism	MetaCyc: CAV1
	HUMANCyc: CAV1
Regulation	Ensembl's Regulation: ENSG00000105974
	miRBase: chr7 :116,166,411-116,201,239
	TargetScan: NM_001172895
	cisRED: ENSG00000105974
Context	iHOP: CAV1
	cancer metabolism search in PubMed: CAV1
	UCL Cancer Institute: CAV1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CAV1 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
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.
Disease	KEGG Disease: CAV1
	MedGen: CAV1 (Human Medical Genetics with Condition)
	ClinVar: CAV1
Phenotype	MGI: CAV1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CAV1 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
BP260187	ANKRD1	1	397	10	92678893	92680843	CAV1	398	584	7	116165090	116166708
BF476043	CHCHD4	13	144	3	14153585	14153716	CAV1	135	441	7	116200112	116200417
BF196928	CAV1	2	182	7	116201048	116201228	MCM9	170	505	6	119134792	119135127
D61924	OXR1	4	146	8	107764771	107764915	CAV1	142	299	7	116201009	116201569
BE930754	CAV1	14	134	7	116184295	116184415	IQGAP2	128	251	5	76003107	76003230

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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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

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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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
chr7:116199315-116199315	p.R171C	2
chr7:116199023-116199023	p.A73A	1
chr7:116199190-116199190	p.A129E	1
chr7:116199067-116199067	p.S88T	1
chr7:116199240-116199240	p.R146C	1
chr7:116166580-116166580	p.G11A	1
chr7:116199070-116199070	p.F89S	1
chr7:116166586-116166586	p.L13H	1
chr7:116199076-116199076	p.T91I	1
chr7:116199329-116199329	p.Q175Q	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	1		1						1							3	4		3
# mutation	1	1		1						1							3	4		3
nonsynonymous SNV		1		1													2	4		3
synonymous SNV	1									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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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
chr7:116199105	p.L13H	1
chr7:116199240	p.T15A	1
chr7:116166586	p.R19Q	1
chr7:116199315	p.D12D,CAV1	1
chr7:116166591	p.L28L,CAV1	1
chr7:116199329	p.S57T,CAV1	1
chr7:116166604	p.F58S,CAV1	1
chr7:116199333	p.T60I,CAV1	1
chr7:116166677	p.T64M,CAV1	1
chr7:116166725	p.R70C,CAV1	1

Other 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

Copy 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

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.

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Protein 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.

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.

: Open all plots for all cancer types

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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

: 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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA26107; -.
Organism-specific databases	CTD	857; -.

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
DB00394	caveolin 1, caveolae protein, 22kDa	approved	Beclomethasone
DB00443	caveolin 1, caveolae protein, 22kDa	approved	Betamethasone
DB01222	caveolin 1, caveolae protein, 22kDa	approved; investigational	Budesonide
DB01410	caveolin 1, caveolae protein, 22kDa	approved; investigational	Ciclesonide
DB01260	caveolin 1, caveolae protein, 22kDa	approved; investigational	Desonide
DB01234	caveolin 1, caveolae protein, 22kDa	approved; investigational	Dexamethasone
DB00180	caveolin 1, caveolae protein, 22kDa	approved; investigational	Flunisolide
DB00588	caveolin 1, caveolae protein, 22kDa	approved; investigational	Fluticasone Propionate
DB00741	caveolin 1, caveolae protein, 22kDa	approved	Hydrocortisone
DB00959	caveolin 1, caveolae protein, 22kDa	approved	Methylprednisolone
DB00764	caveolin 1, caveolae protein, 22kDa	approved	Mometasone
DB01384	caveolin 1, caveolae protein, 22kDa	approved	Paramethasone
DB00860	caveolin 1, caveolae protein, 22kDa	approved	Prednisolone
DB00635	caveolin 1, caveolae protein, 22kDa	approved	Prednisone
DB00896	caveolin 1, caveolae protein, 22kDa	approved	Rimexolone
DB00620	caveolin 1, caveolae protein, 22kDa	approved	Triamcinolone
DB00125	caveolin 1, caveolae protein, 22kDa	approved; nutraceutical	L-Arginine
DB00155	caveolin 1, caveolae protein, 22kDa	approved; nutraceutical	L-Citrulline
DB00435	caveolin 1, caveolae protein, 22kDa	approved	Nitric Oxide
DB00131	caveolin 1, caveolae protein, 22kDa	approved; nutraceutical	Adenosine monophosphate
DB00171	caveolin 1, caveolae protein, 22kDa	approved; nutraceutical	Adenosine triphosphate
DB00360	caveolin 1, caveolae protein, 22kDa	approved; investigational	Tetrahydrobiopterin

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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