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 CPT1A

Basic gene info.	Gene symbol	CPT1A
	Gene name	carnitine palmitoyltransferase 1A (liver)
	Synonyms	CPT1\|CPT1-L\|L-CPT1
	Cytomap	UCSC genome browser: 11q13.2
	Genomic location	chr11 :68522087-68609399
	Type of gene	protein-coding
	RefGenes	NM_001031847.2, NM_001876.3,
	Ensembl id	ENSG00000110090
	Description	CPT ICPTI-Lcarnitine O-palmitoyltransferase 1, liver isoformcarnitine O-palmitoyltransferase I, liver isoformcarnitine palmitoyltransferase I, liver
	Modification date	20141219
dbXrefs	MIM : 600528
	HGNC : HGNC
	Ensembl : ENSG00000110090
	HPRD : 02755
	Vega : OTTHUMG00000167892
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CPT1A
	BioGPS: 1374
	Gene Expression Atlas: ENSG00000110090
	The Human Protein Atlas: ENSG00000110090
Pathway	NCI Pathway Interaction Database: CPT1A
	KEGG: CPT1A
	REACTOME: CPT1A
	ConsensusPathDB
	Pathway Commons: CPT1A
Metabolism	MetaCyc: CPT1A
	HUMANCyc: CPT1A
Regulation	Ensembl's Regulation: ENSG00000110090
	miRBase: chr11 :68,522,087-68,609,399
	TargetScan: NM_001031847
	cisRED: ENSG00000110090
Context	iHOP: CPT1A
	cancer metabolism search in PubMed: CPT1A
	UCL Cancer Institute: CPT1A
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CPT1A in cancer cell metabolism	1. Patsoukis N, Bardhan K, Chatterjee P, Sari D, Liu B, et al. (2015) PD-1 alters T-cell metabolic reprogramming by inhibiting glycolysis and promoting lipolysis and fatty acid oxidation. Nat Commun 6: 6692. doi: 10.1038/ncomms7692. pmid: 4389235. go to article 2. Patella F, Schug ZT, Persi E, Neilson LJ, Erami Z, et al. (2015) Proteomics-based metabolic modeling reveals that fatty acid oxidation (FAO) controls endothelial cell (EC) permeability. Mol Cell Proteomics 14: 621-634. doi: 10.1074/mcp.M114.045575. pmid: 4349982. go to article 3. Roy D, Mondal S, Wang C, He X, Khurana A, et al. (2014) Loss of HSulf-1 promotes altered lipid metabolism in ovarian cancer. Cancer Metab 2: 13. doi: 10.1186/2049-3002-2-13. pmid: 4164348. go to article 4. Schlaepfer IR, Rider L, Rodrigues LU, Gijon MA, Pac CT, et al. (2014) Lipid catabolism via CPT1 as a therapeutic target for prostate cancer. Mol Cancer Ther 13: 2361-2371. doi: 10.1158/1535-7163.MCT-14-0183. pmid: 4185227. go to article 5. Cirillo A, Di Salle A, Petillo O, Melone MA, Grimaldi G, et al. (2014) High grade glioblastoma is associated with aberrant expression of ZFP57, a protein involved in gene imprinting, and of CPT1A and CPT1C that regulate fatty acid metabolism. Cancer Biol Ther 15: 735-741. doi: 10.4161/cbt.28408. pmid: 4049789. go to article

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Phenotypic Information for CPT1A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CPT1A
	Familial Cancer Database: CPT1A

* 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
KEGG_FATTY_ACID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: CPT1A
	MedGen: CPT1A (Human Medical Genetics with Condition)
	ClinVar: CPT1A
Phenotype	MGI: CPT1A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CPT1A

Mutations for CPT1A

* 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

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
haematopoietic_and_lymphoid_tissue	CPT1A	chr11	68567886	68567886	CPT1A	chr11	68567886	68567886

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 CPT1A 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
AK309464	CPT1A	1	1887	11	68540732	68607152	RDH5	1885	2165	12	56117668	56118220
BM970771	CPT1A	15	152	11	68522351	68522488	C16orf72	147	634	16	9210267	9210755
BM041208	CPT1A	2	681	11	68552431	68575053	GAPDH	662	705	12	6647494	6647537
CB154699	CPT1A	15	243	11	68523181	68523409	FGG	232	537	4	155525288	155526135

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=61)	Stat. for Synonymous SNVs (# total SNVs=23)

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
chr11:68566686-68566686	p.Y231Y	3
chr11:68552320-68552320	p.G376R	2
chr11:68579905-68579905	p.A94V	2
chr11:68549256-68549256	p.H445H	2
chr11:68571514-68571514	p.S170L	2
chr11:68552398-68552398	p.D350N	2
chr11:68548126-68548126	p.I480I	2
chr11:68542876-68542876	p.Q495*	2
chr11:68582853-68582853	p.Q30H	2
chr11:68540835-68540835	p.F546F	2

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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=3

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	3	4		18	2		10					10	7	3			15	8		10
# mutation	3	4		18	2		10					11	7	3			15	8		13
nonsynonymous SNV	2	3		14	1		4					10	4	2			9	7		9
synonymous SNV	1	1		4	1		6					1	3	1			6	1		4

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
chr11:68571514	p.S170L,CPT1A	3
chr11:68582853	p.Q30H,CPT1A	2
chr11:68548126	p.H445H,CPT1A	2
chr11:68579905	p.A94V,CPT1A	2
chr11:68549256	p.I480I,CPT1A	2
chr11:68560791	p.A478S,CPT1A	1
chr11:68579981	p.Q364Q,CPT1A	1
chr11:68540781	p.P192R,CPT1A	1
chr11:68566776	p.R89P,CPT1A	1
chr11:68525182	p.T745M,CPT1A	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 CPT1A 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 CPT1A

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.

: 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


BRCA1,CCND1,CHD6,CPT1A,CTTN,DNAJC14,FADD, FITM2,IGHMBP2,KIF3B,MRPL21,MTL5,ORAOV1,PANK3, PPFIA1,PPP6R3,SCD,SUV420H1,TMED10P1,VPS13B,ZNF623	ABL2,ADD2,ANGPT2,ARHGAP23,ATP8B2,BMX,CMIP, CPT1A,DOC2B,ELF4,KCNT2,LHX6,NOD1,PLSCR1, RPGR,SEPT8,SWAP70,TLL1,TMOD2,TRPM6,ZNF385D

AIFM3,AMBRA1,CPT1A,CTTN,DAGLA,FABP1,TMEM236, FZD5,GPD1L,HMGCS2,KALRN,KCNK5,LOC25845,MYB, OVOL1,PITPNM1,PPFIA1,SGK2,SLC35D3,SLC9A3,UBE4A	ABCC3,ACOX1,AGFG2,CD2AP,CDH1,CPT1A,CUL3, EPB41L4B,FLNB,FZD5,HNF4A,PDCD6IP,PDE8A,RAPGEFL1, RBM47,SGK2,SLC41A2,STK38,TMEM63B,TNK1,TRAPPC10

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 CPT1A

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB00583	carnitine palmitoyltransferase 1A (liver)	approved	L-Carnitine
DB01074	carnitine palmitoyltransferase 1A (liver)	approved	Perhexiline

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Cross referenced IDs for CPT1A

* 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