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 LPA

Basic gene info.	Gene symbol	LPA
	Gene name	lipoprotein, Lp(a)
	Synonyms	AK38\|APOA\|LP
	Cytomap	UCSC genome browser: 6q26
	Genomic location	chr6 :160952514-161087407
	Type of gene	protein-coding
	RefGenes	NM_005577.2,
	Ensembl id	ENSG00000198670
	Description	antiangiogenic AK38 proteinapo(a)apolipoprotein(a)lp(a)
	Modification date	20141222
dbXrefs	MIM : 152200
	HGNC : HGNC
	Ensembl : ENSG00000198670
	HPRD : 01063
	Vega : OTTHUMG00000015956
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_LPA
	BioGPS: 4018
	Gene Expression Atlas: ENSG00000198670
	The Human Protein Atlas: ENSG00000198670
Pathway	NCI Pathway Interaction Database: LPA
	KEGG: LPA
	REACTOME: LPA
	ConsensusPathDB
	Pathway Commons: LPA
Metabolism	MetaCyc: LPA
	HUMANCyc: LPA
Regulation	Ensembl's Regulation: ENSG00000198670
	miRBase: chr6 :160,952,514-161,087,407
	TargetScan: NM_005577
	cisRED: ENSG00000198670
Context	iHOP: LPA
	cancer metabolism search in PubMed: LPA
	UCL Cancer Institute: LPA
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: LPA
	Familial Cancer Database: LPA

* 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 REACTOME_LIPOPROTEIN_METABOLISM

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

Mutations for LPA

* 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
ovary	LPA	chr6	161074913	161075113		chr9	82548923	82549123
pancreas	LPA	chr6	160956231	160956251		chr20	60957299	60957319

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 LPA related fusion information.

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

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=8

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=337)	Stat. for Synonymous SNVs (# total SNVs=99)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=1)

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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
chr6:161067344-161067344	p.E98G	5
chr6:160977190-160977190	p.R1614R	5
chr6:161027563-161027563	p.V911F	4
chr6:161032668-161032668	p.T843T	4
chr6:161067377-161067377	p.Y87F	4
chr6:161045160-161045160	p.E554G	4
chr6:161050772-161050772	p.N417K	4
chr6:161067362-161067362	p.D92G	4
chr6:161006078-161006078	p.A1430V	4
chr6:161071386-161071386	p.E65K	3

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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=9

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	7	9		30	3		7		2	1		36	16	9	4	2	39	16		15
# mutation	7	9		29	3		7		2	1		42	17	9	2	2	49	17		19
nonsynonymous SNV	7	8		18	2		6		1	1		35	13	5	2		38	12		14
synonymous SNV		1		12	1		1		1			7	4	4		2	11	5		5

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
chr6:160977190	p.A977E	5
chr6:161026093	p.R1614W	5
chr6:161006078	p.A1430V	4
chr6:160977188	p.V911I	3
chr6:161071386	p.E65K	3
chr6:161027563	p.R1614R	3
chr6:160952893	p.V1026L	2
chr6:161027642	p.P1339P	2
chr6:160999635	p.P1590L	2
chr6:161007593	p.R1016L	2

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 LPA 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 LPA

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


A1CF,APOA1,ASB9,ANKRD30BP2,C3P1,C9,CREB3L3, F2,FABP1,GJB7,HP,LOC100132831,LPA,MCHR2, MT1B,MT1DP,PLG,SERPINA7,SLC17A2,SLC35A3,SULT2A1	ALLC,AQP2,IZUMO2,CDH19,GFRA3,GJD4,GP2, LPA,MC2R,MMP27,NIPAL4,OLFM4,OLIG2,OR9I1, PCP4,PNCK,SNORA2B,SPDYE2,TNP2,UBE2DNL,UMOD

ACTRT1,ALMS1P,ANO7,C1orf100,GABRR1,HSF4,LCE5A, LOC100133308,LOC221122,LOC728276,LPA,NXPH1,OR2C3,OR9Q1, PDXDC2P,PROZ,REP15,RPL13AP17,SH2D6,SNAR-E,SNAR-G2	ACAN,C20orf141,NCOR1P1,CCDC129,CHAT,CLEC4G,GPX5, ITIH3,KPRP,LCE2C,LPA,MEPE,CHODL-AS1,OR2D2, PGLYRP3,POU2F3,SH2D7,SNORA79,TRIM6-TRIM34,TRPM5,ZSWIM2

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 LPA

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
DB00513	lipoprotein, Lp(a)	approved; investigational	Aminocaproic Acid

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Cross referenced IDs for LPA

* 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