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 LIPC

Basic gene info.	Gene symbol	LIPC
	Gene name	lipase, hepatic
	Synonyms	HDLCQ12\|HL\|HTGL\|LIPH
	Cytomap	UCSC genome browser: 15q21-q23
	Genomic location	chr15 :58724174-58861073
	Type of gene	protein-coding
	RefGenes	NM_000236.2,
	Ensembl id	ENSG00000166035
	Description	hepatic lipasehepatic triacylglycerol lipaselipase member C
	Modification date	20141211
dbXrefs	MIM : 151670
	HGNC : HGNC
	Ensembl : ENSG00000166035
	HPRD : 01058
	Vega : OTTHUMG00000132632
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_LIPC
	BioGPS: 3990
	Gene Expression Atlas: ENSG00000166035
	The Human Protein Atlas: ENSG00000166035
Pathway	NCI Pathway Interaction Database: LIPC
	KEGG: LIPC
	REACTOME: LIPC
	ConsensusPathDB
	Pathway Commons: LIPC
Metabolism	MetaCyc: LIPC
	HUMANCyc: LIPC
Regulation	Ensembl's Regulation: ENSG00000166035
	miRBase: chr15 :58,724,174-58,861,073
	TargetScan: NM_000236
	cisRED: ENSG00000166035
Context	iHOP: LIPC
	cancer metabolism search in PubMed: LIPC
	UCL Cancer Institute: LIPC
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: LIPC
	Familial Cancer Database: LIPC

* 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_GLYCEROLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS REACTOME_LIPOPROTEIN_METABOLISM

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

Mutations for LIPC

* 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

* 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
NS	LIPC	chr15	58779827	58779827		chr15	78087289	78087289
ovary	LIPC	chr15	58762626	58762646		chr8	131743487	131743507
ovary	LIPC	chr15	58809649	58809669	LIPC	chr15	58809792	58809812
ovary	LIPC	chr15	58833156	58833176	LIPC	chr15	58833624	58833644
pancreas	LIPC	chr15	58810618	58810638	LIPC	chr15	58786388	58786408
pancreas	LIPC	chr15	58860116	58860136	ADAM10	chr15	58950654	58950674

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 LIPC 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
AI589684	RPS11	28	113	19	50002861	50002946	LIPC	112	334	15	58805185	58805407
T89564	ATP8A1	1	51	4	42437489	42437539	LIPC	47	333	15	58856857	58857141

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=39)	Stat. for Synonymous SNVs (# total SNVs=18)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	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
chr15:58855922-58855922	p.R463fs*2	2
chr15:58840565-58840565	p.S282L	2
chr15:58855764-58855764	p.I410I	2
chr15:58834792-58834792	p.H172H	2
chr15:58855765-58855765	p.G411R	2
chr15:58834808-58834808	p.G178S	2
chr15:58830636-58830636	p.R65*	2
chr15:58855785-58855785	p.K417N	2
chr15:58855879-58855879	p.V449I	2
chr15:58834772-58834772	p.G166W	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=2

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	4	1	1	8			3		2			8	4	2			8	2		9
# mutation	4	1	1	9			3		2			10	4	2			8	2		10
nonsynonymous SNV	4	1		5			3		1			10	2	1			7	2		6
synonymous SNV			1	4					1				2	1			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
chr15:58830668	p.C75C	2
chr15:58834792	p.P387H	1
chr15:58855814	p.Q60H	1
chr15:58838059	p.D212H	1
chr15:58830616	p.D213Y	1
chr15:58853108	p.G393R	1
chr15:58834808	p.D70Y	1
chr15:58855829	p.R225L	1
chr15:58724239	p.T399T	1
chr15:58838067	p.Q73H	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 LIPC 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 LIPC

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


CATSPER1,CPN2,CT55,DEFB108B,DMRTC2,GAGE12D,GAGE2A, GAGE2E,GBX1,GH1,LIPC,LOC146880,LYPD4,OR56A1, PAGE1,PROCA1,PTH1R,SAMD7,SCN4A,SSX7,TMEM174	C11orf87,C1orf68,CNGA2,DEFB118,FAM180A,FBLN1,FGF14, ITGBL1,KCNA6,LIPC,LTBP1,OGN,OLFML1,PROS1, PTGIS,RECK,SHC3,SPOCK1,UST,XG,ZNF521

A4GNT,ACMSD,ACY3,ANXA10,BCAR4,BTBD16,CCER1, CLTC,COX8C,CPS1,CYP2E1,DGCR9,GABRP,GATA4, KY,LIPC,LOC100128239,PDZK1,RPS6KB1,SERPINA4,SLC16A2	AMACR,CACFD1,CAPN2,CCNJL,CLIP2,DTX4,ERBB3, FAM134A,KCNJ2,LIPC,MMP24,MYO1D,NETO2,P2RX4, TINCR,PLCL2,RMND5A,RNASEL,SLC26A2,TSPAN7,WDR78

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 LIPC

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
DB00682	lipase, hepatic	approved	Warfarin
DB01095	lipase, hepatic	approved	Fluvastatin
DB00375	lipase, hepatic	approved	Colestipol
DB00264	lipase, hepatic	approved; investigational	Metoprolol

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Cross referenced IDs for LIPC

* 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