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 LPIN1

Basic gene info.	Gene symbol	LPIN1
	Gene name	lipin 1
	Synonyms	PAP1
	Cytomap	UCSC genome browser: 2p25.1
	Genomic location	chr2 :11886739-11967533
	Type of gene	protein-coding
	RefGenes	NM_001261427.1, NM_001261428.1,NM_001261429.1,NM_145693.2,
	Ensembl id	ENSG00000134324
	Description	lipin-1phosphatidate phosphatase LPIN1
	Modification date	20141207
dbXrefs	MIM : 605518
	HGNC : HGNC
	Ensembl : ENSG00000134324
	HPRD : 09271
	Vega : OTTHUMG00000119082
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_LPIN1
	BioGPS: 23175
	Gene Expression Atlas: ENSG00000134324
	The Human Protein Atlas: ENSG00000134324
Pathway	NCI Pathway Interaction Database: LPIN1
	KEGG: LPIN1
	REACTOME: LPIN1
	ConsensusPathDB
	Pathway Commons: LPIN1
Metabolism	MetaCyc: LPIN1
	HUMANCyc: LPIN1
Regulation	Ensembl's Regulation: ENSG00000134324
	miRBase: chr2 :11,886,739-11,967,533
	TargetScan: NM_001261427
	cisRED: ENSG00000134324
Context	iHOP: LPIN1
	cancer metabolism search in PubMed: LPIN1
	UCL Cancer Institute: LPIN1
Assigned class in ccmGDB	C

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Phenotypic Information for LPIN1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: LPIN1
	Familial Cancer Database: LPIN1

* 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_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: LPIN1
	MedGen: LPIN1 (Human Medical Genetics with Condition)
	ClinVar: LPIN1
Phenotype	MGI: LPIN1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: LPIN1

Mutations for LPIN1

* 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
pancreas	LPIN1	chr2	11889535	11889555		chr2	11870036	11870056
pancreas	LPIN1	chr2	11902827	11902847		chr2	11855171	11855191
pancreas	LPIN1	chr2	11930008	11930028		chr4	162053240	162053260

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 LPIN1 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
DA403287	ARL16	1	163	17	79650564	79650824	LPIN1	161	542	2	11905658	11911581
BF932023	ANKS1B	18	276	12	99145182	99166957	LPIN1	270	422	2	11944623	11945273
BF365751	ARGLU1	1	78	13	107210812	107210889	LPIN1	71	227	2	11938938	11939094
AW889856	ARGLU1	1	78	13	107210812	107210889	LPIN1	71	227	2	11938938	11939094
BF352637	LPIN1	31	231	2	11959372	11959572	LPIN1	230	352	2	11959577	11959699
BF352618	LPIN1	23	223	2	11959372	11959572	LPIN1	222	344	2	11959577	11959699

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=67)	Stat. for Synonymous SNVs (# total SNVs=24)

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

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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
chr2:11943103-11943103	p.P617S	2
chr2:11964803-11964803	p.L853L	2
chr2:11925031-11925031	p.A424T	2
chr2:11943141-11943141	p.R629R	2
chr2:11911528-11911528	p.P107S	2
chr2:11964910-11964910	p.S889L	2
chr2:11911551-11911551	p.S114S	2
chr2:11905715-11905715	p.K16K	2
chr2:11911614-11911614	p.T135T	2
chr2:11911634-11911634	p.P142L	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=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	3	1	14	2		2		4	2		4	4	3		1	17	10		12
# mutation	4	3	1	17	2		2		4	3		4	4	3		1	20	10		16
nonsynonymous SNV	2	3		13	2		1		4	2		2	4	2		1	13	7		11
synonymous SNV	2		1	4			1			1		2		1			7	3		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
chr2:11911614	p.P107S,LPIN1	2
chr2:11911638	p.T135T,LPIN1	2
chr2:11911528	p.S143S,LPIN1	2
chr2:11911613	p.V89I,LPIN1	1
chr2:11925046	p.D210E,LPIN1	1
chr2:11960606	p.R390Q,LPIN1	1
chr2:11913802	p.T627N,LPIN1	1
chr2:11944573	p.K770N,LPIN1	1
chr2:11905843	p.I99I,LPIN1	1
chr2:11923961	p.N216S,LPIN1	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 LPIN1 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 LPIN1

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


CLCN4,CLCN5,AMER1,FAM171A1,FAM49A,FMNL2,GABRP, GPM6B,IFRD1,IL34,KCNQ4,TLDC1,L3MBTL4,LPIN1, LYN,PRKX,RASD2,TBX19,TIGD2,TRIM2,TTLL4	AASS,AGPAT9,ALDH6A1,C6,CALCRL,CYP1A2,DNAH9, ELMOD1,GCK,GLUL,GLYCTK,GYS2,LDHD,LOC149620, LPIN1,MOGAT1,NTSR2,PDK2,PLCXD1,ST3GAL6,STOX1

ADNP2,GDPGP1,CYB5D1,DOCK5,ELOVL6,LIMA1,LPIN1, MLEC,MTHFR,PCSK9,PNPLA3,RAI1,RIMS3,SGPP2, SLC28A3,SREBF1,STARD4,TNFRSF11A,TRIM16,XPNPEP1,ZCCHC2	AKAP2,ARHGAP23,CCDC88A,CELF2,CEP170,CLIP1,FAM120C, FAM65A,HDAC4,LPIN1,MAP4,NCDN,RAB36,RABEP1, RIMKLB,ROBO1,SACS,SLC41A1,SYNE1,TRIB2,ZNF154

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 LPIN1

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
DB00412	lipin 1	approved; investigational	Rosiglitazone

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Cross referenced IDs for LPIN1

* 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