Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolLPIN1
Gene namelipin 1
SynonymsPAP1
CytomapUCSC genome browser: 2p25.1
Genomic locationchr2 :11886739-11967533
Type of geneprotein-coding
RefGenesNM_001261427.1,
NM_001261428.1,NM_001261429.1,NM_145693.2,
Ensembl idENSG00000134324
Descriptionlipin-1phosphatidate phosphatase LPIN1
Modification date20141207
dbXrefs MIM : 605518
HGNC : HGNC
Ensembl : ENSG00000134324
HPRD : 09271
Vega : OTTHUMG00000119082
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LPIN1
BioGPS: 23175
Gene Expression Atlas: ENSG00000134324
The Human Protein Atlas: ENSG00000134324
PathwayNCI Pathway Interaction Database: LPIN1
KEGG: LPIN1
REACTOME: LPIN1
ConsensusPathDB
Pathway Commons: LPIN1
MetabolismMetaCyc: LPIN1
HUMANCyc: LPIN1
RegulationEnsembl's Regulation: ENSG00000134324
miRBase: chr2 :11,886,739-11,967,533
TargetScan: NM_001261427
cisRED: ENSG00000134324
ContextiHOP: LPIN1
cancer metabolism search in PubMed: LPIN1
UCL Cancer Institute: LPIN1
Assigned class in ccmGDBC

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Phenotypic Information for LPIN1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: LPIN1
MedGen: LPIN1 (Human Medical Genetics with Condition)
ClinVar: LPIN1
PhenotypeMGI: LPIN1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasLPIN1chr21188953511889555chr21187003611870056
pancreasLPIN1chr21190282711902847chr21185517111855191
pancreasLPIN1chr21193000811930028chr4162053240162053260
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LPIN1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA403287ARL161163177965056479650824LPIN116154221190565811911581
BF932023ANKS1B18276129914518299166957LPIN127042221194462311945273
BF365751ARGLU117813107210812107210889LPIN17122721193893811939094
AW889856ARGLU117813107210812107210889LPIN17122721193893811939094
BF352637LPIN13123121195937211959572LPIN123035221195957711959699
BF352618LPIN12322321195937211959572LPIN122234421195957711959699

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1                
GAIN (# sample)                 
LOSS (# sample)1                
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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr2:11911551-11911551p.S114S2
chr2:11905715-11905715p.K16K2
chr2:11911614-11911614p.T135T2
chr2:11911634-11911634p.P142L2
chr2:11943084-11943084p.P610P2
chr2:11905738-11905738p.P24L2
chr2:11911638-11911638p.S143R2
chr2:11943103-11943103p.P617S2
chr2:11964803-11964803p.L853L2
chr2:11925031-11925031p.A424T2

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample431142 2 42 443 11710 12
# mutation431172 2 43 443 12010 16
nonsynonymous SNV23 132 1 42 242 1137 11
synonymous SNV2 14  1  1 2 1  73 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr2:11911528p.T135T,LPIN12
chr2:11911614p.S143S,LPIN12
chr2:11911638p.P107S,LPIN12
chr2:11911646p.V811V,LPIN11
chr2:11928551p.G9S,LPIN11
chr2:11964794p.S114S,LPIN11
chr2:11905715p.K267N,LPIN11
chr2:11919762p.P415L,LPIN11
chr2:11944613p.Q654R,LPIN11
chr2:11911506p.G657D,LPIN11

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00412lipin 1approved; investigationalRosiglitazone


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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



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