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 LPA
Basic gene info.Gene symbolLPA
Gene namelipoprotein, Lp(a)
SynonymsAK38|APOA|LP
CytomapUCSC genome browser: 6q26
Genomic locationchr6 :160952514-161087407
Type of geneprotein-coding
RefGenesNM_005577.2,
Ensembl idENSG00000198670
Descriptionantiangiogenic AK38 proteinapo(a)apolipoprotein(a)lp(a)
Modification date20141222
dbXrefs MIM : 152200
HGNC : HGNC
Ensembl : ENSG00000198670
HPRD : 01063
Vega : OTTHUMG00000015956
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LPA
BioGPS: 4018
Gene Expression Atlas: ENSG00000198670
The Human Protein Atlas: ENSG00000198670
PathwayNCI Pathway Interaction Database: LPA
KEGG: LPA
REACTOME: LPA
ConsensusPathDB
Pathway Commons: LPA
MetabolismMetaCyc: LPA
HUMANCyc: LPA
RegulationEnsembl's Regulation: ENSG00000198670
miRBase: chr6 :160,952,514-161,087,407
TargetScan: NM_005577
cisRED: ENSG00000198670
ContextiHOP: LPA
cancer metabolism search in PubMed: LPA
UCL Cancer Institute: LPA
Assigned class in ccmGDBC

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

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS
REACTOME_LIPOPROTEIN_METABOLISM

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

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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryLPAchr6161074913161075113chr98254892382549123
pancreasLPAchr6160956231160956251chr206095729960957319
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 LPA related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 # sample          1  1   
GAIN (# sample)                 
LOSS (# sample)          1  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=8

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check002.gifSomatic 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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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
chr6:161067344-161067344p.E98G5
chr6:160977190-160977190p.R1614R5
chr6:161050772-161050772p.N417K4
chr6:161067362-161067362p.D92G4
chr6:161006078-161006078p.A1430V4
chr6:161027563-161027563p.V911F4
chr6:161032668-161032668p.T843T4
chr6:161067377-161067377p.Y87F4
chr6:161045160-161045160p.E554G4
chr6:161034101-161034101p.A769G3

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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=9

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample79 303 7 21 36169423916 15
# mutation79 293 7 21 42179224917 19
nonsynonymous SNV78 182 6 11 351352 3812 14
synonymous SNV 1 121 1 1  744 2115 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
chr6:160977190p.A977E5
chr6:161026093p.R1614W5
chr6:161006078p.A1430V4
chr6:160977188p.V911I3
chr6:161071386p.E65K3
chr6:161027563p.R1614R3
chr6:160977164p.E1135K2
chr6:160978466p.K2001I2
chr6:161022029p.E1344G2
chr6:161007564p.F1997F2

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 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

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

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
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 LPA
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
DB00513lipoprotein, Lp(a)approved; investigationalAminocaproic 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



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