Cancer Cell Metabolism Gene Database

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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 PLA2G12B
Basic gene info.Gene symbolPLA2G12B
Gene namephospholipase A2, group XIIB
SynonymsGXIIB|GXIIIsPLA2|PLA2G13
CytomapUCSC genome browser: 10q22.1
Genomic locationchr10 :74694937-74714510
Type of geneprotein-coding
RefGenesNM_032562.3,
Ensembl idENSG00000138308
Descriptiongroup XIIB secretory phospholipase A2-like proteingroup XIII secreted phospholipase A2group XIII secretory phospholipase A2-like proteinphospholipase A2, group XIIIsPLA2-GXIIB
Modification date20141207
dbXrefs MIM : 611653
HGNC : HGNC
Ensembl : ENSG00000138308
HPRD : 10155
Vega : OTTHUMG00000018446
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLA2G12B
BioGPS: 84647
Gene Expression Atlas: ENSG00000138308
The Human Protein Atlas: ENSG00000138308
PathwayNCI Pathway Interaction Database: PLA2G12B
KEGG: PLA2G12B
REACTOME: PLA2G12B
ConsensusPathDB
Pathway Commons: PLA2G12B
MetabolismMetaCyc: PLA2G12B
HUMANCyc: PLA2G12B
RegulationEnsembl's Regulation: ENSG00000138308
miRBase: chr10 :74,694,937-74,714,510
TargetScan: NM_032562
cisRED: ENSG00000138308
ContextiHOP: PLA2G12B
cancer metabolism search in PubMed: PLA2G12B
UCL Cancer Institute: PLA2G12B
Assigned class in ccmGDBC

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Phenotypic Information for PLA2G12B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PLA2G12B
Familial Cancer Database: PLA2G12B
* 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
KEGG_GLYCEROPHOSPHOLIPID_METABOLISM
KEGG_ARACHIDONIC_ACID_METABOLISM
KEGG_LINOLEIC_ACID_METABOLISM
KEGG_ALPHA_LINOLENIC_ACID_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PLA2G12B
MedGen: PLA2G12B (Human Medical Genetics with Condition)
ClinVar: PLA2G12B
PhenotypeMGI: PLA2G12B (International Mouse Phenotyping Consortium)
PhenomicDB: PLA2G12B

Mutations for PLA2G12B
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PLA2G12B 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 # sample1                
GAIN (# sample)1                
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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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=7)
Stat. for Synonymous SNVs
(# total SNVs=7)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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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
chr10:74700957-74700957p.R146W2
chr10:74700992-74700992p.R134Q2
chr10:74714297-74714297p.Y49Y2
chr10:74695441-74695441p.C174C1
chr10:74702417-74702417p.P98L1
chr10:74714325-74714325p.R40Q1
chr10:74695458-74695458p.V169M1
chr10:74702434-74702434p.F92F1
chr10:74714335-74714335p.R37W1
chr10:74695492-74695492p.A157A1

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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
# sample 2 3  1    4 2  54 4
# mutation 2 2  1    4 2  84 4
nonsynonymous SNV   1  1    3 1  43 2
synonymous SNV 2 1       1 1  41 2
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
chr10:74714297p.Y49Y2
chr10:74700992p.R37G2
chr10:74714335p.R134Q2
chr10:74714399p.G15G2
chr10:74695458p.G59V1
chr10:74714268p.S52S1
chr10:74714432p.D51Y1
chr10:74695492p.Q181K1
chr10:74714288p.R40Q1
chr10:74700940p.P176P1

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 PLA2G12B 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 PLA2G12B

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

APCS,APOA2,APOA4,APOC3,C8A,C9,CREB3L3,
CRP,F2,FABP1,FGF23,HP,ITIH1,MT1B,
PLA2G12B,PLG,SERPINA7,SERPINC1,SLC17A2,SULT2A1,TM4SF5
ARL6IP6,BCL10,SFR1,KATNBL1,C1orf52,TMEM243,CCDC59,
CGRRF1,CLDND1,CST13P,HMGN4,IL7,MAT2B,MBIP,
MED30,MED4,PLA2G12B,RBM7,SRI,TBPL1,THAP10

ACE2,AHCY,YAE1D1,TMEM252,DDC,FCGRT,FITM2,
GGH,GLCE,HRSP12,OIT3,PLA2G12B,PRAP1,PUS10,
RNFT1,RPS21,SERPINA7,SLC2A8,TP53RK,TSPAN6,ZSWIM3
ACE2,ALPI,AQP11,TMEM253,CHN2,DEPDC7,DGAT1,
FADS6,SLC52A1,KRT14,MS4A8,NAT8B,OIT3,PLA2G12B,
PRAP1,SLC15A1,SLC23A1,TM4SF20,TM6SF2,AGMO,USH1G
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 PLA2G12B


There's no related Drug.
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Cross referenced IDs for PLA2G12B
* 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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