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 PAFAH1B2
Basic gene info.Gene symbolPAFAH1B2
Gene nameplatelet-activating factor acetylhydrolase 1b, catalytic subunit 2 (30kDa)
SynonymsHEL-S-303
CytomapUCSC genome browser: 11q23
Genomic locationchr11 :117014999-117041761
Type of geneprotein-coding
RefGenesNM_001184746.1,
NM_001184747.1,NM_001184748.1,NM_002572.3,NR_110268.1,
NR_110269.1,NR_110282.1,
Ensembl idENSG00000168092
DescriptionPAF acetylhydrolase 30 kDa subunitPAF-AH 30 kDa subunitPAF-AH subunit betaPAF-AH1b alpha 2 subunitPAFAH subunit betaepididymis secretory protein Li 303intracellular platelet-activating factor acetylhydrolase alpha 2 subunitplatelet-activating facto
Modification date20141207
dbXrefs MIM : 602508
HGNC : HGNC
Ensembl : ENSG00000168092
HPRD : 03940
Vega : OTTHUMG00000167064
ProteinUniProt: P68402
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PAFAH1B2
BioGPS: 5049
Gene Expression Atlas: ENSG00000168092
The Human Protein Atlas: ENSG00000168092
PathwayNCI Pathway Interaction Database: PAFAH1B2
KEGG: PAFAH1B2
REACTOME: PAFAH1B2
ConsensusPathDB
Pathway Commons: PAFAH1B2
MetabolismMetaCyc: PAFAH1B2
HUMANCyc: PAFAH1B2
RegulationEnsembl's Regulation: ENSG00000168092
miRBase: chr11 :117,014,999-117,041,761
TargetScan: NM_001184746
cisRED: ENSG00000168092
ContextiHOP: PAFAH1B2
cancer metabolism search in PubMed: PAFAH1B2
UCL Cancer Institute: PAFAH1B2
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PAFAH1B2 in cancer cell metabolism1. Kohnz RA, Mulvihill MM, Chang JW, Hsu K-L, Sorrentino A, et al. (2015) Activity-Based Protein Profiling of Oncogene-Driven Changes in Metabolism Reveals Broad Dysregulation of PAFAH1B2 and 1B3 in Cancer. ACS chemical biology. go to article

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Phenotypic Information for PAFAH1B2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PAFAH1B2
Familial Cancer Database: PAFAH1B2
* 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
Nat Rev Drug Discovery, 2013, 12: 829, doi: 10.1038/nrd4145

check002.gifOthers
OMIM 602508; gene.
602508; gene.
Orphanet
DiseaseKEGG Disease: PAFAH1B2
MedGen: PAFAH1B2 (Human Medical Genetics with Condition)
ClinVar: PAFAH1B2
PhenotypeMGI: PAFAH1B2 (International Mouse Phenotyping Consortium)
PhenomicDB: PAFAH1B2

Mutations for PAFAH1B2
* 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
There's no inter-chromosomal structural variation.
- 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
ovaryPAFAH1B2chr11117019839117019859CDCA5chr116484540964845429
ovaryPAFAH1B2chr11117029961117029981chr11116988146116988166
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 PAFAH1B2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CT002325PAFAH1B219511117015040117015134ARID5A9669429721313997215971
CB528508PAFAH1B2161311117040748117041360ZFAND561066597497436174974416
BC064340PAFAH1B2110811117015115117023244FOXR110674811118849489118851995
AW629132TBL1X10155X96876339687778PAFAH1B213848811117038809117039159
BE177628PAFAH1B2147311117026779117027249PAFAH1B246065711117022690117022887
AA318969LIN92791226453685226453762PAFAH1B27729511117039777117039995
BU662239CDC25A21323934821550048215526PAFAH1B223670911117039756117040228

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
There's no copy number variation information in COSMIC data for this gene.

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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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=1)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no s-snv.
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr11:117038249-117038249p.T175S1

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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
# sample1  1    1  21   21 3
# mutation1  1    1  21   21 3
nonsynonymous SNV1       1  21   21 3
synonymous SNV   1                
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
chr11:117038270p.G200W1
chr11:117038271p.C206Y1
chr11:117038293p.R23P,PAFAH1B21
chr11:117038323p.S26Y,PAFAH1B21
chr11:117023231p.G46R,PAFAH1B21
chr11:117038342p.G74W,PAFAH1B21
chr11:117023240p.G88R,PAFAH1B21
chr11:117030704p.G116A,PAFAH1B21
chr11:117031909p.G143C1
chr11:117031951p.S182L1

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 PAFAH1B2 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 PAFAH1B2

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

ARHGEF12,ASXL2,CBL,CCNT1,CLOCK,CUL5,DDX6,
GTF2A1,MAP3K2,KMT2A,MPZL3,NPAT,PAFAH1B2,PPP4R2,
PRKAR2A,REST,RIF1,SON,STRN,TBCEL,UBE4A
ASXL2,ATF2,BROX,CLCN3,DPY19L3,FAM168A,GTF2A1,
MGAT5,MOB1A,PAFAH1B2,PDZD8,PPP4R2,REST,RHBDD1,
SBNO1,SLC30A6,STRN,TMEM184C,TRIM44,UTP14C,WDFY3

ATE1,CCNT1,DDI2,EYA3,GTF2A1,HIPK3,KLHL11,
LATS1,LIMS1,NHLRC2,PAFAH1B2,PPP4R2,PPTC7,PRKAR2A,
PTPLB,REST,RNF168,RQCD1,SBNO1,UHMK1,ZFP91
ALG2,BAG4,C2orf43,C9orf41,CDC40,CEP76,COPB1,
DCBLD1,DEPDC4,ERLIN1,CCSER1,HSDL2,LOC729082,PAFAH1B2,
RSPRY1,SLC25A40,SLC30A5,SMEK2,STT3B,USP33,ZDHHC20
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 PAFAH1B2


There's no related Drug.
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Cross referenced IDs for PAFAH1B2
* 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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