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 PAFAH1B2

Basic gene info.	Gene symbol	PAFAH1B2
	Gene name	platelet-activating factor acetylhydrolase 1b, catalytic subunit 2 (30kDa)
	Synonyms	HEL-S-303
	Cytomap	UCSC genome browser: 11q23
	Genomic location	chr11 :117014999-117041761
	Type of gene	protein-coding
	RefGenes	NM_001184746.1, NM_001184747.1,NM_001184748.1,NM_002572.3,NR_110268.1, NR_110269.1,NR_110282.1,
	Ensembl id	ENSG00000168092
	Description	PAF 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 date	20141207
dbXrefs	MIM : 602508
	HGNC : HGNC
	Ensembl : ENSG00000168092
	HPRD : 03940
	Vega : OTTHUMG00000167064
Protein	UniProt: P68402 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PAFAH1B2
	BioGPS: 5049
	Gene Expression Atlas: ENSG00000168092
	The Human Protein Atlas: ENSG00000168092
Pathway	NCI Pathway Interaction Database: PAFAH1B2
	KEGG: PAFAH1B2
	REACTOME: PAFAH1B2
	ConsensusPathDB
	Pathway Commons: PAFAH1B2
Metabolism	MetaCyc: PAFAH1B2
	HUMANCyc: PAFAH1B2
Regulation	Ensembl's Regulation: ENSG00000168092
	miRBase: chr11 :117,014,999-117,041,761
	TargetScan: NM_001184746
	cisRED: ENSG00000168092
Context	iHOP: PAFAH1B2
	cancer metabolism search in PubMed: PAFAH1B2
	UCL Cancer Institute: PAFAH1B2
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PAFAH1B2 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
Nat Rev Drug Discovery, 2013, 12: 829, doi: 10.1038/nrd4145

Others
OMIM	602508; gene. 602508; gene.
Orphanet
Disease	KEGG Disease: PAFAH1B2
	MedGen: PAFAH1B2 (Human Medical Genetics with Condition)
	ClinVar: PAFAH1B2
Phenotype	MGI: PAFAH1B2 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	PAFAH1B2	chr11	117019839	117019859	CDCA5	chr11	64845409	64845429
ovary	PAFAH1B2	chr11	117029961	117029981		chr11	116988146	116988166

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 PAFAH1B2 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
CT002325	PAFAH1B2	1	95	11	117015040	117015134	ARID5A	96	694	2	97213139	97215971
CB528508	PAFAH1B2	1	613	11	117040748	117041360	ZFAND5	610	665	9	74974361	74974416
BC064340	PAFAH1B2	1	108	11	117015115	117023244	FOXR1	106	748	11	118849489	118851995
AW629132	TBL1X	10	155	X	9687633	9687778	PAFAH1B2	138	488	11	117038809	117039159
BE177628	PAFAH1B2	1	473	11	117026779	117027249	PAFAH1B2	460	657	11	117022690	117022887
AA318969	LIN9	2	79	1	226453685	226453762	PAFAH1B2	77	295	11	117039777	117039995
BU662239	CDC25A	213	239	3	48215500	48215526	PAFAH1B2	236	709	11	117039756	117040228

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

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

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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=1

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Somatic 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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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
chr11:117038249-117038249	p.T175S	1

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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	1			1					1			2	1				2	1		3
# mutation	1			1					1			2	1				2	1		3
nonsynonymous SNV	1								1			2	1				2	1		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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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
chr11:117038271	p.R23P,PAFAH1B2	1
chr11:117038293	p.S26Y,PAFAH1B2	1
chr11:117038323	p.G46R,PAFAH1B2	1
chr11:117023231	p.G74W,PAFAH1B2	1
chr11:117038342	p.G88R,PAFAH1B2	1
chr11:117023240	p.G116A,PAFAH1B2	1
chr11:117030704	p.G143C	1
chr11:117031909	p.S182L	1
chr11:117031951	p.S182S	1
chr11:117034544	p.D190N	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 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

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


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

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 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