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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PAFAH1B1 |
Basic gene info. | Gene symbol | PAFAH1B1 |
Gene name | platelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa) | |
Synonyms | LIS1|LIS2|MDCR|MDS|PAFAH | |
Cytomap | UCSC genome browser: 17p13.3 | |
Genomic location | chr17 :2496922-2588909 | |
Type of gene | protein-coding | |
RefGenes | NM_000430.3, | |
Ensembl id | ENSG00000007168 | |
Description | lissencephaly 1 proteinplatelet-activating factor acetylhydrolase IB subunit alphaplatelet-activating factor acetylhydrolase, isoform Ib, alpha subunit (45kD)platelet-activating factor acetylhydrolase, isoform Ib, subunit 1 (45kDa) | |
Modification date | 20141219 | |
dbXrefs | MIM : 601545 | |
HGNC : HGNC | ||
Ensembl : ENSG00000007168 | ||
HPRD : 03329 | ||
Vega : OTTHUMG00000177574 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PAFAH1B1 | |
BioGPS: 5048 | ||
Gene Expression Atlas: ENSG00000007168 | ||
The Human Protein Atlas: ENSG00000007168 | ||
Pathway | NCI Pathway Interaction Database: PAFAH1B1 | |
KEGG: PAFAH1B1 | ||
REACTOME: PAFAH1B1 | ||
ConsensusPathDB | ||
Pathway Commons: PAFAH1B1 | ||
Metabolism | MetaCyc: PAFAH1B1 | |
HUMANCyc: PAFAH1B1 | ||
Regulation | Ensembl's Regulation: ENSG00000007168 | |
miRBase: chr17 :2,496,922-2,588,909 | ||
TargetScan: NM_000430 | ||
cisRED: ENSG00000007168 | ||
Context | iHOP: PAFAH1B1 | |
cancer metabolism search in PubMed: PAFAH1B1 | ||
UCL Cancer Institute: PAFAH1B1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PAFAH1B1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PAFAH1B1 |
Familial Cancer Database: PAFAH1B1 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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 |
Mutations for PAFAH1B1 |
* 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 | Top |
- 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 | PAFAH1B1 | chr17 | 2548765 | 2548785 | PAFAH1B1 | chr17 | 2528640 | 2528660 |
ovary | PAFAH1B1 | chr17 | 2586566 | 2586586 | PAFAH1B1 | chr17 | 2587319 | 2587339 |
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 PAFAH1B1 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 |
L25107 | PAFAH1B1 | 1 | 1322 | 17 | 2570446 | 2585537 | ADNP | 1320 | 1451 | 20 | 49508499 | 49508633 | |
AI934581 | PAFAH1B1 | 14 | 130 | 17 | 2497210 | 2541418 | ELOVL7 | 130 | 550 | 5 | 60047749 | 60048169 | |
BM969831 | PAFAH1B1 | 18 | 378 | 17 | 2588549 | 2588909 | PAFAH1B1 | 373 | 442 | 17 | 2588476 | 2588545 | |
L13387 | PRKCA | 1 | 682 | 17 | 64410407 | 64411088 | PAFAH1B1 | 683 | 2749 | 17 | 2570340 | 2586175 | |
BE768768 | ACPP | 8 | 233 | 3 | 132076886 | 132077108 | PAFAH1B1 | 232 | 301 | 17 | 2578664 | 2578733 | |
BE504849 | PAFAH1B1 | 2 | 185 | 17 | 2587611 | 2587794 | TAP1 | 178 | 570 | 6 | 4247569 | 4249586 | |
BQ372756 | ACPP | 11 | 261 | 3 | 132076858 | 132077108 | PAFAH1B1 | 260 | 329 | 17 | 2578664 | 2578733 | |
BF750913 | ATP6V0E1 | 12 | 145 | 5 | 172461667 | 172461800 | PAFAH1B1 | 134 | 245 | 17 | 2585022 | 2585134 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   |   |   |   |   | 3 |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   | 3 |   |   |   |   |   |   |   |   |   |   |
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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=22) | (# total SNVs=3) |
(# total SNVs=1) | (# total SNVs=1) |
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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 |
chr17:2570389-2570389 | p.P99L | 2 |
chr17:2570445-2570445 | p.P118S | 2 |
chr17:2570374-2570374 | p.W94* | 2 |
chr17:2583502-2583502 | p.G349G | 1 |
chr17:2568691-2568691 | p.R20C | 1 |
chr17:2576008-2576008 | p.A210P | 1 |
chr17:2583506-2583506 | p.K351E | 1 |
chr17:2568692-2568692 | p.R20H | 1 |
chr17:2570398-2570398 | p.Y102C | 1 |
chr17:2576020-2576020 | p.K214E | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 | 2 |   | 7 |   |   |   |   | 2 |   |   | 1 | 1 |   |   |   | 6 | 3 |   | 4 |
# mutation | 1 | 2 |   | 6 |   |   |   |   | 2 |   |   | 1 | 1 |   |   |   | 6 | 3 |   | 4 |
nonsynonymous SNV | 1 | 2 |   | 5 |   |   |   |   | 1 |   |   |   | 1 |   |   |   | 4 | 3 |   | 3 |
synonymous SNV |   |   |   | 1 |   |   |   |   | 1 |   |   | 1 |   |   |   |   | 2 |   |   | 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 |
chr17:2573488 | p.R144Q | 2 |
chr17:2568691 | p.Y102C | 1 |
chr17:2573468 | p.L354F | 1 |
chr17:2583502 | p.A103P | 1 |
chr17:2568692 | p.R371Q | 1 |
chr17:2583517 | p.R108R | 1 |
chr17:2569362 | p.A378A | 1 |
chr17:2575983 | p.V124I | 1 |
chr17:2583567 | p.P393L | 1 |
chr17:2569384 | p.Y137Y | 1 |
Other DBs for Point Mutations |
Copy Number for PAFAH1B1 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 PAFAH1B1 |
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. |
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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 |
AKAP11,ANKFY1,ASXL2,C17orf85,CRK,DHX33,DPP8, EXOC6B,KRBA2,METTL16,NCOR1,PAFAH1B1,PRPF8,RPA1, SMYD4,TSR1,TTBK2,UBE2G1,VPS53,ZFP3,ZZEF1 | CDC27,DNM1L,EEA1,EIF4G2,EXOC5,FBXW11,HIPK1, HIPK3,ITCH,KIF5B,LOC647979,MEF2A,NCKAP1,PAFAH1B1, PIAS2,SLC25A46,SYNJ2BP,UHRF1BP1L,USP12,USP9X,ZFP91 |
ANKFY1,C17orf85,CRK,FLII,FXR2,MAP2K4,METTL16, MYO1C,NCOR1,NDEL1,PAFAH1B1,PITPNA,PRPF8,RABEP1, RPA1,SMCR8,SMG6,SMYD4,UBE2G1,WDR81,ZBTB4 | AAK1,AFF4,C16orf72,DDX6,FBXW11,FMR1,GRB2, HEXIM1,KIF1B,LARGE,LHFPL2,PAFAH1B1,PDLIM5,PELI2, PICALM,RANBP9,RAPGEF2,SPAG9,STAU1,USP9X,ZFAND3 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for PAFAH1B1 |
There's no related Drug. |
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Cross referenced IDs for PAFAH1B1 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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