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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PAFAH2 |
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Phenotypic Information for PAFAH2(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: PAFAH2 |
Familial Cancer Database: PAFAH2 |
* 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/ |
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Nat Rev Drug Discovery, 2013, 12: 829, doi: 10.1038/nrd4145 |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: PAFAH2 |
MedGen: PAFAH2 (Human Medical Genetics with Condition) | |
ClinVar: PAFAH2 | |
Phenotype | MGI: PAFAH2 (International Mouse Phenotyping Consortium) |
PhenomicDB: PAFAH2 |
Mutations for PAFAH2 |
* 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. |
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- Statistics for Tissue and Mutation type | Top |
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- For Inter-chromosomal Variations |
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'. |
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- For Intra-chromosomal Variations |
There's no intra-chromosomal structural variation. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
pancreas | PAFAH2 | chr1 | 26304802 | 26304822 | chr11 | 87519189 | 87519209 |
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) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PAFAH2 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 |
AI218124 | C20orf62 | 24 | 351 | 20 | 43090411 | 43090738 | PAFAH2 | 349 | 546 | 1 | 26299106 | 26301071 | |
AW449898 | ROBO2 | 206 | 227 | 3 | 76950568 | 76950589 | PAFAH2 | 225 | 411 | 1 | 26287619 | 26287805 | |
AK129536 | ZEB2 | 1 | 351 | 2 | 145267236 | 145267586 | PAFAH2 | 346 | 1590 | 1 | 26286260 | 26287504 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=23) | (# total SNVs=9) |
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(# total SNVs=0) | (# total SNVs=1) |
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* 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 |
chr1:26315958-26315958 | p.L75L | 2 |
chr1:26315993-26315993 | p.E64K | 2 |
chr1:26311004-26311004 | p.A119A | 2 |
chr1:26314754-26314754 | p.L103F | 2 |
chr1:26301136-26301136 | p.A255V | 1 |
chr1:26317306-26317306 | p.? | 1 |
chr1:26310483-26310483 | p.R169H | 1 |
chr1:26288568-26288568 | p.K364T | 1 |
chr1:26314809-26314809 | p.R85H | 1 |
chr1:26303174-26303174 | p.R253W | 1 |
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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 |   |   | 8 | 1 |   | 1 |   | 2 |   |   | 3 |   | 2 |   |   | 6 | 1 |   | 2 |
# mutation | 1 |   |   | 8 | 2 |   | 1 |   | 2 |   |   | 3 |   | 2 |   |   | 6 | 1 |   | 3 |
nonsynonymous SNV | 1 |   |   | 5 | 1 |   | 1 |   | 2 |   |   | 3 |   | 2 |   |   | 2 | 1 |   | 1 |
synonymous SNV |   |   |   | 3 | 1 |   |   |   |   |   |   |   |   |   |   |   | 4 |   |   | 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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* 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 |
chr1:26311004 | p.A119A | 2 |
chr1:26303246 | p.V350I | 1 |
chr1:26314785 | p.A142S | 1 |
chr1:26299085 | p.P342P | 1 |
chr1:26303254 | p.R127C | 1 |
chr1:26314809 | p.S316S | 1 |
chr1:26299107 | p.F120L | 1 |
chr1:26310447 | p.S316N | 1 |
chr1:26315944 | p.H301Q | 1 |
chr1:26299185 | p.L103F | 1 |
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* 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. |
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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 PAFAH2 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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SMIM14,DNAJC16,EIF4G3,FBXL5,HMGCL,KIAA0232,KIAA0319L, LRBA,LRRFIP1,PAFAH2,PDIK1L,PDPK1,PIGV,RBM47, RSC1A1,SPG11,TBC1D9,TMBIM6,TMEM57,VPS13D,WDR31 | AP1M2,ARSD,ASTN2,C9orf152,CAPN13,CORO2A,CYP2J2, DLG3,EPCAM,ETNK2,FAM174B,ILDR1,KIAA0319L,LEO1, PAFAH2,PPM1H,SLC38A1,SLC39A11,STYK1,TMEM63C,ZNF652 |
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ABCD3,ABHD3,ATP8B1,BCAS1,STPG1,C1orf210,C4orf19, CDS1,CPT2,DHDDS,FUCA1,GGT6,GPA33,HMGCL, NR3C2,PAFAH2,RBM47,RPS6KA1,SLC35A3,SULT1B1,TSPAN1 | ACADS,ACSF2,AP1M2,KDF1,C1orf210,CBLC,CPT2, EPB41L4B,ESRRA,GPBP1L1,HDHD3,KLC4,LCMT1,MARVELD3, NAT2,PAFAH2,PROSC,SH3BGRL2,SLC35D2,STAP2,TMEM144 |
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* 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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Pharmacological Information for PAFAH2 |
There's no related Drug. |
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Cross referenced IDs for PAFAH2 |
* 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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