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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PCYT2 |
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Phenotypic Information for PCYT2(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PCYT2 |
Familial Cancer Database: PCYT2 |
* 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 | |
KEGG_GLYCEROPHOSPHOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: PCYT2 |
MedGen: PCYT2 (Human Medical Genetics with Condition) | |
ClinVar: PCYT2 | |
Phenotype | MGI: PCYT2 (International Mouse Phenotyping Consortium) |
PhenomicDB: PCYT2 |
Mutations for PCYT2 |
* 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 |
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'. |
- 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 | PCYT2 | chr17 | 79862377 | 79862397 | chr20 | 44733434 | 44733454 | |
ovary | PCYT2 | chr17 | 79863063 | 79863083 | MED1 | chr17 | 37586229 | 37586249 |
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 PCYT2 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 |
Other DBs for Structural Variants |
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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 |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=17) | (# total SNVs=10) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr17:79867402-79867402 | p.V56M | 3 |
chr17:79864762-79864762 | p.R184W | 2 |
chr17:79866482-79866482 | p.R123R | 2 |
chr17:79866776-79866776 | p.N106H | 1 |
chr17:79863320-79863320 | p.D303N | 1 |
chr17:79864701-79864701 | p.A204V | 1 |
chr17:79866785-79866785 | p.D103H | 1 |
chr17:79863585-79863585 | p.A288A | 1 |
chr17:79864720-79864720 | p.Q198E | 1 |
chr17:79862724-79862724 | p.R385R | 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 | 2 | 1 |   | 1 | 1 |   | 2 |   | 2 |   |   | 2 |   |   |   |   | 4 | 5 |   | 3 |
# mutation | 2 | 1 |   | 1 | 1 |   | 2 |   | 2 |   |   | 2 |   |   |   |   | 4 | 6 |   | 3 |
nonsynonymous SNV | 1 | 1 |   | 1 | 1 |   | 1 |   |   |   |   | 1 |   |   |   |   | 2 | 5 |   | 1 |
synonymous SNV | 1 |   |   |   |   |   | 1 |   | 2 |   |   | 1 |   |   |   |   | 2 | 1 |   | 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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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 |
chr17:79867402 | p.V56M,PCYT2 | 2 |
chr17:79864762 | p.N306K,PCYT2 | 1 |
chr17:79867409 | p.I83I,PCYT2 | 1 |
chr17:79864773 | p.A304A,PCYT2 | 1 |
chr17:79867430 | p.G67G,PCYT2 | 1 |
chr17:79862799 | p.F277F,PCYT2 | 1 |
chr17:79865452 | p.T58I,PCYT2 | 1 |
chr17:79867459 | p.A223S,PCYT2 | 1 |
chr17:79862805 | p.F171F,PCYT2 | 1 |
chr17:79865653 | p.I53I,PCYT2 | 1 |
Other DBs for Point Mutations |
Copy Number for PCYT2 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 PCYT2 |
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 |
ANAPC11,ARHGDIA,ARL16,ASPSCR1,C17orf89,OXLD1,CCDC137, DCXR,DUS1L,FAM195B,GPS1,HGS,LRRC45,MRPL12, MRPL38,PCYT2,RAC3,RFNG,SIRT7,SLC25A10,STRA13 | ALDH1L1,ASS1,C17orf53,IZUMO4,C20orf27,APMAP,ECHDC3, FASN,GCDH,GLUL,GLYCTK,MPST,NDRG4,PC, PCYT2,PMM1,PXMP2,RASL10B,SHMT1,SLC25A1,TMEM120A | ||||
ATP5D,UQCC3,COX8A,DCXR,DUS1L,GPS1,LRRC45, MRPL12,MRPL38,NAPRT,NDUFS8,NT5C,PCYT2,PYCR1, RFNG,RNF126,SIRT7,SLC25A10,SLC25A39,SURF2,TSEN54 | AGMAT,AIMP2,AKR7A3,DNPH1,CENPV,CISD3,COQ4, FAM195A,FAM35A,FAM35BP,HADH,IMP3,MTCH2,NDUFC2, OXNAD1,PCYT2,PRR5,SHMT1,SLC25A10,SUCLG1,TRAF4 |
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 PCYT2 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00709 | phosphate cytidylyltransferase 2, ethanolamine | approved; investigational | Lamivudine |
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Cross referenced IDs for PCYT2 |
* 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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