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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PLD4 |
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Phenotypic Information for PLD4(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PLD4 |
Familial Cancer Database: PLD4 |
* This gene is included in those cancer gene databases. |
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 | |
REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: PLD4 |
MedGen: PLD4 (Human Medical Genetics with Condition) | |
ClinVar: PLD4 | |
Phenotype | MGI: PLD4 (International Mouse Phenotyping Consortium) |
PhenomicDB: PLD4 |
Mutations for PLD4 |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PLD4 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=24) | (# total SNVs=8) |
(# total SNVs=1) | (# 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 |
chr14:105397224-105397224 | p.R271H | 3 |
chr14:105396392-105396392 | p.R206W | 2 |
chr14:105395273-105395273 | p.? | 2 |
chr14:105394092-105394092 | p.P41L | 1 |
chr14:105398382-105398382 | p.A347A | 1 |
chr14:105396340-105396340 | p.M188I | 1 |
chr14:105397102-105397102 | p.I230I | 1 |
chr14:105394151-105394151 | p.P61S | 1 |
chr14:105398383-105398383 | p.A348S | 1 |
chr14:105396341-105396341 | p.G189W | 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 | 3 |   |   | 2 | 3 |   |   |   | 1 |   |   | 4 | 4 |   |   |   | 3 | 2 |   | 3 |
# mutation | 3 |   |   | 2 | 3 |   |   |   | 1 |   |   | 4 | 4 |   |   |   | 4 | 2 |   | 3 |
nonsynonymous SNV | 1 |   |   | 1 | 2 |   |   |   | 1 |   |   | 2 | 3 |   |   |   | 3 | 1 |   | 2 |
synonymous SNV | 2 |   |   | 1 | 1 |   |   |   |   |   |   | 2 | 1 |   |   |   | 1 | 1 |   | 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 |
chr14:105395177 | p.P78S | 1 |
chr14:105397224 | p.S330S | 1 |
chr14:105399118 | p.L126V | 1 |
chr14:105395231 | p.A331T | 1 |
chr14:105397232 | p.G144W | 1 |
chr14:105399139 | p.A365S | 1 |
chr14:105395257 | p.S152S | 1 |
chr14:105397263 | p.F367L | 1 |
chr14:105399197 | p.V219A | 1 |
chr14:105396381 | p.R372R | 1 |
Other DBs for Point Mutations |
Copy Number for PLD4 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 PLD4 |
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 |
ABI3,CCDC88B,EBI3,GAPT,GIMAP1,HLA-DPB1,HMHA1, PALD1,LAT2,LY86,LYL1,MFNG,MYO1F,NAPSB, P2RY13,PLD4,PRAM1,RASAL3,SELPLG,SNAI3,TNFSF12 | ACTL10,CAPN1,CARD9,DEF6,GRK6,IL27RA,IL34, MICALL2,NFKBIE,PITPNM1,PLD4,PLEKHN1,RELB,RHBDF2, SEPT9,SH3BP1,SPNS3,ST14,SYTL1,TMEM102,YDJC |
AMICA1,ARHGAP15,DCANP1,CCR4,CD1C,CD1E,CD200R1, CLEC10A,CX3CR1,CXorf21,CYSLTR1,DOCK10,FCER1A,GAPT, LSP1,NAPSB,P2RY12,PLD4,PTGDS,SCN4B,TLR7 | SOWAHD,BTN1A1,CD207,CD27,CYFIP2,GPR114,GPR18, HLA-DPB2,HMHA1,ICAM3,LY9,P2RY10,PLD4,PTPN6, RHOH,RUNX3,SIGLEC10,SYK,TEC,TMEM156,ZNF180 |
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 PLD4 |
There's no related Drug. |
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Cross referenced IDs for PLD4 |
* 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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