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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PIKFYVE |
Basic gene info. | Gene symbol | PIKFYVE |
Gene name | phosphoinositide kinase, FYVE finger containing | |
Synonyms | CFD|FAB1|HEL37|PIP5K|PIP5K3|ZFYVE29 | |
Cytomap | UCSC genome browser: 2q34 | |
Genomic location | chr2 :209130990-209170271 | |
Type of gene | protein-coding | |
RefGenes | NM_001178000.1, NM_015040.3,NM_152671.3,NM_001002881.1, | |
Ensembl id | ENSG00000115020 | |
Description | 1-phosphatidylinositol 3-phosphate 5-kinase1-phosphatidylinositol-3-phosphate 5-kinasePIPkin-IIIepididymis luminal protein 37phosphatidylinositol 3-phosphate 5-kinase type IIIphosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type IIIty | |
Modification date | 20141207 | |
dbXrefs | MIM : 609414 | |
HGNC : HGNC | ||
Ensembl : ENSG00000115020 | ||
HPRD : 17852 | ||
Vega : OTTHUMG00000132945 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PIKFYVE | |
BioGPS: 200576 | ||
Gene Expression Atlas: ENSG00000115020 | ||
The Human Protein Atlas: ENSG00000115020 | ||
Pathway | NCI Pathway Interaction Database: PIKFYVE | |
KEGG: PIKFYVE | ||
REACTOME: PIKFYVE | ||
ConsensusPathDB | ||
Pathway Commons: PIKFYVE | ||
Metabolism | MetaCyc: PIKFYVE | |
HUMANCyc: PIKFYVE | ||
Regulation | Ensembl's Regulation: ENSG00000115020 | |
miRBase: chr2 :209,130,990-209,170,271 | ||
TargetScan: NM_001178000 | ||
cisRED: ENSG00000115020 | ||
Context | iHOP: PIKFYVE | |
cancer metabolism search in PubMed: PIKFYVE | ||
UCL Cancer Institute: PIKFYVE | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PIKFYVE(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PIKFYVE |
Familial Cancer Database: PIKFYVE |
* 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 | |
KEGG_INOSITOL_PHOSPHATE_METABOLISM KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_PI_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Mutations for PIKFYVE |
* 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 PIKFYVE 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 |
AA578440 | PIKFYVE | 8 | 58 | 2 | 209221813 | 209221863 | PIKFYVE | 54 | 309 | 2 | 209221563 | 209221818 | |
BX640810 | PIKFYVE | 4 | 2651 | 2 | 209184109 | 209186753 | SMR3B | 2647 | 3011 | 4 | 71255597 | 71255961 |
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 | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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=188) | (# total SNVs=47) |
(# total SNVs=2) | (# 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 |
chr2:209177007-209177007 | p.A562T | 3 |
chr2:209191056-209191056 | p.K1174M | 3 |
chr2:209185035-209185035 | p.L714L | 3 |
chr2:209190697-209190697 | p.L1054L | 3 |
chr2:209218727-209218727 | p.R1984* | 3 |
chr2:209136403-209136403 | p.R54C | 3 |
chr2:209188947-209188947 | p.R758W | 2 |
chr2:209209849-209209849 | p.R1681Q | 2 |
chr2:209191017-209191017 | p.R1161I | 2 |
chr2:209190652-209190652 | p.K1039K | 2 |
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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 | 5 | 9 |   | 33 | 3 |   | 8 |   | 7 |   |   | 22 | 14 | 6 |   | 3 | 18 | 10 |   | 28 |
# mutation | 6 | 9 |   | 41 | 3 |   | 8 |   | 7 |   |   | 27 | 16 | 6 |   | 3 | 24 | 13 |   | 42 |
nonsynonymous SNV | 5 | 6 |   | 31 | 3 |   | 6 |   | 6 |   |   | 16 | 12 | 6 |   | 3 | 16 | 7 |   | 34 |
synonymous SNV | 1 | 3 |   | 11 |   |   | 2 |   | 1 |   |   | 11 | 4 |   |   |   | 8 | 6 |   | 8 |
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 |
chr2:209204148 | p.R1560H | 3 |
chr2:209195376 | p.R758W | 2 |
chr2:209188947 | p.R1161I | 2 |
chr2:209190805 | p.G789C | 2 |
chr2:209189668 | p.K1039N | 2 |
chr2:209190652 | p.T800T | 2 |
chr2:209177007 | p.L1090L | 2 |
chr2:209189703 | p.L252V,PIKFYVE | 2 |
chr2:209191017 | p.Q1307H | 2 |
chr2:209163498 | p.A562T | 2 |
Other DBs for Point Mutations |
Copy Number for PIKFYVE 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 PIKFYVE |
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 |
ASXL2,BIRC6,BMPR2,BOD1L1,ERCC6L2,CREB1,FAM126B, INO80D,KIAA1109,MAP3K2,NBEAL1,NR2C2,PIKFYVE,RIF1, SETX,SON,TRIP12,TTBK2,USP34,ZNF699,ZNF81 | AKAP11,ANKIB1,ATP11B,DICER1,DMXL1,AGO3,FRYL, GAPVD1,HELZ,HOOK3,RIC1,MAP3K2,PBRM1,PCNX, PIK3C2A,PIKFYVE,PKN2,RC3H2,SECISBP2L,UBE4A,VPS13C |
ASXL2,ATAD2B,ATM,BIRC6,CBL,CLASP1,HERC1, ITSN2,NR2C2,PIKFYVE,PLEKHM3,SF3B1,SHPRH,SOS1, TAOK1,TET3,TRIP12,TTBK2,UBXN7,USP34,ZKSCAN8 | BRWD1,BTAF1,CHD9,DMXL2,DOPEY1,HELZ,MED13L, KMT2C,NKTR,PIKFYVE,PRDM2,RBM33,RBM6,RPL32P3, SMG1,TNKS2,TRIM52,USP34,ZC3H11A,ZNF236,ZSCAN29 |
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 PIKFYVE |
There's no related Drug. |
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Cross referenced IDs for PIKFYVE |
* 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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