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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PHKA2 |
Basic gene info. | Gene symbol | PHKA2 |
Gene name | phosphorylase kinase, alpha 2 (liver) | |
Synonyms | GSD9A|PHK|PYK|PYKL|XLG|XLG2 | |
Cytomap | UCSC genome browser: Xp22.2-p22.1 | |
Genomic location | chrX :18910415-19002480 | |
Type of gene | protein-coding | |
RefGenes | NM_000292.2, | |
Ensembl id | ENSG00000044446 | |
Description | phosphorylase b kinase regulatory subunit alpha liver isoformphosphorylase b kinase regulatory subunit alpha, liver isoformphosphorylase kinase alpha L subunitphosphorylase kinase alpha-subunit | |
Modification date | 20141219 | |
dbXrefs | MIM : 300798 | |
HGNC : HGNC | ||
Ensembl : ENSG00000044446 | ||
HPRD : 02380 | ||
Vega : OTTHUMG00000021222 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PHKA2 | |
BioGPS: 5256 | ||
Gene Expression Atlas: ENSG00000044446 | ||
The Human Protein Atlas: ENSG00000044446 | ||
Pathway | NCI Pathway Interaction Database: PHKA2 | |
KEGG: PHKA2 | ||
REACTOME: PHKA2 | ||
ConsensusPathDB | ||
Pathway Commons: PHKA2 | ||
Metabolism | MetaCyc: PHKA2 | |
HUMANCyc: PHKA2 | ||
Regulation | Ensembl's Regulation: ENSG00000044446 | |
miRBase: chrX :18,910,415-19,002,480 | ||
TargetScan: NM_000292 | ||
cisRED: ENSG00000044446 | ||
Context | iHOP: PHKA2 | |
cancer metabolism search in PubMed: PHKA2 | ||
UCL Cancer Institute: PHKA2 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PHKA2(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PHKA2 |
Familial Cancer Database: PHKA2 |
* 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 | |
REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: PHKA2 |
MedGen: PHKA2 (Human Medical Genetics with Condition) | |
ClinVar: PHKA2 | |
Phenotype | MGI: PHKA2 (International Mouse Phenotyping Consortium) |
PhenomicDB: PHKA2 |
Mutations for PHKA2 |
* 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 PHKA2 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=108) | (# total SNVs=24) |
(# 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 |
chr23:18924631-18924631 | p.R930W | 3 |
chr23:18918808-18918808 | p.R1013W | 2 |
chr23:18923936-18923936 | p.D950N | 2 |
chr23:18911622-18911622 | p.S1230L | 2 |
chr23:18913297-18913297 | p.S1099A | 2 |
chr23:18959735-18959735 | p.L259R | 2 |
chr23:18938281-18938281 | p.S611L | 2 |
chr23:18959751-18959751 | p.E254* | 2 |
chr23:18912471-18912471 | p.R1130G | 2 |
chr23:18915316-18915316 | p.G1083* | 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 | 1 | 6 | 2 | 24 |   |   | 7 |   | 2 |   |   | 15 | 5 |   |   |   | 11 | 7 | 1 | 11 |
# mutation | 1 | 6 | 2 | 23 |   |   | 7 |   | 2 |   |   | 16 | 5 |   |   |   | 11 | 8 | 1 | 17 |
nonsynonymous SNV |   | 3 | 1 | 16 |   |   | 5 |   | 2 |   |   | 12 | 5 |   |   |   | 6 | 5 | 1 | 13 |
synonymous SNV | 1 | 3 | 1 | 8 |   |   | 2 |   |   |   |   | 4 |   |   |   |   | 5 | 3 |   | 4 |
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 |
chrX:18911701 | p.A1204T | 3 |
chrX:18924631 | p.S1230L | 2 |
chrX:18911622 | p.D950N | 2 |
chrX:18961840 | p.T507T | 2 |
chrX:18924858 | p.I155I | 2 |
chrX:18923936 | p.R930W | 2 |
chrX:18943834 | p.V1124V | 2 |
chrX:18912487 | p.T891M | 2 |
chrX:18966934 | p.V235V | 2 |
chrX:18944619 | p.M183I | 1 |
Other DBs for Point Mutations |
Copy Number for PHKA2 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 PHKA2 |
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 |
CTPS2,CXorf23,FAM156A,GEMIN8,HDAC6,KLHL15,LPIN3, MBTPS2,OGT,PDHA1,PHKA2,PMS2P3,PNPLA7,POLA1, TCEANC,TRAPPC2,TTLL3,TXLNG,ZNF182,ZNF491,ZRSR2 | ABCD2,ADCY6,ADIPOQ,ANO6,GPATCH11,EHHADH,GABRE, GYG2,HK2,LPL,MESTIT1,MARC1,PCYOX1,PDE3B, PDP2,PEX19,PHKA2,PRKAR2B,PTPLB,SIK2,SLC16A7 |
CASK,CCDC22,CLCN5,AMER1,GRIPAP1,HDAC6,LAS1L, NONO,OTUD5,JADE3,PHF8,PHKA2,POLA1,SCML1, TAB3,TSR2,USP27X,ZNF182,ZNF275,KRBOX4,ZNF674 | ACAD10,C11orf49,DTX4,ERBB2,FAM53B,FOXO4,INSR, KIAA0195,LRP4,MAML3,MYO1D,NDRG1,PAQR5,PFKL, PHKA2,POMT1,PRKCSH,PTPRF,SCARB1,SORL1,ZNF395 |
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 PHKA2 |
There's no related Drug. |
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Cross referenced IDs for PHKA2 |
* 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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