|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PRKAB1 |
Basic gene info. | Gene symbol | PRKAB1 |
Gene name | protein kinase, AMP-activated, beta 1 non-catalytic subunit | |
Synonyms | AMPK|HAMPKb | |
Cytomap | UCSC genome browser: 12q24.1-q24.3 | |
Genomic location | chr12 :120105760-120119429 | |
Type of gene | protein-coding | |
RefGenes | NM_006253.4, | |
Ensembl id | ENSG00000111725 | |
Description | 5'-AMP-activated protein kinase beta-1 subunit5'-AMP-activated protein kinase subunit beta-1AMP-activated protein kinase beta subunitAMPK beta -1 chainAMPK beta 1AMPK subunit beta-1AMPKbprotein kinase, AMP-activated, noncatalytic, beta-1 | |
Modification date | 20141207 | |
dbXrefs | MIM : 602740 | |
HGNC : HGNC | ||
Ensembl : ENSG00000111725 | ||
HPRD : 04116 | ||
Vega : OTTHUMG00000168954 | ||
Protein | UniProt: Q9Y478 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PRKAB1 | |
BioGPS: 5564 | ||
Gene Expression Atlas: ENSG00000111725 | ||
The Human Protein Atlas: ENSG00000111725 | ||
Pathway | NCI Pathway Interaction Database: PRKAB1 | |
KEGG: PRKAB1 | ||
REACTOME: PRKAB1 | ||
ConsensusPathDB | ||
Pathway Commons: PRKAB1 | ||
Metabolism | MetaCyc: PRKAB1 | |
HUMANCyc: PRKAB1 | ||
Regulation | Ensembl's Regulation: ENSG00000111725 | |
miRBase: chr12 :120,105,760-120,119,429 | ||
TargetScan: NM_006253 | ||
cisRED: ENSG00000111725 | ||
Context | iHOP: PRKAB1 | |
cancer metabolism search in PubMed: PRKAB1 | ||
UCL Cancer Institute: PRKAB1 | ||
Assigned class in ccmGDB | B - This gene belongs to cancer gene. |
Top |
Phenotypic Information for PRKAB1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PRKAB1 |
Familial Cancer Database: PRKAB1 |
* 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 | |
Nat Rev Drug Discovery, 2013, 12: 829, doi: 10.1038/nrd4145 |
Others | |
OMIM | 602740; gene. |
Orphanet | |
Disease | KEGG Disease: PRKAB1 |
MedGen: PRKAB1 (Human Medical Genetics with Condition) | |
ClinVar: PRKAB1 | |
Phenotype | MGI: PRKAB1 (International Mouse Phenotyping Consortium) |
PhenomicDB: PRKAB1 |
Mutations for PRKAB1 |
* 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 PRKAB1 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 |
Top |
Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
Top |
SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
|
Top |
Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=19) | (# total SNVs=8) |
(# total SNVs=0) | (# total SNVs=2) |
Top |
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 |
chr12:120114410-120114410 | p.R201W | 2 |
chr12:120106082-120106082 | p.L11L | 2 |
chr12:120117793-120117793 | p.A241V | 2 |
chr12:120110208-120110208 | p.G88R | 2 |
chr12:120106160-120106160 | p.L37L | 2 |
chr12:120110270-120110270 | p.? | 1 |
chr12:120114386-120114386 | p.V193I | 1 |
chr12:120106178-120106178 | p.D43D | 1 |
chr12:120111817-120111817 | p.Q124H | 1 |
chr12:120114396-120114397 | p.P196L | 1 |
Top |
SNV Counts per Each Loci in TCGA data |
|
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 |   | 5 |   |   | 2 |   |   |   |   | 3 |   |   |   |   | 1 | 2 |   | 7 |
# mutation | 2 | 1 |   | 5 |   |   | 2 |   |   |   |   | 3 |   |   |   |   | 1 | 2 |   | 8 |
nonsynonymous SNV |   | 1 |   | 4 |   |   | 2 |   |   |   |   | 1 |   |   |   |   | 1 | 2 |   | 6 |
synonymous SNV | 2 |   |   | 1 |   |   |   |   |   |   |   | 2 |   |   |   |   |   |   |   | 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]) |
Top |
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 |
chr12:120110208 | p.L37L | 2 |
chr12:120117793 | p.A241V | 2 |
chr12:120106160 | p.G88R | 2 |
chr12:120114410 | p.N110S | 1 |
chr12:120117782 | p.E120Q | 1 |
chr12:120110257 | p.Q124H | 1 |
chr12:120111774 | p.E139D | 1 |
chr12:120118103 | p.I152I | 1 |
chr12:120106129 | p.D175N | 1 |
chr12:120111803 | p.G27D | 1 |
Other DBs for Point Mutations |
Copy Number for PRKAB1 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] |
Top |
Gene Expression for PRKAB1 |
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)) |
Top |
CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
Top |
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 |
ANKRA2,APH1B,C12orf43,C12orf76,COQ5,DAZAP2,DNALI1, FAM47E,KCNJ11,MLPH,P2RX4,PCBD2,PRKAB1,RNF10, SUOX,TCTN1,TCTN2,TMEM116,TTC8,UBE3B,USP30 | BCL2L1,AAR2,CCDC115,GLOD4,CERS5,LHPP,MANBAL, MESDC2,PDCD6,PDIA3,POLR2G,PRKAB1,PSME1,RHBDD2, RPN1,STX5,TBL2,TMEM179B,TSPAN31,UFC1,WDR61 | ||||
ACOX1,ACVR1B,CD24,CDX2,COG1,ENPP5,GPR160, HOXB9,IHH,MANSC1,NUDT4,PCTP,PRKAB1,PRR15, RAB5B,RXFP4,SHROOM1,SPAG1,USP30,WIPI1,WNK4 | ADORA3,B4GALNT2,LINC01559,PPP1R36,SETD9,CELA3B,DEFB1, FAM195A,FAM45B,FUCA1,GDE1,LOC100216001,NMNAT1,NRAS, PHYH,PRKAB1,PTGER2,SPAG4,SRI,UOX,YBX2 |
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 |
Top |
Interacting Genes (from Pathway Commons) |
Top |
Pharmacological Information for PRKAB1 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Chemistry | BindingDB | Q9Y478; -. |
Chemistry | ChEMBL | CHEMBL2096907; -. |
Organism-specific databases | PharmGKB | PA33746; -. |
Organism-specific databases | CTD | 5564; -. |
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 |
DB00131 | protein kinase, AMP-activated, beta 1 non-catalytic subunit | approved; nutraceutical | Adenosine monophosphate | ||
DB00331 | protein kinase, AMP-activated, beta 1 non-catalytic subunit | approved | Metformin | ||
DB00877 | protein kinase, AMP-activated, beta 1 non-catalytic subunit | approved; investigational | Sirolimus | ||
DB00171 | protein kinase, AMP-activated, beta 1 non-catalytic subunit | approved; nutraceutical | Adenosine triphosphate | ||
DB00412 | protein kinase, AMP-activated, beta 1 non-catalytic subunit | approved; investigational | Rosiglitazone | ||
DB01132 | protein kinase, AMP-activated, beta 1 non-catalytic subunit | approved; investigational | Pioglitazone |
Top |
Cross referenced IDs for PRKAB1 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |