Atlas of Genetics and Cytogenetics in Oncology and Haematology


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PDGFA (platelet derived growth factor subunit A)

Identity

Alias_namesplatelet-derived growth factor alpha polypeptide
Alias_symbol (synonym)PDGF1
PDGF-A
Other alias
HGNC (Hugo) PDGFA
LocusID (NCBI) 5154
Atlas_Id 41679
Location 7p22.3  [Link to chromosome band 7p22]
Location_base_pair Starts at 536897 and ends at 559481 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
PDGFA (7p22.3) / NT5C3A (7p14.3)PDGFA 7p22.3 NT5C3

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  idic(7)(q11.2)
t(5;16)(q32;p13) NDE1/PDGFRB


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 2 ]
  Gastric Tumors: an overview
Kidney: Nephroblastoma (Wilms tumor)


External links

Nomenclature
HGNC (Hugo)PDGFA   8799
Cards
Entrez_Gene (NCBI)PDGFA  5154  platelet derived growth factor subunit A
AliasesPDGF-A; PDGF1
GeneCards (Weizmann)PDGFA
Ensembl hg19 (Hinxton)ENSG00000197461 [Gene_View]  chr7:536897-559481 [Contig_View]  PDGFA [Vega]
Ensembl hg38 (Hinxton)ENSG00000197461 [Gene_View]  chr7:536897-559481 [Contig_View]  PDGFA [Vega]
ICGC DataPortalENSG00000197461
TCGA cBioPortalPDGFA
AceView (NCBI)PDGFA
Genatlas (Paris)PDGFA
WikiGenes5154
SOURCE (Princeton)PDGFA
Genetics Home Reference (NIH)PDGFA
Genomic and cartography
GoldenPath hg19 (UCSC)PDGFA  -     chr7:536897-559481 -  7p22.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)PDGFA  -     7p22.3   [Description]    (hg38-Dec_2013)
EnsemblPDGFA - 7p22.3 [CytoView hg19]  PDGFA - 7p22.3 [CytoView hg38]
Mapping of homologs : NCBIPDGFA [Mapview hg19]  PDGFA [Mapview hg38]
OMIM173430   
Gene and transcription
Genbank (Entrez)A09204 AB451309 AB451439 AK292217 AU118732
RefSeq transcript (Entrez)NM_002607 NM_033023
RefSeq genomic (Entrez)NC_000007 NC_018918 NG_029727 NT_007819 NW_004929329
Consensus coding sequences : CCDS (NCBI)PDGFA
Cluster EST : UnigeneHs.535898 [ NCBI ]
CGAP (NCI)Hs.535898
Alternative Splicing GalleryENSG00000197461
Gene ExpressionPDGFA [ NCBI-GEO ]   PDGFA [ EBI - ARRAY_EXPRESS ]   PDGFA [ SEEK ]   PDGFA [ MEM ]
Gene Expression Viewer (FireBrowse)PDGFA [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5154
GTEX Portal (Tissue expression)PDGFA
Protein : pattern, domain, 3D structure
UniProt/SwissProtP04085   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP04085  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP04085
Splice isoforms : SwissVarP04085
PhosPhoSitePlusP04085
Domaine pattern : Prosite (Expaxy)PDGF_1 (PS00249)    PDGF_2 (PS50278)   
Domains : Interpro (EBI)Cystine-knot_cytokine    PD_growth_factor_CS    PDGF/VEGF_dom    PDGF_N   
Domain families : Pfam (Sanger)PDGF (PF00341)    PDGF_N (PF04692)   
Domain families : Pfam (NCBI)pfam00341    pfam04692   
Domain families : Smart (EMBL)PDGF (SM00141)  
Conserved Domain (NCBI)PDGFA
DMDM Disease mutations5154
Blocks (Seattle)PDGFA
PDB (SRS)3MJK   
PDB (PDBSum)3MJK   
PDB (IMB)3MJK   
PDB (RSDB)3MJK   
Structural Biology KnowledgeBase3MJK   
SCOP (Structural Classification of Proteins)3MJK   
CATH (Classification of proteins structures)3MJK   
SuperfamilyP04085
Human Protein AtlasENSG00000197461
Peptide AtlasP04085
HPRD01424
IPIIPI00021833   IPI00220454   IPI00655954   IPI00816049   IPI00022037   IPI00892963   IPI00787244   IPI00892738   
Protein Interaction databases
DIP (DOE-UCLA)P04085
IntAct (EBI)P04085
FunCoupENSG00000197461
BioGRIDPDGFA
STRING (EMBL)PDGFA
ZODIACPDGFA
Ontologies - Pathways
QuickGOP04085
Ontology : AmiGOGolgi membrane  MAPK cascade  angiogenesis  response to hypoxia  cell activation  hair follicle development  positive regulation of mesenchymal cell proliferation  platelet degranulation  Ras guanyl-nucleotide exchange factor activity  platelet-derived growth factor receptor binding  platelet-derived growth factor receptor binding  protein binding  collagen binding  extracellular region  extracellular space  endoplasmic reticulum lumen  microvillus  transforming growth factor beta receptor signaling pathway  cell-cell signaling  growth factor activity  positive regulation of cell proliferation  response to wounding  organ morphogenesis  cell surface  response to inorganic substance  negative regulation of phosphatidylinositol biosynthetic process  negative regulation of platelet activation  regulation of phosphatidylinositol 3-kinase signaling  positive regulation of phosphatidylinositol 3-kinase signaling  regulation of smooth muscle cell migration  cell projection assembly  actin cytoskeleton organization  extracellular matrix organization  positive regulation of cell migration  platelet alpha granule lumen  positive regulation of protein autophosphorylation  response to estradiol  response to retinoic acid  regulation of actin cytoskeleton organization  positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway  wound healing  response to drug  protein homodimerization activity  positive regulation of MAP kinase activity  positive regulation of MAPK cascade  positive regulation of GTPase activity  skin development  positive regulation of DNA replication  phosphatidylinositol phosphorylation  phosphatidylinositol-4,5-bisphosphate 3-kinase activity  protein heterodimerization activity  platelet-derived growth factor receptor signaling pathway  phosphatidylinositol-mediated signaling  positive regulation of fibroblast proliferation  lung alveolus development  platelet-derived growth factor binding  inner ear development  regulation of peptidyl-tyrosine phosphorylation  negative chemotaxis  positive regulation of cell division  positive regulation of protein kinase B signaling  regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling  positive regulation of ERK1 and ERK2 cascade  regulation of glomerular mesangial cell proliferation  embryonic lung development  regulation of DNA biosynthetic process  
Ontology : EGO-EBIGolgi membrane  MAPK cascade  angiogenesis  response to hypoxia  cell activation  hair follicle development  positive regulation of mesenchymal cell proliferation  platelet degranulation  Ras guanyl-nucleotide exchange factor activity  platelet-derived growth factor receptor binding  platelet-derived growth factor receptor binding  protein binding  collagen binding  extracellular region  extracellular space  endoplasmic reticulum lumen  microvillus  transforming growth factor beta receptor signaling pathway  cell-cell signaling  growth factor activity  positive regulation of cell proliferation  response to wounding  organ morphogenesis  cell surface  response to inorganic substance  negative regulation of phosphatidylinositol biosynthetic process  negative regulation of platelet activation  regulation of phosphatidylinositol 3-kinase signaling  positive regulation of phosphatidylinositol 3-kinase signaling  regulation of smooth muscle cell migration  cell projection assembly  actin cytoskeleton organization  extracellular matrix organization  positive regulation of cell migration  platelet alpha granule lumen  positive regulation of protein autophosphorylation  response to estradiol  response to retinoic acid  regulation of actin cytoskeleton organization  positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway  wound healing  response to drug  protein homodimerization activity  positive regulation of MAP kinase activity  positive regulation of MAPK cascade  positive regulation of GTPase activity  skin development  positive regulation of DNA replication  phosphatidylinositol phosphorylation  phosphatidylinositol-4,5-bisphosphate 3-kinase activity  protein heterodimerization activity  platelet-derived growth factor receptor signaling pathway  phosphatidylinositol-mediated signaling  positive regulation of fibroblast proliferation  lung alveolus development  platelet-derived growth factor binding  inner ear development  regulation of peptidyl-tyrosine phosphorylation  negative chemotaxis  positive regulation of cell division  positive regulation of protein kinase B signaling  regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling  positive regulation of ERK1 and ERK2 cascade  regulation of glomerular mesangial cell proliferation  embryonic lung development  regulation of DNA biosynthetic process  
Pathways : BIOCARTAMechanism of Gene Regulation by Peroxisome Proliferators via PPARa(alpha) [Genes]    PDGF Signaling Pathway [Genes]    Cytokines and Inflammatory Response [Genes]    Phospholipids as signalling intermediaries [Genes]   
Pathways : KEGGMAPK signaling pathway    Ras signaling pathway    Rap1 signaling pathway    Cytokine-cytokine receptor interaction    PI3K-Akt signaling pathway    Focal adhesion    Gap junction    Regulation of actin cytoskeleton    HTLV-I infection    Pathways in cancer    Transcriptional misregulation in cancer    MicroRNAs in cancer    Glioma    Prostate cancer    Melanoma   
NDEx NetworkPDGFA
Atlas of Cancer Signalling NetworkPDGFA
Wikipedia pathwaysPDGFA
Orthology - Evolution
OrthoDB5154
GeneTree (enSembl)ENSG00000197461
Phylogenetic Trees/Animal Genes : TreeFamPDGFA
HOVERGENP04085
HOGENOMP04085
Homologs : HomoloGenePDGFA
Homology/Alignments : Family Browser (UCSC)PDGFA
Gene fusions - Rearrangements
Fusion : MitelmanPDGFA/NT5C3A [7p22.3/7p14.3]  
Fusion: TCGAPDGFA 7p22.3 NT5C3 BRCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPDGFA [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PDGFA
dbVarPDGFA
ClinVarPDGFA
1000_GenomesPDGFA 
Exome Variant ServerPDGFA
ExAC (Exome Aggregation Consortium)PDGFA (select the gene name)
Genetic variants : HAPMAP5154
Genomic Variants (DGV)PDGFA [DGVbeta]
DECIPHER (Syndromes)7:536897-559481  ENSG00000197461
CONAN: Copy Number AnalysisPDGFA 
Mutations
ICGC Data PortalPDGFA 
TCGA Data PortalPDGFA 
Broad Tumor PortalPDGFA
OASIS PortalPDGFA [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPDGFA  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPDGFA
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch PDGFA
DgiDB (Drug Gene Interaction Database)PDGFA
DoCM (Curated mutations)PDGFA (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PDGFA (select a term)
intoGenPDGFA
Cancer3DPDGFA(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM173430   
Orphanet
MedgenPDGFA
Genetic Testing Registry PDGFA
NextProtP04085 [Medical]
TSGene5154
GENETestsPDGFA
Huge Navigator PDGFA [HugePedia]
snp3D : Map Gene to Disease5154
BioCentury BCIQPDGFA
ClinGenPDGFA
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5154
Chemical/Pharm GKB GenePA33144
Clinical trialPDGFA
Miscellaneous
canSAR (ICR)PDGFA (select the gene name)
Probes
Litterature
PubMed139 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePDGFA
EVEXPDGFA
GoPubMedPDGFA
iHOPPDGFA
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Thu Mar 30 15:13:53 CEST 2017

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