How to Build CHD@ZJU

CHD related Articles were retrieved from Pubmed, by entering keywords "coronary heart disease" and constrict the publish date from 2000/1/1 to now (2013/1/23). As a result, totally 115898 articles were found and their abstracts were downloaded for text mining. Since some articles didn't contain abstracts, only 88396 abstracts remained.

The text-mining process to get CHD related genes could be divided in to 5 following steps:

  • 1) Extracting all keywords from abstracts and ignoring those keywords start with numbers. 101402 keywords were extracted.

  • 2) Input these keywords into Gene library in ArrayTrack and find possible related genes. 4674 genes were then found.

  • 3) Put these 4674 genes again into pubmed abstracts to find related aticles. Only genes which offical name or there keyword description (such as prolactin for gene PRL) could be found in the abstract would be remained. As a result, 1247 genes were remained.

  • 4) Manually examined on the 1247 genes to validate it was acutally related to CHD. Some genes would be filtered if it represents other meanings (such as gene CAD, Entrez ID:790, carbamoyl-phosphate synthetase 2, is mostly meant coronary arterial disease in articles). 681 genes were then validated with at least one reference.

  • 5) All genes was compared with 1078 CHD genes in RGD database, and 370 genes were overlapped. These 370 genes were labels as "RGD_Supported" and the other 293 genes were labels as "REFERED". All 663 genes had supported references in CHD@ZJU which were examined by step 4.
  • How To contact Us

    Collaboration Information: Prof. Xiaohui Fan (fanxh@zju.edu.cn)

    Website using assistance : Leihong Wu (11019004@zju.edu.cn)



    Basic Information

    Gene Name: PDGFD

    Description: platelet derived growth factor D

    Entrez Gene ID: 80310

    SwissProt Acc Number: Q9GZP0

    RefSeq: NM_025208

    It was supported literatures to be a novel CHD related gene:

    ..The CAD-associated SNP in the PDGFD locus showed tissue-specific cis expression quantitative trait locus effects. These findings implicate new pathways for CAD susceptibility...

    From PMID: 21378988, in Journal Nat Genet. , 2011


    References

    There were 4 potential papers with PDGFD and CHD.

    PMIDTitleJournalsDetails
    23364394 A genome-wide association study of a coronary artery disease risk variant.Journal of human geneticsMore Details
    22704460 A case-control study provides evidence of association for a common SNP rs974819 in PDGFD to coronary heart disease and suggests a sex-dependent effect.Thrombosis researchMore Details
    22476029 Genome-wide studies of gene expression relevant to coronary artery disease.Current opinion in cardiologyMore Details
    21378988 A genome-wide association study in Europeans and South Asians identifies five new loci for coronary artery disease.Nature geneticsMore Details

    NOTEs: These result is mostly from TEXT-MINING and there might have mismatches.



    PPI interactions

    There were totally 2 unique genes interacted with PDGFD. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PDGFRB in vivo14514732 No
    UBC Affinity Capture-MS21890473 No


    Involved FDA drugs

    There was no drug associated with PDGFD