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: GAP43

    Description: growth associated protein 43

    Entrez Gene ID: 2596

    SwissProt Acc Number: P17677

    RefSeq: NM_001130064

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

    ..The density of biatrial tyrosine hydroxylase (TH) and growth-associated protein43 (GAP43) nerves were 5- to 8-fold higher and were more heterogeneous in MI compared with control dogs...

    From PMID: 12835207, in Journal Circulation. , 2003


    References

    There were 4 potential papers with GAP43 and CHD.

    PMIDTitleJournalsDetails
    22001051 Acute myocardial infarction induces bilateral stellate ganglia neural remodeling in rabbits.Cardiovascular pathology : the official journal of the Society for CardiovascularMore Details
    15607663 Sympathetic nerve sprouting after orthotopic heart transplantation.The Journal of heart and lung transplantation : the official publication of theMore Details
    12714561 "Sympathetic nerve sprouting, electrical remodeling, and increased vulnerability to ventricular fibrillation in hypercholesterolemic rabbits."Circulation researchMore Details
    12835207 Altered atrial electrical restitution and heterogeneous sympathetic hyperinnervation in hearts with chronic left ventricular myocardial infarction: implications for atrial fibrillation.CirculationMore Details

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



    PPI interactions

    There were totally 8 unique genes interacted with GAP43. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PLCD1 Affinity Capture-Western12805215 CHD related
    RABEP1 Reconstituted Complex9742146 No
    CALM1 Two-hybrid8872303|8900147|12805215,8900147 No
    ELAVL4 in vitro12034726 No
    CSNK2A1 in vitro1828073 CHD related
    PRKCD in vitro;in vivo9139733 CHD related
    PRKCB in vitro8694767,2140056 CHD related
    SPTAN1 in vivo10521589 No


    Involved FDA drugs

    There was no drug associated with GAP43