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: NF1

    Description: neurofibromin 1

    Entrez Gene ID: 4763

    SwissProt Acc Number: P21359

    RefSeq: NM_000267

    It was suspected to be CHD related:

    ..Our results demonstrate a regulatory role for Nf1 during epicardial EMT and provide insights into the susceptibility of patients with disrupted NF1 signaling to cardiovascular disease...

    From PMID: 22535408, in Journal Development , 2012


    References

    There were 3 potential papers with NF1 and CHD.

    PMIDTitleJournalsDetails
    22535408 Nf1 limits epicardial derivative expansion by regulating epithelial to mesenchymal transition and proliferation."Development (Cambridge, England)"More Details
    20130469 Genetic variants promoting smooth muscle cell proliferation can result in diffuse and diverse vascular diseases: evidence for a hyperplastic vasculomyopathy.Genetics in medicine : official journal of the American College of MedicalMore Details
    17095352 Sudden cardiac death in young children with neurofibromatosis type 1.The Journal of pediatricsMore Details

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



    PPI interactions

    There were totally 20 unique genes interacted with NF1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SMAD4 Affinity Capture-Western18215124 No
    VCP Affinity Capture-Western22105171|22105171 No
    NSFL1C Affinity Capture-Western22105171 No
    TBPL1 in vivo15767669 No
    APP in vivo16374483 No
    SDC2 in vitro;in vivo;yeast 2-hybrid11356864 No
    MYOG Reconstituted Complex1329097 No
    HRAS Two-hybrid8628317|8628317 No
    SMARCA4 Affinity Capture-Western15999204 No
    POLR2A Affinity Capture-Western15999204 No
    SMAD2 Reconstituted Complex18215124 CHD related
    SMAD3 Reconstituted Complex18215124 CHD related
    TIRAP Affinity Capture-MS21903422 No
    UBC Affinity Capture-MS21139048|21890473 No
    SIRT7 Affinity Capture-MS22586326 No
    MIS12 Co-purification21199919 No
    NSL1 Affinity Capture-Western21199919 No
    GRIN2D in vivo10862698 No
    DNAJC7 in vivo8836031 No
    GRIN1 in vivo10862698 No


    Involved FDA drugs

    There was no drug associated with NF1