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: CYR61

    Description: "cysteine-rich, angiogenic inducer, 61"

    Entrez Gene ID: 3491

    SwissProt Acc Number: O00622

    RefSeq: NM_001554

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

    .."HRG may, therefore, play an important role in the development of coronary artery disease and the expansion of the atherosclerotic plaque and may locally regulate the expression of the angiogenetic factor CYR61."..

    From PMID: 16155362, in Journal J Vasc Res. , 2005


    References

    There were 2 potential papers with CYR61 and CHD.

    PMIDTitleJournalsDetails
    18505769 Serial analysis of the vascular endothelial transcriptome under static and shear stress conditions.Physiological genomicsMore Details
    16155362 Expression of heregulin in human coronary atherosclerotic lesions.Journal of vascular researchMore Details

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



    PPI interactions

    There were totally 8 unique genes interacted with CYR61. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    ITGAV Reconstituted Complex11287419 CHD related
    ITGB5 Reconstituted Complex11287419|11287419 No
    MYC Affinity Capture-MS17314511 CHD related
    ZWINT Affinity Capture-MS20360068 No
    Mis12 Affinity Capture-MS20360068 No
    UBC Affinity Capture-MS21139048 No
    YWHAZ Affinity Capture-MS17361185 No
    UBD Affinity Capture-MS22797925 No


    Involved FDA drugs

    There was no drug associated with CYR61