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: SCAP

    Description: SREBF chaperone

    Entrez Gene ID: 22937

    SwissProt Acc Number: Q12770

    RefSeq: NM_012235

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

    .."involving SREBP2,SCAP, INSIG1 and INSIG2 genes, were associated with coronary heart disease (CHD) of Chinese Han population individually or interactively."..

    From PMID: 19740467, in Journal Atherosclerosis. , 2010


    References

    There were 4 potential papers with SCAP and CHD.

    PMIDTitleJournalsDetails
    20111910 "Sterol regulatory element-binding transcription factor (SREBF)-2, SREBF cleavage-activating protein (SCAP), and premature coronary artery disease in a Chinese population."Molecular biology reportsMore Details
    19740467 Interactions among genetic variants from SREBP2 activating-related pathway on risk of coronary heart disease in Chinese Han population.AtherosclerosisMore Details
    18068195 Enhanced sterol response element-binding protein in postintervention restenotic blood vessels plays an important role in vascular smooth muscle proliferation.Life sciencesMore Details
    12436350 "Effects of SREBF-1a and SCAP polymorphisms on plasma levels of lipids, severity, progression and regression of coronary atherosclerosis and response to therapy with fluvastatin.""Journal of molecular medicine (Berlin, Germany)"More Details

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



    PPI interactions

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

    Gene nameInteraction typereference PMIDCHD relation
    SEC24B Reconstituted Complex19706601 No
    SREBF1 Affinity Capture-Western9242699 No
    SCAP in vivo15782218 CHD related
    INSIG1 Affinity Capture-Western12842885|18835813|17043353|12242332|12842885,12202038,12482938 CHD related
    INSIG2 Affinity Capture-Western16549805|12242332|12482938,12242332 No
    RNF139 Affinity Capture-Western19706601 No
    UBC Affinity Capture-MS21139048|21906983 No
    PGRMC1 in vivo15782218 No


    Involved FDA drugs

    There was no drug associated with SCAP