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: IGFBP3

    Description: insulin-like growth factor binding protein 3

    Entrez Gene ID: 3486

    SwissProt Acc Number: P17936

    RefSeq: NM_000598

    It was suspected to be CHD related:

    .."high IGFBP-1 and?IGFBP-3?were found associated with increased cardiovascular, ischaemic?heart?disease?and total mortality and incidence of?coronary?events"..

    From PMID: 18513511, in Journal Am Heart J. , 2008


    References

    There were 4 potential papers with IGFBP3 and CHD.

    PMIDTitleJournalsDetails
    22113073 Associations of IGF1 and its binding proteins with abdominal aortic aneurysm and aortic diameter in older men.European journal of endocrinology / European Federation of Endocrine SocietiesMore Details
    21046444 Are elevated levels of IGF-1 caused by coronary arteriesoclerosis?: Molecular and clinical analysis.The protein journalMore Details
    19626396 Presence of irregularity in region between -1115 and -784 nt in P1 promoter of insulin-like growth factor-1 gene may indicate beneficial effect on coronary arteries in a group of patients with stable angina: preliminary data.Heart and vesselsMore Details
    17763192 "Insulin-like growth factor (IGF)-I, IGF-II and IGF-binding protein (IGFBP)-3 levels in Arab subjects with coronary heart disease."Scandinavian journal of clinical and laboratory investigationMore Details

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



    PPI interactions

    There were totally 30 unique genes interacted with IGFBP3. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    COL1A1 Two-hybrid12735930|12735930|12735930 CHD related
    Ltbp1 Two-hybrid12962157 No
    Igf2 Two-hybrid12962157 No
    POLA2 Two-hybrid16169070|16169070 No
    GTF3C1 Two-hybrid16169070 No
    IGF1R Co-purification9389554 CHD related
    CD44 Reconstituted Complex12127836|12127836 CHD related
    FN1 Reconstituted Complex12127836|11344214|11344214|11344214|11344214 CHD related
    ADAM12 Two-hybrid10849447|10849447 CHD related
    TF Affinity Capture-Western11297622|11297622 No
    CAV1 in vitro14576164 CHD related
    F2 in vitro;in vivo8843739,7538844 CHD related
    IGF1 Reconstituted Complex12735930|10823924|9497324|11600567 CHD related
    IGF2 Reconstituted Complex11749962|9497324|10407151 CHD related
    PLG Reconstituted Complex9688635|9688635 No
    PAPPA2 Biochemical Activity11264294|11264294 No
    RXRA Reconstituted Complex10874028|10874028|10874028 CHD related
    IGFALS Reconstituted Complex9497324|9446566|9446566,9497324 CHD related
    CSNK2A1 in vitro;in vivo10650937 CHD related
    CTSG in vitro;in vivo10512690 No
    CTSD in vitro9275067 No
    CTSL1 in vitro11801256 No
    GPI in vitro15059907 No
    MMP1 in vitro7523391 CHD related
    MMP2 in vitro7523391 CHD related
    KLK3 in vitro10218588,7538844 No
    LTBP1 yeast 2-hybrid12962157 CHD related
    MMP3 in vitro7523391 CHD related
    KLKB1 in vivo10226805 No
    KPNB1 in vitro10811646 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB01277Mecasermin"For the long-term treatment of growth failure in pediatric patients with Primary IGFD or with GH gene deletion who have developed neutralizing antibodies to GH. It is not indicated to treat Secondary IGFD resulting from GH deficiency, malnutrition, hypothyroidism or other causes; it is not a substitute for GH therapy."H01AC03