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: FGF1

    Description: fibroblast growth factor 1 (acidic)

    Entrez Gene ID: 2246

    SwissProt Acc Number: P05230

    RefSeq: NM_000800

    It was suspected to be CHD related:

    ..Autologous transplantation of EPCs encoding FGF1 gene promotes neovascularization in a porcine model of chronic myocardial ischemia...

    From PMID: 19181401, in Journal Int J Cardiol.? , 2009


    References

    There were 2 potential papers with FGF1 and CHD.

    PMIDTitleJournalsDetails
    19181401 Autologous transplantation of EPCs encoding FGF1 gene promotes neovascularization in a porcine model of chronic myocardial ischemia.International journal of cardiologyMore Details
    12907464 Ethanol inhibits fibroblast growth factor-induced proliferation of aortic smooth muscle cells."Arteriosclerosis, thrombosis, and vascular biology"More Details

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



    PPI interactions

    There were totally 15 unique genes interacted with FGF1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CSNK2B Affinity Capture-MS12145206|12145206|12145206 No
    CSNK2A1 Reconstituted Complex12145206|12145206 CHD related
    CSNK2A2 Reconstituted Complex12145206|12145206 No
    FGFR2 Co-crystal Structure10618369|11069186 No
    HSPA9 Affinity Capture-MS10510314|10510314|10510314|10510314 No
    FGFR1 Co-crystal Structure11030354 No
    FIBP Two-hybrid9806903|9806903 No
    FGF1 Co-crystal Structure9655399|11069186,9655399 CHD related
    FGFR4 Reconstituted Complex10736564|10336501 CHD related
    NRP1 in vitro15695515 CHD related
    S100A13 Co-purification9712836|11432880|11432880,9712836 No
    FGFR3 Reconstituted Complex8576175|10574949|10574949,14732692 No
    SYT1 Reconstituted Complex11432880|11432880 No
    FGFBP1 Reconstituted Complex11509569|11509569 No
    UBC Affinity Capture-MS21139048 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00686Pentosan PolysulfateFor the relief of bladder pain or discomfort associated with interstitial cystitis.C05BA04
    approvedDB01025AmlexanoxUsed as a paste in the mouth to treat aphthous ulcers (canker sores). A01AD07;R03DX01
    experimentalDB01901Sucrose Octasulfate
    experimentalDB01942Formic Acid
    experimentalDB02264O2-Sulfo-Glucuronic Acid
    experimentalDB03959"N,O6-Disulfo-Glucosamine"
    experimentalDB04409Naphthalene Trisulfonate
    experimentalDB082385-AMINO-NAPHTALENE-2-MONOSULFONATE