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: FGF2

    Description: fibroblast growth factor 2 (basic)

    Entrez Gene ID: 2247

    SwissProt Acc Number: P09038

    RefSeq: NM_002006

    It was suspected to be CHD related:

    ..The fibroblast growth factor 2 (FGF2) is involved in various processes possibly leading to the development of complex diseases such as atherosclerosis...

    From PMID: 15882674, in Journal Int J Cardiol , 2005


    References

    There were 4 potential papers with FGF2 and CHD.

    PMIDTitleJournalsDetails
    23578358 Janus-like role of fibroblast growth factor 2 in arteriosclerotic coronary artery disease: atherogenesis and angiogenesis.AtherosclerosisMore Details
    16271723 A strategy of retrograde injection of bone marrow mononuclear cells into the myocardium for the treatment of ischemic heart disease.Journal of molecular and cellular cardiologyMore Details
    15882674 The human FGF2 level is influenced by genetic predisposition.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 32 unique genes interacted with FGF2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SDC1 Co-purification16982797|16982797 CHD related
    SDC2 Co-purification16982797|16982797 No
    SDC4 Co-purification16982797 CHD related
    RPS19 Co-purification11716516|11716516 No
    THBS1 Reconstituted Complex17996481 CHD related
    NRP1 in vitro15695515 CHD related
    FGF2 in vitro9558385 CHD related
    FGFR3 in vivo10574949 No
    RPS6KA3 in vitro15879597 No
    CD44 in vivo7532176 CHD related
    CSNK2A1 Reconstituted Complex12145206|12145206 CHD related
    CSNK2A2 Reconstituted Complex12145206 No
    CSNK2B Reconstituted Complex12145206|12145206 No
    GPC3 Affinity Capture-Western12478660|12478660 CHD related
    VTN Reconstituted Complex11796824|11796824 CHD related
    FGFBP1 Reconstituted Complex11509569|11509569 No
    SDC3 Reconstituted Complex8344959 No
    FGFR1 Reconstituted Complex10950949|10950949,11030354 No
    GPC4 Reconstituted Complex11066092|11066092 No
    RPL6 Two-hybrid9826564|9826564|9826564 No
    UBC Affinity Capture-MS21139048 No
    CRYAB Protein-peptide17487982 No
    PTX3 in vitro16020751 CHD related
    CASP1 in vivo18329368 CHD related
    FGFR4 in vitro8530375 CHD related
    HSPG2 in vivo11847221 No
    PF4 in vitro;in vivo9558385 CHD related
    PRMT1 in vitro10652299 No
    CXCL13 in vitro11708770 No
    FGFRL1 in vitro11418238 No
    CEP57 in vitro;in vivo;yeast 2-hybrid12717444 No
    API5 in vitro;in vivo;yeast 2-hybrid11075807 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00364Sucralfate"For the short-term treatment (up to 8 weeks) of active duodenal ulcer, as well as maintenance therapy for duodenal ulcer patients at reduced dosage (1 gram twice a day) after healing of acute ulcers. Also used for the short-term treatment of gastric ulcer."A02BX02
    approvedDB00686Pentosan PolysulfateFor the relief of bladder pain or discomfort associated with interstitial cystitis.C05BA04
    approvedDB00877SirolimusFor the prophylaxis of organ rejection in patients receiving renal transplants.L04AA10
    experimentalDB03935"1,4-Dideoxy-O2-Sulfo-Glucuronic Acid"
    experimentalDB03959"N,O6-Disulfo-Glucosamine"
    experimentalDB03981"1,4-Dideoxy-5-Dehydro-O2-Sulfo-Glucuronic Acid"