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: S100A1

    Description: S100 calcium binding protein A1

    Entrez Gene ID: 6271

    SwissProt Acc Number: P23297

    RefSeq: NM_006271

    It was suspected to be CHD related:

    .."S100A1, a positive inotropic regulator of myocardial contractility, becomes depleted in failing cardiomyocytes in humans and animals, and myocardial-targeted S100A1 gene transfer rescues cardiac contractile function by restoring sarcoplasmic reticulum calcium (Ca(2+)) handling in acutely and chronically failing hearts in small animal models."..

    From PMID: 21775667, in Journal Sci Transl Med.? , 2011


    References

    There were 4 potential papers with S100A1 and CHD.

    PMIDTitleJournalsDetails
    23683996 Immunohistochemical detection of S100A1 in the postmortem diagnosis of acute myocardial infarction.Diagnostic pathologyMore Details
    21775667 Cardiac AAV9-S100A1 gene therapy rescues post-ischemic heart failure in a preclinical large animal model.Science translational medicineMore Details
    16952982 Cardiac S100A1 protein levels determine contractile performance and propensity toward heart failure after myocardial infarction.CirculationMore Details
    10924368 "S100A1, a new marker for acute myocardial ischemia."Biochemical and biophysical research communicationsMore Details

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



    PPI interactions

    There were totally 22 unique genes interacted with S100A1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    S100P Two-hybrid16189514|16189514,15171681 CHD related
    S100A1 Two-hybrid16189514|9803314|16169012,16189514,15171681 CHD related
    NIF3L1 Two-hybrid16189514|16189514 No
    S100B Two-hybrid16189514 CHD related
    S100A4 Two-hybrid16189514|10753920|10753920 No
    PYGM Affinity Capture-Western12804600 CHD related
    GJA1 Affinity Capture-Western12804600|12804600 CHD related
    ATP2A2 Affinity Capture-Western12804600|12804600 CHD related
    PLB1 Affinity Capture-Western12804600 No
    RYR1 Reconstituted Complex9298970 No
    PLN in vitro;in vivo12804600 CHD related
    ACTA1 in vivo9645951 CHD related
    GFAP in vitro10510252 CHD related
    ANXA6 Reconstituted Complex9883272 No
    PGM1 Far Western8894274 No
    CAPZA2 Far Western9803314 No
    DES Reconstituted Complex8641565 No
    MDM2 Reconstituted Complex20591429 CHD related
    AGER in vivo11007787 CHD related
    CAPZA1 in vitro9803314 No
    CACYBP in vivo12042313 CHD related
    SYN1 in vitro;in vivo15147519 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00768OlopatadineFor the treatment of ocular itching associated with allergic conjunctivitis.S01GX09;R01AC08