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.

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  • 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.

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  • 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: TRPC1

    Description: "transient receptor potential cation channel, subfamily C, member 1"

    Entrez Gene ID: 7220

    SwissProt Acc Number: P48995

    RefSeq: NM_003304

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

    .."Smooth muscle cell proliferation, a major mechanism of CAD, is mediated partly by myoplasmic Ca2+?dysregulation and store-operated Ca2+?entry (SOCE) via canonical transient receptor potential 1 (TRPC1) channels is proposed to play a key role."..

    From PMID: 19744946, in Journal Cardiovasc Res. , 2010


    References

    There were 3 potential papers with TRPC1 and CHD.

    PMIDTitleJournalsDetails
    20431989 Expression levels of TRPC1 and TRPC6 ion channels are reciprocally altered in aging rat aorta: implications for age-related vasospastic disorders."Age (Dordrecht, Netherlands)"More Details
    19744946 Exercise training decreases store-operated Ca2+entry associated with metabolic syndrome and coronary atherosclerosis.Cardiovascular researchMore Details
    16439693 Upregulated TRPC1 channel in vascular injury in vivo and its role in human neointimal hyperplasia.Circulation researchMore Details

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



    PPI interactions

    There were totally 21 unique genes interacted with TRPC1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    GRM1 Affinity Capture-Western14614461 No
    TRPC6 Affinity Capture-Western12857742 CHD related
    TRPC3 Affinity Capture-Western12857742|9215637 CHD related
    TRPC1 FRET12032305 CHD related
    ITPR3 Affinity Capture-Western10980191|10980191,11290752 CHD related
    CAV1 Affinity Capture-Western10980191|12732636 CHD related
    BMPR2 in vitro15188402 No
    MDFI in vitro;in vivo;yeast 2-hybrid14530267 No
    GRIA1 in vitro;in vivo14614461 No
    PKD2 Two-hybrid10097141|10097141 No
    HOMER1 Affinity Capture-Western14505576 No
    HOMER3 Affinity Capture-Western14505576|14505576 No
    ITPR1 Affinity Capture-Western14505576 No
    TRPC4 Affinity Capture-Western12857742 No
    TRPC5 Affinity Capture-Western12857742 No
    RHOA Affinity Capture-Western12766172|12766172 CHD related
    ELAVL1 Affinity Capture-RNA19322201 No
    TRPC4AP Affinity Capture-Western20458742 No
    TNFRSF1A Affinity Capture-Western20458742 CHD related
    ITPR2 in vitro;in vivo11336651,10970773 No
    MX1 in vitro;in vivo15757897 No


    Involved FDA drugs

    There was no drug associated with TRPC1