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: CD59

    Description: "CD59 molecule, complement regulatory protein"

    Entrez Gene ID: 966

    SwissProt Acc Number: P13987

    RefSeq: NM_000611

    It was suspected to be CHD related:

    ..although loss of CD59 (protectin) from cells compromised by ischemia/reperfusion may contribute to direct damage of the coronary vascular bed by the terminal complement complex...

    From PMID: 11080612, in Journal Cell Signal. , 2000


    References

    There were 2 potential papers with CD59 and CHD.

    PMIDTitleJournalsDetails
    19131645 Complement regulator CD59 protects against atherosclerosis by restricting the formation of complement membrane attack complex.Circulation researchMore Details
    12015747 A possible role for complement in the pathogenesis of chronic chagasic cardiomyopathy.The Journal of pathologyMore Details

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



    PPI interactions

    There were totally 14 unique genes interacted with CD59. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    C9 Reconstituted Complex7523406 CHD related
    gag Co-fractionation10708443 No
    env Co-fractionation10708443 No
    NCR1 Affinity Capture-Western14635045|14635045 No
    NCR3 Affinity Capture-Western14635045|14635045 No
    C8A Reconstituted Complex7544344|7544344 CHD related
    CD8A Reconstituted Complex1377690 No
    Htt Affinity Capture-MS17500595 No
    GNAI3 in vitro;in vivo8650218 No
    CD9 in vitro1377690 CHD related
    CD2 in vitro1377404 No
    SRC in vivo12219031 CHD related
    SLC6A8 in vivo12219031 No
    SMAD4 yeast 2-hybrid15231748 No


    Involved FDA drugs

    There was no drug associated with CD59