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: CMA1

    Description: "chymase 1, mast cell"

    Entrez Gene ID: 1215

    SwissProt Acc Number: P23946

    RefSeq: NM_001836

    It was suspected to be CHD related:

    .."The gene for mast cell chymase (CMA1) is an ideal candidate for investigating the genetic predisposition to coronary heart disease (CHD),"..

    From PMID: 21796807, in Journal J Zhejiang Univ Sci B , 2011


    References

    There were 1 potential papers with CMA1 and CHD.

    PMIDTitleJournalsDetails
    21796807 "Association between SNP rs1800875, serum chymase and immunoglobulin E levels in patients with coronary heart disease."Journal of Zhejiang University. Science. BMore Details

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



    PPI interactions

    There were totally 8 unique genes interacted with CMA1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SERPINA3 in vitro8226889 CHD related
    MMP1 in vitro;in vivo8027075 CHD related
    EDN3 in vitro9257865 No
    PFN1 in vitro11751973 No
    KITLG in vitro10224464 No
    EDN1 in vitro9257865 CHD related
    EDN2 in vitro9675146 CHD related
    AGT in vitro10899625 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB03149Phenylalanylmethane
    experimentalDB03297Benzylsulfinic Acid
    experimentalDB038142-(N-Morpholino)-Ethanesulfonic Acid
    experimentalDB040162-[3-({Methyl[1-(2-Naphthoyl)Piperidin-4-Yl]Amino}Carbonyl)-2-Naphthyl]-1-(1-Naphthyl)-2-Oxoethylphosphonic Acid
    experimentalDB07680[(1S)-1-(5-CHLORO-1-BENZOTHIEN-3-YL)-2-(2-NAPHTHYLAMINO)-2-OXOETHYL]PHOSPHONIC ACID