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: PCSK2

    Description: proprotein convertase subtilisin/kexin type 2

    Entrez Gene ID: 5126

    SwissProt Acc Number: P16519

    RefSeq: NM_002594

    It was suspected to be CHD related:

    ..the C-->G polymorphism of PCSK2 (rs6080699) were significantly (false discovery rate for allele frequencies of <0.05) associated with MI. ..

    From PMID: 20036365, in Journal Atherosclerosis , 2010


    References

    There were 2 potential papers with PCSK2 and CHD.

    PMIDTitleJournalsDetails
    20036365 "Association of genetic variants in SEMA3F, CLEC16A, LAMA3, and PCSK2 with myocardial infarction in Japanese individuals."AtherosclerosisMore Details
    17903303 Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study.BMC medical geneticsMore Details

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



    PPI interactions

    There were totally 3 unique genes interacted with PCSK2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PMCH in vivo10037747 No
    IAPP in vitro;in vivo3053705,8557106,11246872,10931181 No
    SCG5 in vitro;in vivo11439082,7722516 No


    Involved FDA drugs

    There was no drug associated with PCSK2