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: LOX

    Description: lysyl oxidase

    Entrez Gene ID: 4015

    SwissProt Acc Number: P28300

    RefSeq: NM_002317

    It was suspected to be CHD related:

    ..Lysyl oxidase (LOX) plays a crucial role in the maintenance of extracellular matrix stability and could participate in vascular remodelling associated with cardiovascular diseases...

    From PMID: 18469024, in Journal Cardiovasc Res , 2008


    References

    There were 6 potential papers with LOX and CHD.

    PMIDTitleJournalsDetails
    21612403 Lysyl oxidase G473A polymorphism is associated with increased risk of coronary artery diseases.DNA and cell biologyMore Details
    20435853 "Role of arachidonic acid, lipoxygenase, and mitochondrial depolarization in reperfusion arrhythmias."American journal of physiology. Heart and circulatory physiologyMore Details
    20093560 "LOX index, a novel predictive biochemical marker for coronary heart disease and stroke."Clinical chemistryMore Details
    18469024 Regulation of lysyl oxidase in vascular cells: lysyl oxidase as a new player in cardiovascular diseases.Cardiovascular researchMore Details
    17164132 Role of epoxyeicosatrienoic acids in protecting the myocardium following ischemia/reperfusion injury.Prostaglandins & other lipid mediatorsMore Details
    15831618 Lysyl oxidase deficiency: a new cause of human arterial dissection.Heart (British Cardiac Society)More Details

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



    PPI interactions

    There were totally 6 unique genes interacted with LOX. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    DPT in vivo8082810 No
    ELN in vivo6912069 CHD related
    HIST1H1B in vitro12686141 No
    LOX in vitro;in vivo;yeast 2-hybrid15110773 CHD related
    DHDDS Two-hybrid15110773|15110773 No
    HIST1H2BJ in vitro12686141 No


    Involved FDA drugs

    There was no drug associated with LOX