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: MSR1

    Description: macrophage scavenger receptor 1

    Entrez Gene ID: 4481

    SwissProt Acc Number: P21757

    RefSeq: NM_002445

    It was suspected to be CHD related:

    ..These findings point to a significant role of MSR1 in atherosclerosis...

    From PMID: 19715475, in Journal Genet Test Mol Biomarkers , 2009


    References

    There were 5 potential papers with MSR1 and CHD.

    PMIDTitleJournalsDetails
    23739627 Monocyte gene expression and coronary artery disease.Current opinion in clinical nutrition and metabolic careMore Details
    23554780 Genetic variants of the class A scavenger receptor gene are associated with coronary artery disease in Chinese.Journal of biomedical researchMore Details
    20410100 "Genetic variation in APOJ, LPL, and TNFRSF10B affects plasma fatty acid distribution in Alaskan Eskimos."The American journal of clinical nutritionMore Details
    19715475 Increased risk for atherosclerosis of various macrophage scavenger receptor 1 alleles.Genetic testing and molecular biomarkersMore Details
    18067591 CD36 mRNA expression is increased in CD14+ monocytes of patients with coronary heart disease.Clinical and experimental pharmacology & physiologyMore Details

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



    PPI interactions

    There were totally 2 unique genes interacted with MSR1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    TRAF6 Affinity Capture-Western21460221 No
    HSPA1A Affinity Capture-Western11785981|11785981 CHD related


    Involved FDA drugs

    There was no drug associated with MSR1