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: FAM5C

    Description: "family with sequence similarity 5, member C"

    Entrez Gene ID: 339479

    SwissProt Acc Number: Q76B58

    RefSeq: NM_199051

    It was supported literatures to be a novel CHD related gene:

    .."Polymorphisms in the family with sequence similarity 5, member C' (FAM5C) gene have been associated with myocardial infarction (MI)."..

    From PMID: 18430236, in Journal BMC Med Genet. , 2008


    References

    There were 2 potential papers with FAM5C and CHD.

    PMIDTitleJournalsDetails
    22013132 The relationships between FAM5C SNP (rs10920501) variability and metabolic syndrome and inflammation in women with coronary heart disease.Biological research for nursingMore Details
    18430236 Genetic and functional association of FAM5C with myocardial infarction.BMC medical geneticsMore Details

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



    PPI interactions

    There were totally 2 unique genes interacted with FAM5C. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    HGS Reconstituted Complex19019082 No
    UBC Affinity Capture-MS20972266 No


    Involved FDA drugs

    There was no drug associated with FAM5C