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: SAA1

    Description: serum amyloid A1

    Entrez Gene ID: 6288

    SwissProt Acc Number: P02735

    RefSeq: NM_000331

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

    .."In Chinese Han people, the genetic polymorphism of SAA1 may reflect the serum concentration of HDL-C"..

    From PMID: 20979827, in Journal Zhonghua Yi Xue Za Zhi. , 2010


    References

    There were 2 potential papers with SAA1 and CHD.

    PMIDTitleJournalsDetails
    23357645 Variant screening of the serum amyloid A1 gene and functional study of the p.Gly90Asp variant for its role in atherosclerosis.AtherosclerosisMore Details
    20677144 [Distribution of genetic polymorphisms of serum amyloid protein A1 in healthy Chinese Han and Uighur populations in Xinjiang].Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = ChineseMore Details

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



    PPI interactions

    There were totally 7 unique genes interacted with SAA1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SELS Reconstituted Complex12031974 CHD related
    COL4A3 in vitro8995276 No
    COL4A2 in vitro8995276 No
    COL4A1 in vitro8995276 CHD related
    COL4A4 in vitro8995276 No
    FPR1 in vitro10753626 No
    LAMA1 in vitro8995276 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00062Human Serum Albumin"For treatment of severe blood loss, hypervolemia, hypoproteinemia"
    approvedDB00064Serum albumin iodonatedFor determination of total blood and plasma volumes