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: FGG

    Description: fibrinogen gamma chain

    Entrez Gene ID: 2266

    SwissProt Acc Number: P02679

    RefSeq: NM_000509

    It was suspected to be CHD related:

    .."FGA and FGG SNPs as well as FGA, FGB, FGG and FGA-FGG haplotypes do not seem to be important contributors to CAD occurrence in our sample.//Plasma fibrinogen gamma' concentration influences the risk of MI,and this relationship seems to be strengthened by the presence of an elevated total plasma fibrinogen concentration and the FGG 9340T and FGA 2224G alleles."..

    From PMID: 20167083, in Journal BMC Med Genet.? , 2010


    References

    There were 4 potential papers with FGG and CHD.

    PMIDTitleJournalsDetails
    22388766 A genetic instrument for Mendelian randomization of fibrinogen.European journal of epidemiologyMore Details
    20167083 Fibrinogen beta variants confer protection against coronary artery disease in a Greek case-control study.BMC medical geneticsMore Details
    17263791 Elevated plasma fibrinogen gamma' concentration is associated with myocardial infarction: effects of variation in fibrinogen genes and environmental factors.Journal of thrombosis and haemostasis : JTHMore Details
    16706972 Association between patterns of nucleotide variation across the three fibrinogen genes and plasma fibrinogen levels: the Coronary Artery Risk Development in Young Adults (CARDIA) study.Journal of thrombosis and haemostasis : JTHMore Details

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



    PPI interactions

    There were totally 11 unique genes interacted with FGG. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    FGA Co-crystal Structure12356313|12356313 CHD related
    FGB Co-crystal Structure12356313|12356313 CHD related
    FGG Co-crystal Structure12501189|9333233|12501189,9333233 CHD related
    ITGAM in vivo11073102,9712878 CHD related
    F13A1 in vitro8905624,10828988 CHD related
    F13B Co-purification8756701 CHD related
    KHDRBS2 Affinity Capture-MS17643375 No
    ICAM1 in vitro;in vivo7822297 CHD related
    ITGB3 in vitro10747940 CHD related
    VTN in vitro;in vivo11744726 CHD related
    SERPINA5 in vitro8384496 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00364Sucralfate"For the short-term treatment (up to 8 weeks) of active duodenal ulcer, as well as maintenance therapy for duodenal ulcer patients at reduced dosage (1 gram twice a day) after healing of acute ulcers. Also used for the short-term treatment of gastric ulcer."A02BX02