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: FGB

    Description: fibrinogen beta chain

    Entrez Gene ID: 2244

    SwissProt Acc Number: P02675

    RefSeq: NM_005141

    It was suspected to be CHD related:

    .."The minor alleles of four SNPs from the FGB gene, two from the FGA gene, and one from the FGG gene were associated with higher plasma fibrinogen levels."..

    From PMID: 22388766, in Journal Eur J Epidemiol , 2012


    References

    There were 8 potential papers with FGB and CHD.

    PMIDTitleJournalsDetails
    23129316 "Apo A5 -1131T/C, FgB -455G/A, -148C/T, and CETP TaqIB gene polymorphisms and coronary artery disease in the Chinese population: a meta-analysis of 15,055 subjects."Molecular biology reportsMore Details
    22388766 A genetic instrument for Mendelian randomization of fibrinogen.European journal of epidemiologyMore Details
    21332313 "Sequence variations in the FII, FV, F13A1, FGB and PAI-1 genes are associated with differences in myocardial perfusion."PharmacogenomicsMore Details
    20167083 Fibrinogen beta variants confer protection against coronary artery disease in a Greek case-control study.BMC medical geneticsMore Details
    19352213 "Antihypertensive pharmacogenetic effect of fibrinogen-beta variant -455G>A on cardiovascular disease, end-stage renal disease, and mortality: the GenHAT study."Pharmacogenetics and genomicsMore 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
    16776623 Polymorphisms associated with apolipoprotein B levels in Greek patients with familial hypercholesterolemia.Clinical chemistry and laboratory medicine : CCLM / FESCCMore Details

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



    PPI interactions

    There were totally 16 unique genes interacted with FGB. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CALR Affinity Capture-MS7592883|7592883 No
    FGG Co-crystal Structure12356313|12356313 CHD related
    FGA Co-crystal Structure12356313 CHD related
    NID1 Reconstituted Complex1680863 No
    FBLN1 Reconstituted Complex7642629|7642629 CHD related
    LPA Reconstituted Complex10980194|10980194|10980194 CHD related
    KHDRBS2 Affinity Capture-MS17643375 No
    MIS12 Affinity Capture-MS20360068 No
    GRB7 Two-hybrid21900206 No
    AIMP2 Two-hybrid21900206 No
    TK1 Two-hybrid21900206 No
    CDKN1A Two-hybrid21900206 CHD related
    SMN1 Two-hybrid21900206 No
    PIK3R3 Two-hybrid21900206 No
    ANXA7 Two-hybrid21900206 No
    SERPINA5 in vitro8148485,8384496 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