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: BDNF

    Description: brain-derived neurotrophic factor

    Entrez Gene ID: 627

    SwissProt Acc Number: P23560

    RefSeq: NM_001143805

    It was suspected to be CHD related:

    .."In this issue of the Journal, Jiang and colleagues report a strong association between brain derived neurotrophic factor (BDNF) Val66Met polymorphism and CAD. "..

    From PMID: 19013442, in Journal Clin Chim Acta , 2009


    References

    There were 13 potential papers with BDNF and CHD.

    PMIDTitleJournalsDetails
    21624682 Type A behavior pattern and hyperthymic temperament: possible association with bipolar IV disorder.Journal of affective disordersMore Details
    22020095 Association of plasma brain-derived neurotrophic factor and cardiovascular risk factors and prognosis in angina pectoris.Biochemical and biophysical research communicationsMore Details
    20702043 Determinants of serum brain-derived neurotrophic factor.PsychoneuroendocrinologyMore Details
    21554945 "Brain derived neurotrophic factor, cardiopulmonary fitness and cognition in patients with coronary artery disease.""Brain, behavior, and immunity"More Details
    19059263 Chronic intermittent fasting improves the survival following large myocardial ischemia by activation of BDNF/VEGF/PI3K signaling pathway.Journal of molecular and cellular cardiologyMore Details
    19013140 BDNF Val66Met polymorphism is associated with unstable angina.Clinica chimica acta; international journal of clinical chemistryMore Details
    19013442 The brain and heart: dancing in unison?Clinica chimica acta; international journal of clinical chemistryMore Details
    16904693 Application of bFGF and BDNF to improve angiogenesis and cardiac function.The Journal of surgical researchMore Details
    16352696 BDNF-mediated enhancement of inflammation and injury in the aging heart.Physiological genomicsMore Details
    16186425 Possible role of brain-derived neurotrophic factor in the pathogenesis of coronary artery disease.CirculationMore Details
    15939120 Reduced plasma levels of NGF and BDNF in patients with acute coronary syndromes.International journal of cardiologyMore Details
    14699970 Neurotrophin presence in human coronary atherosclerosis and metabolic syndrome: a role for NGF and BDNF in cardiovascular disease?Progress in brain researchMore Details
    11935372 "NGF, BDNF, leptin, and mast cells in human coronary atherosclerosis and metabolic syndrome."Archives of physiology and biochemistryMore Details

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



    PPI interactions

    There were totally 13 unique genes interacted with BDNF. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    NTRK2 Reconstituted Complex9312147|11855816 No
    APP Reconstituted Complex21832049 No
    CPE in vitro15664176 CHD related
    BDNF in vitro8174548,7961712 CHD related
    SORT1 in vitro;in vivo15987945 CHD related
    CADPS2 in vitro;in vivo14715936 No
    Ntrk2 Affinity Capture-Western1645620 No
    ELAVL1 Affinity Capture-RNA19322201 No
    NCAM1 in vitro10760298 CHD related
    ESR1 in vitro11923430 CHD related
    NTF3 in vitro7703225 No
    NOS3 in vitro10493752 CHD related
    MBTPS1 in vitro9990022 No


    Involved FDA drugs

    There was no drug associated with BDNF