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: ACTA2

    Description: "actin, alpha 2, smooth muscle, aorta"

    Entrez Gene ID: 59

    SwissProt Acc Number: P62736

    RefSeq: NM_001141945

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

    ..We report a young adult who presented with an acute brachial artery occlusion and was subsequently found to have aortopathy and an ACTA2 mutation. ..

    From PMID: 22946110, in Journal Vasc Med. , 2012


    References

    There were 7 potential papers with ACTA2 and CHD.

    PMIDTitleJournalsDetails
    24243736 Acute aortic dissections with pregnancy in women with ACTA2 mutations.American journal of medical genetics. Part AMore Details
    23175675 Mitogen-activated protein kinase 14 is a novel negative regulatory switch for the vascular smooth muscle cell contractile gene program."Arteriosclerosis, thrombosis, and vascular biology"More Details
    23591991 "Smooth muscle hyperplasia due to loss of smooth muscle alpha-actin is driven by activation of focal adhesion kinase, altered p53 localization and increased levels of platelet-derived growth factor receptor-beta."Human molecular geneticsMore Details
    22946110 Brachial artery occlusion in a young adult with an ACTA2 thoracic aortic aneurysm."Vascular medicine (London, England)"More Details
    21248741 Three novel mutations in the ACTA2 gene in German patients with thoracic aortic aneurysms and dissections.European journal of human genetics : EJHGMore Details
    20130469 Genetic variants promoting smooth muscle cell proliferation can result in diffuse and diverse vascular diseases: evidence for a hyperplastic vasculomyopathy.Genetics in medicine : official journal of the American College of MedicalMore Details
    19409525 "Mutations in smooth muscle alpha-actin (ACTA2) cause coronary artery disease, stroke, and Moyamoya disease, along with thoracic aortic disease."American journal of human geneticsMore Details

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



    PPI interactions

    There were totally 56 unique genes interacted with ACTA2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CCT4 Co-crystal Structure11580270 No
    PCYT1B Co-crystal Structure11580270 No
    CCT5 Co-crystal Structure11580270 No
    MYH9 Co-fractionation22939629 No
    MYH11 Co-fractionation22939629 No
    RPL10A Co-fractionation22939629 No
    RPL18 Co-fractionation22939629 No
    RPS23 Co-fractionation22939629 No
    RPL14 Co-fractionation22939629 No
    RPL7A Co-fractionation22939629 No
    RPS15A Co-fractionation22939629 No
    RPL17 Co-fractionation22939629 No
    RPS16 Co-fractionation22939629 No
    RPS26 Co-fractionation22939629 No
    RPS4X Co-fractionation22939629 No
    MYH10 Co-fractionation22939629 No
    ACTC1 Co-fractionation22939629 CHD related
    MYO1C Co-fractionation22939629 No
    TPM1 Co-fractionation22939629 CHD related
    MRPL47 Co-fractionation22939629 No
    AARS Co-fractionation22939629 No
    FSCN1 Co-fractionation22939629 No
    UBAP1 Co-fractionation22939629 No
    ZYX Co-fractionation22939629 No
    MRPS2 Co-fractionation22939629 No
    MRPS7 Co-fractionation22939629 No
    GSTP1 Co-fractionation22939629 No
    SPTAN1 Co-fractionation22939629 No
    CNN2 Co-fractionation22939629 No
    YWHAQ Affinity Capture-MS20618440 No
    EP300 Affinity Capture-MS16051665 CHD related
    CREBBP Affinity Capture-MS16051665 No
    NOP56 Affinity Capture-MS12777385 No
    EGFR Affinity Capture-MS19531499 CHD related
    UBC Affinity Capture-MS20639865|18781797|21963094|21906983|22505724 No
    KIAA0101 Affinity Capture-MS21628590 No
    CUL3 Affinity Capture-MS21145461 No
    CUL4B Affinity Capture-MS21145461 No
    CUL2 Affinity Capture-MS21145461 No
    CUL1 Affinity Capture-MS21145461 No
    COPS5 Affinity Capture-MS21145461 No
    CAND1 Affinity Capture-MS21145461 No
    SHBG Two-hybrid15862967 CHD related
    MYOC Two-hybrid16289162|16289162 No
    LRRK2 Affinity Capture-MS20876399 No
    CRYAB Reconstituted Complex17590381 No
    YWHAB Co-fractionation22939629 No
    YWHAE Co-fractionation22939629 No
    DNASE1 in vitro11707283 No
    GC in vitro12119014 No
    MYL1 in vitro11707283 No
    PRKCD in vitro10628374 CHD related
    TMSB4X in vitro11812134 No
    SNTA1 in vitro9512352 No
    CFL1 in vitro11707283 No
    MINK1 yeast 2-hybrid15032605 No


    Involved FDA drugs

    There was no drug associated with ACTA2