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: MKL1

    Description: megakaryoblastic leukemia (translocation) 1

    Entrez Gene ID: 57591

    SwissProt Acc Number: Q969V6

    RefSeq: NM_020831

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

    ..Subsequent single nucleotide polymorphism (SNP) association studies revealed an association between CAD and megakaryoblastic leukemia factor-1 gene (MKL1)..

    From PMID: 19513752, in Journal Hum Genet. , 2009


    References

    There were 3 potential papers with MKL1 and CHD.

    PMIDTitleJournalsDetails
    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
    20816842 Megakaryoblastic leukemia protein-1 (MKL1): Increasing evidence for an involvement in cancer progression and metastasis.The international journal of biochemistry & cell biologyMore Details
    19513752 Megakaryoblastic leukemia factor-1 gene in the susceptibility to coronary artery disease.Human geneticsMore Details

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



    PPI interactions

    There were totally 16 unique genes interacted with MKL1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SRF Affinity Capture-Western14565952|17599918|21965288|12397177,14565952 CHD related
    MKL2 Affinity Capture-Western14565952 No
    SUPT16H Affinity Capture-Western18036521 No
    SSRP1 Affinity Capture-Western18036521 No
    SMARCA4 Affinity Capture-Western17599918|17599918 No
    UBC Affinity Capture-Western21965288 No
    GSK3B Affinity Capture-Western21965288 CHD related
    SMAD3 Affinity Capture-Western21965288 CHD related
    ACTB Affinity Capture-Western21670154 No
    MKL1 in vitro14565952 CHD related
    UBE2I in vitro;yeast 2-hybrid16098147 No
    SUMO1 in vitro;in vivo16098147 No
    MYOCD Reconstituted Complex14970199 No
    KDM3A Reconstituted Complex17991879 No
    SUMO2 Affinity Capture-MS21693764|19471022 No
    NCOA3 Affinity Capture-Luminescence17360478 No


    Involved FDA drugs

    There was no drug associated with MKL1