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: BMP4

    Description: bone morphogenetic protein 4

    Entrez Gene ID: 652

    SwissProt Acc Number: P12644

    RefSeq: NM_001202

    It was suspected to be CHD related:

    .."We suggest that BMP4 is a mechanosensitive, inflammatory factor playing a critical role in early steps of atherogenesis in the lesion-prone areas."..

    From PMID: 12766166, in Journal J Biol Chem , 2003


    References

    There were 9 potential papers with BMP4 and CHD.

    PMIDTitleJournalsDetails
    23559633 Anti-inflammatory and antiatherogenic role of BMP receptor II in endothelial cells."Arteriosclerosis, thrombosis, and vascular biology"More Details
    24119764 Bone morphogenic protein-4: A potential novel target for preventing vein graft failure in coronary revascularization.Medical hypothesesMore Details
    22681982 [Hypertension-induced fibrosis: a balance story].Annales de cardiologie et d'angeiologieMore Details
    20551377 Discovery of novel mechanosensitive genes in vivo using mouse carotid artery endothelium exposed to disturbed flow.BloodMore Details
    20665672 Chondro/osteoblastic and cardiovascular gene modulation in human artery smooth muscle cells that calcify in the presence of phosphate and calcitriol or paricalcitol.Journal of cellular biochemistryMore Details
    19453255 Bone morphogenetic protein 7 (BMP7) gene polymorphisms are associated with inverse relationships between vascular calcification and BMD: the Diabetes Heart Study.Journal of bone and mineral research : the official journal of the AmericanMore Details
    17950562 Induction of vascular atrophy as a novel approach to treating restenosis. A review.Journal of vascular surgeryMore Details
    15464586 GATA4 is a dosage-sensitive regulator of cardiac morphogenesis.Developmental biologyMore Details
    12766166 Bone morphogenic protein 4 produced in endothelial cells by oscillatory shear stress stimulates an inflammatory response.The Journal of biological chemistryMore Details

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



    PPI interactions

    There were totally 17 unique genes interacted with BMP4. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    BMPR1A Reconstituted Complex8006002 No
    BMPR1B Reconstituted Complex8006002 No
    ZFYVE9 yeast 2-hybrid15231748 No
    BMP4 in vivo7644468,7673243 CHD related
    BGN in vivo15775969,15173106 No
    SOSTDC1 Affinity Capture-Western15020244|15020244 No
    BMPR2 Affinity Capture-Western7644468|7644468,8702914 No
    TWSG1 Reconstituted Complex11260715 No
    UBC Affinity Capture-MS21906983 No
    HTRA1 in vitro14973287 No
    BMP8B in vitro;in vivo11427739,10894154 No
    NOG in vivo10657699,11706034 No
    STAP2 in vivo7644468 No
    CHRDL2 in vivo14660436 No
    BMPER in vivo12897139 No
    GREM2 in vivo15039429 No
    CHRDL1 in vitro;in vivo11441185 No


    Involved FDA drugs

    There was no drug associated with BMP4