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: COL3A1

    Description: "collagen, type III, alpha 1"

    Entrez Gene ID: 1281

    SwissProt Acc Number: P02461

    RefSeq: NM_000090

    It was suspected to be CHD related:

    .."We conclude that variants in the COL3A1 gene, the product of which is a vessel-wall protein and platelet ligand, modulate the risk of coronary artery disease and could also modulate the response to antithrombotic therapy. "..

    From PMID: 12149201, in Journal Blood.? , 2002


    References

    There were 5 potential papers with COL3A1 and CHD.

    PMIDTitleJournalsDetails
    22403797 Impact of salt on cardiac differential gene expression and coronary lesion in normotensive mineralocorticoid-treated mice."American journal of physiology. Regulatory, integrative and comparative"More Details
    20117381 Growth differentiation factor 5 regulates cardiac repair after myocardial infarction.Journal of the American College of CardiologyMore Details
    19477391 Vascular Ehlers-Danlos syndrome--all three coronary artery spontaneous dissections.Journal of cardiologyMore Details
    15905966 "Biomedicine and diseases: the Klippel-Trenaunay syndrome, vascular anomalies and vascular morphogenesis."Cellular and molecular life sciences : CMLSMore Details
    12149201 Genetic variability in the extracellular matrix as a determinant of cardiovascular risk: association of type III collagen COL3A1 polymorphisms with coronary artery disease.BloodMore Details

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



    PPI interactions

    There were totally 12 unique genes interacted with COL3A1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SPARC Reconstituted Complex2745554 CHD related
    THBS1 Reconstituted Complex3571333|3571333 CHD related
    MAG Reconstituted Complex2446864|2446864 No
    SP1 Affinity Capture-MS22266860 No
    CAND1 Affinity Capture-MS21145461 No
    MYOC Two-hybrid16289162|16289162 No
    PCOLCE in vitro12105202 No
    CAPN1 yeast 2-hybrid12358155 No
    FGF7 in vitro11973338 No
    DDR2 in vitro9659899 No
    DDR1 in vivo9659900 CHD related
    HTRA1 in vitro;in vivo;yeast 2-hybrid15101818 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00048CollagenaseUsed to promote debridement of necrotic tissue in the treatment of severe burns and dermal ulcers including decubitus ulcers.D03BA02