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: LRP6

    Description: low density lipoprotein receptor-related protein 6

    Entrez Gene ID: 4040

    SwissProt Acc Number: O75581

    RefSeq: NM_002336

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

    ..The C allele of the rs11054731 within the LRP6 gene was associated with increased risk and extent of CAD in Chinese...

    From PMID: 22490400, in Journal Chin Med J (Engl). , 2012


    References

    There were 6 potential papers with LRP6 and CHD.

    PMIDTitleJournalsDetails
    23703864 Rare nonconservative LRP6 mutations are associated with metabolic syndrome.Human mutationMore Details
    23395167 LRP6 enhances glucose metabolism by promoting TCF7L2-dependent insulin receptor expression and IGF receptor stabilization in humans.Cell metabolismMore Details
    19833493 Carotid artery atherosclerosis in hypertensive patients with a functional LDL receptor-related protein 6 gene variant."Nutrition, metabolism, and cardiovascular diseases : NMCD"More Details
    19667113 A common variant in low-density lipoprotein receptor-related protein 6 gene (LRP6) is associated with LDL-cholesterol."Arteriosclerosis, thrombosis, and vascular biology"More Details
    17622581 "Gone with the Wnts: beta-catenin, T-cell factor, forkhead box O, and oxidative stress in age-dependent diseases of bone, lipid, and glucose metabolism.""Molecular endocrinology (Baltimore, Md.)"More Details
    17332414 LRP6 mutation in a family with early coronary disease and metabolic risk factors."Science (New York, N.Y.)"More Details

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



    PPI interactions

    There were totally 20 unique genes interacted with LRP6. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    MESDC2 Affinity Capture-Western12581525 No
    DKK1 Affinity Capture-Western11448771 CHD related
    WNT1 Affinity Capture-Western11448771 No
    UBC Affinity Capture-Western18378904 No
    NPC1 Affinity Capture-Western18948618 CHD related
    ZNRF3 Affinity Capture-Western22575959 No
    WNT3A Affinity Capture-Western19910923|14739301,12897152 CHD related
    WNT5A Affinity Capture-Western19910923 CHD related
    LRP6 in vivo12897152 CHD related
    ANTXR1 in vitro;in vivo16564009 No
    ANTXR2 in vitro;in vivo16564009 No
    FZD8 Affinity Capture-Western11448771 No
    APOB Reconstituted Complex18948618 CHD related
    AXIN1 Affinity Capture-Western20128690 No
    LRRK2 Co-localization22899650 No
    ATP13A2 Two-hybrid22645275 No
    DKK2 in vivo11742004,11357136 No
    FZD5 in vivo12857724 No
    GSK3B in vitro16365045 CHD related
    MESDC1 in vivo16989816 No


    Involved FDA drugs

    There was no drug associated with LRP6