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: LRP1

    Description: low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor)

    Entrez Gene ID: 4035

    SwissProt Acc Number: Q07954

    RefSeq: NM_002332

    It was suspected to be CHD related:

    ..LDL receptor-related protein 1 (LRP1) is highly expressed in the vascular wall and is mainly associated with macrophages and vascular smooth muscle cells (VSMCs). ..

    From PMID: 15705932, in Journal Arterioscler Thromb Vasc Biol , 2005


    References

    There were 4 potential papers with LRP1 and CHD.

    PMIDTitleJournalsDetails
    22055160 Abdominal aortic aneurysm is associated with a variant in low-density lipoprotein receptor-related protein 1.American journal of human geneticsMore Details
    21252261 Association of anti-oxidized LDL and candidate genes with severity of coronary stenosis in the Women's Ischemia Syndrome Evaluation study.Journal of lipid researchMore Details
    20360257 Opposing effects of apolipoprotein m on catabolism of apolipoprotein B-containing lipoproteins and atherosclerosis.Circulation researchMore Details
    15705932 LDL receptor-related protein and the vascular wall: implications for atherothrombosis."Arteriosclerosis, thrombosis, and vascular biology"More Details

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



    PPI interactions

    There were totally 69 unique genes interacted with LRP1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SERPINE1 Affinity Capture-Western15001579 CHD related
    CANX Affinity Capture-Western14980518 No
    CALR Affinity Capture-Western14980518 No
    PDIA2 Affinity Capture-Western14980518 No
    MMP14 Affinity Capture-Western14645246 CHD related
    GIPC1 Two-hybrid10827173 No
    MAPK8IP1 Two-hybrid10827173|20205790 No
    DLG4 Two-hybrid10827173 No
    MAPK8IP2 Two-hybrid10827173 No
    SYNJ2BP Two-hybrid10827173 No
    NOS1AP Two-hybrid10827173 CHD related
    SCN3A Two-hybrid10827173 No
    APBA2 Two-hybrid10827173 No
    DAB1 Two-hybrid10827173|9837937 No
    ITGB1BP1 Two-hybrid10827173 No
    ANAPC10 Two-hybrid10827173 No
    A2M Co-crystal Structure10652313|10652313,12194978 No
    PDGFB Reconstituted Complex11854294 CHD related
    F8 Reconstituted Complex12522143 No
    GULP1 Reconstituted Complex11729193 No
    PLAUR Affinity Capture-Western11359936|11359936 CHD related
    LRPAP1 Reconstituted Complex1374383|10747918,1374383,1718973 CHD related
    LIPC Reconstituted Complex7721852 CHD related
    SNX17 Reconstituted Complex12169628 No
    APBB1 Two-hybrid9837937 No
    RIC8B Two-hybrid20205790 No
    CC2D1A Two-hybrid20205790 No
    SNRNP70 Two-hybrid20205790 No
    ANKS1B Two-hybrid20205790 No
    PID1 Two-hybrid20205790|20205790 No
    HNRPDL Two-hybrid20205790 No
    MAPRE1 Two-hybrid20205790 No
    LRP1 in vitro8703036 CHD related
    CAV1 in vivo14593097 CHD related
    WNT3A in vitro;in vivo14739301 CHD related
    SERPINA1 in vitro15131125 CHD related
    CTSG in vitro15131125 No
    ELANE in vitro15131125 CHD related
    APP in vivo12212791,7543026 No
    SKIL yeast 2-hybrid15231748 No
    KAT5 FRET12888553|12888553 No
    CALCR Reconstituted Complex12821648 No
    SHC1 Affinity Capture-Western12789267|12789267|12789267,12069755 No
    THBS1 Reconstituted Complex14991768|9045712|9045712,14991768 CHD related
    SRC Biochemical Activity11854294|12789267,11854294 CHD related
    DAB2 Reconstituted Complex11247302 CHD related
    MDK Affinity Capture-MS10772929|10772929 CHD related
    PLAT Reconstituted Complex10632583|1502153|10632583,1502153 CHD related
    F9 Reconstituted Complex12522212|12522212 No
    LPL Reconstituted Complex7510694|7989348|1281473,7510694,7989348 CHD related
    USP3 Affinity Capture-MS19615732 No
    CACNA1A Two-hybrid21078624 No
    APOE Affinity Capture-Western2779654 CHD related
    UBC Affinity Capture-MS21139048 No
    FBXO6 Affinity Capture-MS22268729 No
    C3 in vivo10608878 CHD related
    C4BPA in vitro;in vivo11705989 No
    CTGF in vivo14585398 CHD related
    FURIN in vitro;in vivo8546712,2112085 No
    LTF in vivo1464627 No
    HSP90B1 in vivo11861214 No
    MMP13 in vitro;in vivo10514495 CHD related
    PRKACA in vitro11158305 CHD related
    GTPBP1 in vitro;in vivo9820815 No
    MMP15 in vitro14645246 No
    MMP16 in vitro14645246 No
    MMP17 in vitro14645246 No
    CD82 in vitro;in vivo9804823 No
    BACE1 in vivo15749709 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00025Antihemophilic Factor"For the treatment of hemophilia A, von Willebrand diseae and Factor XIII deficiency"B02BD02
    approvedDB00031TenecteplaseFor treatment of myocardial infarction and lysis of intracoronary emboliB01AD11
    approvedDB00100Coagulation Factor IXFor treatment of hemophilia (Christmas disease).B02BD04