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: PLAT

    Description: "plasminogen activator, tissue"

    Entrez Gene ID: 5327

    SwissProt Acc Number: P00750

    RefSeq: NM_000930

    It was suspected to be CHD related:

    .."Polymorphic markers of ACE and F13, NOS3 and F13, ACE and PLAT loci were in gametic disequilibrium in the patients."..

    From PMID: 11507973, in Journal Int J Circumpolar Health , 2001


    References

    There were 1 potential papers with PLAT and CHD.

    PMIDTitleJournalsDetails
    16248996 Prevalence of genetic risk factors for coronary artery disease in Corsica island (France).Experimental and molecular pathologyMore Details

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



    PPI interactions

    There were totally 29 unique genes interacted with PLAT. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PLAU Reconstituted Complex7721771 CHD related
    SERPINI1 Biochemical Activity12354288|12354288|12354288,12228252 No
    F2 Co-crystal Structure10543954 CHD related
    LRP1 Reconstituted Complex10632583|1502153|10632583,1502153 CHD related
    PDGFC Biochemical Activity22035541 No
    PLG in vitro11928826 No
    GRIN1 in vitro15448144 No
    PLAT in vitro8613982,9268299,9434908 CHD related
    CLEC3B Reconstituted Complex12694198|12694198 No
    CALR Reconstituted Complex9359841 No
    KRT8 Reconstituted Complex9988531 No
    ANXA2 Reconstituted Complex12468550 No
    SERPINA5 Reconstituted Complex2551064|2551064 No
    LAMA5 Reconstituted Complex10956663 No
    SERPINE1 Reconstituted Complex2110366 CHD related
    FGA Reconstituted Complex11170397 CHD related
    HMGB1 Co-purification8366113 CHD related
    F10 Reconstituted Complex11371191|11371191 No
    FN1 Reconstituted Complex8360181 CHD related
    LAMA1 Reconstituted Complex8360181 CHD related
    TERF2 Affinity Capture-MS20811636 No
    POT1 Affinity Capture-MS20811636 No
    MAPK1 in vitro15861134 CHD related
    SPARC in vitro2745554 CHD related
    LAMA3 in vitro10956663 CHD related
    MAPK3 in vitro15861134 CHD related
    SERPING1 in vivo7586269 No
    LRP1B in vivo11384978 No
    CKAP4 in vitro;in vivo12913003 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00013Urokinase"Urokinase can be used for the treatment of pulminary embolism, coronary artery thrombosis, IV catheter clearance, and venous and arterial blood clots."B01AD04
    approvedDB00513Aminocaproic AcidFor use in the treatment of excessive postoperative bleeding.B02AA01
    approvedDB01088IloprostUsed for the treatment of pulmonary arterial hypertension.B01AC11
    experimentalDB041346-Amino Hexanoic Acid
    experimentalDB076845-(DIMETHYLAMINO)-2-NAPHTHALENESULFONIC ACID