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: CD9

    Description: CD9 molecule

    Entrez Gene ID: 928

    SwissProt Acc Number: P21926

    RefSeq: NM_001769

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

    .."Surface expression of CD9 (P =0.004), GP Ib (P = 0.0001), GP IIb/IIIa (P = 0.007), VLA-2 (P = 0.01), P-selectin (P = 0.02), and PECAM-1 (P = 0.01), but not the vitronectin receptor, was also reduced in sertraline and NDMS pretreated washed platelets. "..

    From PMID: 11394937, in Journal Pharmacol Res. , 2001


    References

    There were 1 potential papers with CD9 and CHD.

    PMIDTitleJournalsDetails
    11394937 "Platelet inhibition by sertraline and N-desmethylsertraline: a possible missing link between depression, coronary events, and mortality benefits of selective serotonin reuptake inhibitors."Pharmacological research : the official journal of the Italian PharmacologicalMore Details

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



    PPI interactions

    There were totally 25 unique genes interacted with CD9. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    ITGB1 Affinity Capture-Western8630057|12175627|9812906,9813091 CHD related
    IGSF8 Affinity Capture-Western11504738 No
    CD46 Affinity Capture-Western10741407 No
    PTGFRN Affinity Capture-Western11278880|11087758 No
    CD53 Affinity Capture-Western11959120 No
    SERPINH1 Affinity Capture-Western10227388 No
    PRKCA Affinity Capture-Western11325968 CHD related
    CD59 in vitro1377690 CHD related
    ITGA2 in vivo9812906,9813091 CHD related
    HBEGF in vivo;yeast 2-hybrid1939101,11735113,11846885,8194524 No
    CD82 Affinity Capture-Western15492270 No
    KIT Affinity Capture-Western12036870|12036870 No
    CD63 Affinity Capture-Western8630057|8630057,11204565,12175627 CHD related
    CD81 Affinity Capture-Western8630057|9804823|8630057 No
    ITGA3 Affinity Capture-Western10694273|10065872|10065872,10694273 CHD related
    ITGA5 Affinity Capture-Western10065872 CHD related
    TSPAN4 Affinity Capture-Western9360996|9360996 No
    CD19 Affinity Capture-Western9804823 No
    CD36 Affinity Capture-Western11238109|11238109 CHD related
    UBC Affinity Capture-MS21139048|21906983 No
    ELAVL1 Affinity Capture-RNA19322201 No
    LGALS3BP Affinity Capture-Western20581239 No
    ATP6V1B1 Affinity Capture-MS21674799 No
    CD38 in vivo15941914 CHD related
    ADAM2 in vivo10518536 No


    Involved FDA drugs

    There was no drug associated with CD9