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: NPC1

    Description: "Niemann-Pick disease, type C1"

    Entrez Gene ID: 4864

    SwissProt Acc Number: O15118

    RefSeq: NM_000271

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

    ..The results of the present study suggest that NPC1 variants seem to be contributors to coronary heart disease occurrence in Chinese population...

    From PMID: 20955564, in Journal BMC Med Genet. , 2010


    References

    There were 3 potential papers with NPC1 and CHD.

    PMIDTitleJournalsDetails
    24296264 "NPC1, intracellular cholesterol trafficking and atherosclerosis."Clinica chimica acta; international journal of clinical chemistryMore Details
    20955564 Interaction of functional NPC1 gene polymorphism with smoking on coronary heart disease.BMC medical geneticsMore Details
    17984379 "Spontaneous atherothrombosis and medial degradation in Apoe-/-, Npc1-/- mice."CirculationMore Details

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



    PPI interactions

    There were totally 9 unique genes interacted with NPC1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    UBC Affinity Capture-Western16757520 No
    MRPS28 Co-fractionation22939629 No
    TMOD3 Co-fractionation22939629 No
    VPS4A Affinity Capture-Western16757520|16757520|16757520 No
    OSBPL5 Affinity Capture-Western21220512 No
    LRP6 Affinity Capture-Western18948618 CHD related
    TMEM173 Affinity Capture-MS21903422 No
    UNC93B1 Affinity Capture-MS21903422 No
    FBXO6 Affinity Capture-MS22268729 No


    Involved FDA drugs

    There was no drug associated with NPC1