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: PALLD

    Description: "palladin, cytoskeletal associated protein"

    Entrez Gene ID: 23022

    SwissProt Acc Number: Q8WX93

    RefSeq: NM_001166108

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

    .."A single-nucleotide polymorphism (SNP) in the palladin gene (PALLD, rs7439293) has recently been reported to be associated with coronary heart disease (CHD) in two case-control studies as well as in a large population-based cohort (Atherosclerosis Risk in Communities study, ARIC). "..

    From PMID: 21054356, in Journal Eur J Clin Invest , 2011


    References

    There were 2 potential papers with PALLD and CHD.

    PMIDTitleJournalsDetails
    21054356 Polymorphism of the palladin gene and cardiovascular outcome in patients with atherosclerosis.European journal of clinical investigationMore Details
    18073581 Five common gene variants identify elevated genetic risk for coronary heart disease.Genetics in medicine : official journal of the American College of MedicalMore Details

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



    PPI interactions

    There were totally 14 unique genes interacted with PALLD. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    ACTN1 Affinity Capture-Western16125169|15147863 No
    SARS Co-fractionation22939629 No
    ACTN2 in vivo10931874 No
    EZR Two-hybrid11598191|11598191|11598191 No
    UBC Affinity Capture-MS21139048|21906983 No
    ISG15 Affinity Capture-MS16009940 No
    SORBS2 Reconstituted Complex16125169 No
    ACOX1 Co-fractionation22939629 No
    HSP90AA4P Co-fractionation22939629 No
    IGBP1 Co-fractionation22939629 No
    DSTN Co-fractionation22939629 No
    HSPB1 Co-fractionation22939629 No
    NDUFV1 Co-fractionation22939629 No
    ITGB5 yeast 2-hybrid16355270 No


    Involved FDA drugs

    There was no drug associated with PALLD