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: PSRC1

    Description: proline/serine-rich coiled-coil 1

    Entrez Gene ID: 84722

    SwissProt Acc Number: Q6PGN9

    RefSeq: NM_001005290

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

    .."Loci corresponding to CDKN2A/CDKN2B/ANRIL, MTHFD1L, CELSR2, PSRC1 and SORT1 genes have been associated with CHD, "..

    From PMID: 21860704, in Journal World J Cardiol. , 2011


    References

    There were 5 potential papers with PSRC1 and CHD.

    PMIDTitleJournalsDetails
    24005217 From genotype to phenotype in human atherosclerosis--recent findings.Current opinion in lipidologyMore Details
    21860704 Implications of discoveries from genome-wide association studies in current cardiovascular practice.World journal of cardiologyMore Details
    18649068 The novel genetic variant predisposing to coronary artery disease in the region of the PSRC1 and CELSR2 genes on chromosome 1 associates with serum cholesterol."Journal of molecular medicine (Berlin, Germany)"More Details
    18179892 Genome-wide association study identifies genes for biomarkers of cardiovascular disease: serum urate and dyslipidemia.American journal of human geneticsMore Details
    18193044 "Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans."Nature geneticsMore Details

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



    PPI interactions

    There were totally 9 unique genes interacted with PSRC1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    APP Reconstituted Complex21832049 No
    S100A9 Co-fractionation22939629 CHD related
    PTMA Co-fractionation22939629 No
    AURKA Co-fractionation22939629 No
    SRGN Two-hybrid21900206 No
    SH3KBP1 Affinity Capture-MS19531213 No
    IGBP1 Co-fractionation22939629 No
    PSME1 Co-fractionation22939629 No
    PRDX5 Co-fractionation22939629 No


    Involved FDA drugs

    There was no drug associated with PSRC1