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: SHH

    Description: sonic hedgehog homolog (Drosophila)

    Entrez Gene ID: 6469

    SwissProt Acc Number: Q15465

    RefSeq: NM_000193

    It was suspected to be CHD related:

    .."Interestingly, we found an asymmetric reduction in SHH signaling in cardiac myocytes, as compared with perivascular cells, resulting in excessive coronary artery formation in the Gpc3-deficient animals."..

    From PMID: 19733558, in Journal Dev Biol. , 2009


    References

    There were 3 potential papers with SHH and CHD.

    PMIDTitleJournalsDetails
    20720195 Sonic hedgehog signaling induces vascular smooth muscle cell proliferation via induction of the G1 cyclin-retinoblastoma axis."Arteriosclerosis, thrombosis, and vascular biology"More Details
    19629560 Sonic hedgehog is a potent chemoattractant for human monocytes: diabetes mellitus inhibits Sonic hedgehog-induced monocyte chemotaxis.Basic research in cardiologyMore Details
    19733558 Loss of glypican-3 function causes growth factor-dependent defects in cardiac and coronary vascular development.Developmental biologyMore Details

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



    PPI interactions

    There were totally 8 unique genes interacted with SHH. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SHH Co-purification11395778|11395778|11395778 CHD related
    UBC Affinity Capture-Western21357747 No
    ADCYAP1 in vitro12417650 No
    HHIP in vivo10050855 No
    SYVN1 Affinity Capture-Western21357747 No
    PTCH1 in vivo9811851 No
    PTCH2 in vivo9811851 No
    GAS1 in vitro;in vivo11572986 No


    Involved FDA drugs

    There was no drug associated with SHH