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: SH2B1

    Description: SH2B adaptor protein 1

    Entrez Gene ID: 25970

    SwissProt Acc Number: Q9NRF2

    RefSeq: NM_001145795

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

    ..Variability at the SH2B1 obesity locus is associated with MI in diabetic patients and with reduced insulin-stimulated NOS activity in human endothelial cells...

    From PMID: 21907990, in Journal Atherosclerosis. , 2011


    References

    There were 1 potential papers with SH2B1 and CHD.

    PMIDTitleJournalsDetails
    21907990 The SH2B1 obesity locus is associated with myocardial infarction in diabetic patients and with NO synthase activity in endothelial cells.AtherosclerosisMore Details

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



    PPI interactions

    There were totally 7 unique genes interacted with SH2B1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    FGFR3 Affinity Capture-Western11827956|11827956 No
    GRB2 Affinity Capture-Western9856458|9856458 CHD related
    NTRK1 Two-hybrid9856458|10708759 No
    JAK2 Two-hybrid9343427|12551917,10757801,9343427 CHD related
    INSR Affinity Capture-Western9742218|9742218|10594240 No
    NTRK2 Two-hybrid12074588 No
    KIAA0319 Two-hybrid12421765 No


    Involved FDA drugs

    There was no drug associated with SH2B1