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: IGF2

    Description: insulin-like growth factor 2 (somatomedin A)

    Entrez Gene ID: 3481

    SwissProt Acc Number: P01344

    RefSeq: NM_000612

    It was suspected to be CHD related:

    .."IGF2 could be considered as a candidate gene for future research on mechanisms for the association between height and chronic diseases, such as cancer, diabetes, and coronary heart disease."..

    From PMID: 17488802, in Journal J Clin Endocrinol Metab , 2007


    References

    There were 2 potential papers with IGF2 and CHD.

    PMIDTitleJournalsDetails
    17488802 Study of association between common variation in the insulin-like growth factor 2 gene and indices of obesity and body size in middle-aged men and women.The Journal of clinical endocrinology and metabolismMore Details
    16166779 Single-nucleotide polymorphisms and haplotype LD analysis of the 29-kb IGF2 region on chromosome 11p15.5 in the Korean population.Human heredityMore Details

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



    PPI interactions

    There were totally 21 unique genes interacted with IGF2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    IGFBP1 Reconstituted Complex10810289|10810289 CHD related
    IGFBP3 Reconstituted Complex11749962|9497324|10407151 CHD related
    IGFBP6 Reconstituted Complex7683646|7683646 No
    IGFBP5 Reconstituted Complex9497324|9497324 CHD related
    BAG6 Two-hybrid21900206 No
    ITGB1BP3 Two-hybrid21900206 No
    FAF1 Two-hybrid21900206 No
    PLG in vitro15642732 No
    IGFBP2 in vitro;in vivo1714916,8781553,2465304 No
    IGF2R in vitro;in vivo7797478,9722981 No
    IGF1R in vivo9972281 CHD related
    NOV Reconstituted Complex10084601|10084601 No
    IGFBP7 Reconstituted Complex8939990|8939990 No
    TF Reconstituted Complex11749962 No
    VTN Reconstituted Complex10342887|10342887 CHD related
    IDE Reconstituted Complex1733942 No
    IGFBP4 Reconstituted Complex9722589 No
    PCSK4 Biochemical Activity16040806|16040806 No
    WISP2 in vitro10358067 No
    INSR in vivo9722981 No
    GPC3 in vivo8589713 CHD related


    Involved FDA drugs

    There was no drug associated with IGF2