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: NOTCH2

    Description: Notch homolog 2 (Drosophila)

    Entrez Gene ID: 4853

    SwissProt Acc Number: Q04721

    RefSeq: NM_024408

    It was suspected to be CHD related:

    .."Recently, various human studies have revealed a high coincidence of VEGF and NOTCH polymorphisms with cardiovascular outflow tract anomalies,"..

    From PMID: 22683047, in Journal Differentiation , 2012


    References

    There were 3 potential papers with NOTCH2 and CHD.

    PMIDTitleJournalsDetails
    23967210 17beta-estradiol enhances signalling mediated by VEGF-A-delta-like ligand 4-notch1 axis in human endothelial cells.PloS oneMore Details
    21860640 Deoxyribonucleic Acid copy number aberrations in vasospastic angina patients using an array comparative genomic hybridization.Korean circulation journalMore Details
    18802018 Impaired Notch4 activity elicits endothelial cell activation and apoptosis: implication for transplant arteriosclerosis."Arteriosclerosis, thrombosis, and vascular biology"More Details

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



    PPI interactions

    There were totally 27 unique genes interacted with NOTCH2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CNTN1 Affinity Capture-Western14567914 No
    RBPJ Two-hybrid9032325|9032325 No
    JAG2 Affinity Capture-Western10958687|10958687 No
    SEC24C Co-fractionation22939629 No
    PCMT1 Co-fractionation22939629 No
    PSMB1 Co-fractionation22939629 No
    TJP1 Co-fractionation22939629 No
    SIN3A Co-fractionation22939629 No
    PLAUR Co-fractionation22939629 CHD related
    PSEN2 in vivo11518718 No
    MAML2 in vivo12370315 No
    MAML3 in vivo12370315 No
    SMAD1 yeast 2-hybrid15231748 CHD related
    GSK3B Biochemical Activity12794074|12794074|12794074 CHD related
    JAG1 Affinity Capture-Western11346656|10551863|10551863|10551863,10958687 CHD related
    DLL1 Affinity Capture-Western11346656|9244302|10958687 CHD related
    MAML1 Reconstituted Complex11101851|11101851 No
    UBC Affinity Capture-MS21139048|21890473 No
    CRKL Two-hybrid18654987 No
    MYOC Two-hybrid16289162|16289162 No
    SPEN Co-fractionation22939629 No
    NDUFV2 Co-fractionation22939629 No
    NDUFV1 Co-fractionation22939629 No
    LFNG in vitro;in vivo11346656 No
    MFNG in vitro;in vivo11346656 No
    DTX1 in vivo9244302 No
    PSEN1 in vivo11518718 No


    Involved FDA drugs

    There was no drug associated with NOTCH2