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: NOTCH3

    Description: Notch homolog 3 (Drosophila)

    Entrez Gene ID: 4854

    SwissProt Acc Number: Q9UM47

    RefSeq: NM_000435

    It was suspected to be CHD related:

    ..Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is an angiopathy caused by mutations in the NOTCH3 gene...

    From PMID: 12861102, in Journal Medicine (Baltimore) , 2003


    References

    There were 6 potential papers with NOTCH3 and CHD.

    PMIDTitleJournalsDetails
    22752632 Apelin-13 increases myocardial progenitor cells and improves repair postmyocardial infarction.American journal of physiology. Heart and circulatory physiologyMore Details
    22204979 The role of endothelial cell-bound Jagged1 in Notch3-induced human coronary artery smooth muscle cell differentiation.BiomaterialsMore Details
    21330605 Soluble Jagged-1 inhibits neointima formation by attenuating Notch-Herp2 signaling."Arteriosclerosis, thrombosis, and vascular biology"More Details
    16514092 Electrocardiogram in cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy patients without any clinical evidence of coronary artery disease: a case-control study.Stroke; a journal of cerebral circulationMore Details
    15905966 "Biomedicine and diseases: the Klippel-Trenaunay syndrome, vascular anomalies and vascular morphogenesis."Cellular and molecular life sciences : CMLSMore Details
    12861102 Myocardial infarction in cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL).MedicineMore Details

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



    PPI interactions

    There were totally 20 unique genes interacted with NOTCH3. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SNW1 Reconstituted Complex11404076 No
    DLL1 Reconstituted Complex11006133 CHD related
    JAG1 Reconstituted Complex11006133 CHD related
    JAG2 Reconstituted Complex11006133 No
    GSK3B Affinity Capture-Western21502811 CHD related
    STRAP Affinity Capture-Western21502811 No
    CBL Affinity Capture-Western19966856 No
    PSEN2 in vivo11518718 No
    MAML2 in vivo12370315 No
    MAML3 in vivo12370315 No
    CHUK in vivo17289033 CHD related
    RBPJ in vivo11404076 No
    NOTCH1 Phenotypic Suppression11404076 CHD related
    MAML1 Reconstituted Complex11101851|11101851 No
    UBC Affinity Capture-Western21502811|21139048|21890473 No
    CSNK2B Two-hybrid21900206 No
    PSMA1 Affinity Capture-Western17292860 No
    PTCRA Affinity Capture-Western19966856 No
    KAT2B in vitro;in vivo;yeast 2-hybrid11404076 No
    PSEN1 in vivo11518718 No


    Involved FDA drugs

    There was no drug associated with NOTCH3