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: CCL21

    Description: chemokine (C-C motif) ligand 21

    Entrez Gene ID: 6366

    SwissProt Acc Number: O00585

    RefSeq: NM_002989

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

    ..The abnormal regulation of CCL19 and CCL21 and their common receptor in atherosclerosis could contribute to disease progression by recruiting T-cells and macrophages to the atherosclerotic lesions and by promoting inflammatory responses in these cells...

    From PMID: 17170367, in Journal Arterioscler Thromb Vasc Biol. , 2007


    References

    There were 3 potential papers with CCL21 and CHD.

    PMIDTitleJournalsDetails
    20373128 Inflammatory response to percutaneous coronary intervention in stable coronary artery disease.Journal of thrombosis and thrombolysisMore Details
    20231178 Inflammatory markers in patients with coronary artery disease with and without inflammatory rheumatic disease."Rheumatology (Oxford, England)"More Details
    17170367 Enhanced expression of the homeostatic chemokines CCL19 and CCL21 in clinical and experimental atherosclerosis: possible pathogenic role in plaque destabilization."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 10 unique genes interacted with CCL21. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    GOT2 Two-hybrid21900206 No
    CCR7 in vivo9507024,9585422 CHD related
    CCRL1 in vitro10706668 No
    Igfbp7 Reconstituted Complex12847218 No
    CCR10 Reconstituted Complex10706668 No
    VCAN Reconstituted Complex11083865 CHD related
    UBQLN4 Two-hybrid16713569 No
    CCBP2 in vivo10706668 No
    CTSD in vitro12651610 No
    CXCL13 in vitro;in vivo15546958 No


    Involved FDA drugs

    There was no drug associated with CCL21