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: CCL19

    Description: chemokine (C-C motif) ligand 19

    Entrez Gene ID: 6363

    SwissProt Acc Number: Q99731

    RefSeq: NM_006274

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

    .."While monocyte chemoattractant protein, CCL21 and CXCL16 increased rapidly in response to PCI, Interleukin-8, CCL19 and RANTES decreased."..

    From PMID: 20373128, in Journal J Thromb Thrombolysis. , 2011


    References

    There were 2 potential papers with CCL19 and CHD.

    PMIDTitleJournalsDetails
    20373128 Inflammatory response to percutaneous coronary intervention in stable coronary artery disease.Journal of thrombosis and thrombolysisMore 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 8 unique genes interacted with CCL19. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CCL19 in vitro9153236 CHD related
    CCRL1 in vitro10706668 No
    CCR10 Reconstituted Complex10706668 No
    CCR7 Reconstituted Complex9153236 CHD related
    UBC Affinity Capture-MS21139048 No
    CCBP2 in vivo10706668 No
    CXCL13 in vitro;in vivo15546958,16678487 No
    CCL22 in vitro;in vivo15714581 No


    Involved FDA drugs

    There was no drug associated with CCL19