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: CXCL1

    Description: "chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha)"

    Entrez Gene ID: 2919

    SwissProt Acc Number: P09341

    RefSeq: NM_001511

    It was suspected to be CHD related:

    .."hypertension and diabetes were associated with the absence of collaterals (ROC area 0.91). When analyzed according to extent of collateralization, higher Rentrop scores were significantly associated with increased concentration of the angiogenic ligand CXCL1 (p<0.0001),"..

    From PMID: 21731663, in Journal PLoS One , 2011


    References

    There were 4 potential papers with CXCL1 and CHD.

    PMIDTitleJournalsDetails
    23925450 Treatment with the CC chemokine-binding protein Evasin-4 improves post-infarction myocardial injury and survival in mice.Thrombosis and haemostasisMore Details
    22030025 Enhanced IL-17 signalling following myocardial ischaemia/reperfusion injury.International journal of cardiologyMore Details
    21731663 Plasma chemokine levels are associated with the presence and extent of angiographic coronary collaterals in chronic ischemic heart disease.PloS oneMore Details
    19162037 CB(2) cannabinoid receptor activation is cardioprotective in a mouse model of ischemia/reperfusion.Journal of molecular and cellular cardiologyMore Details

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



    PPI interactions

    There were totally 6 unique genes interacted with CXCL1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    DARC Reconstituted Complex13679391|7592830 No
    CXCL1 Co-crystal Structure8397104|7806518,8089846,8397104 CHD related
    CXCR2 in vivo8550564,8940121,8702798,1379593 CHD related
    CXCR1 in vivo1379593,8702798 CHD related
    HIPK2 Affinity Capture-Western15896780|15896780 No
    MMP9 in vitro11023497 CHD related


    Involved FDA drugs

    There was no drug associated with CXCL1