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: CSF1

    Description: colony stimulating factor 1 (macrophage)

    Entrez Gene ID: 1435

    SwissProt Acc Number: P09603

    RefSeq: NM_000757

    It was suspected to be CHD related:

    .."In severely obese women (mean body mass index = 43.0 +/- 1.1 kg/m(2)), higher protein expression of both MCP1 and CSF1 was detected in OM vs. sc fat. "..

    From PMID: 17374712, in Journal J Clin Endocrinol Metab , 2007


    References

    There were 1 potential papers with CSF1 and CHD.

    PMIDTitleJournalsDetails
    17374712 Macrophage infiltration into omental versus subcutaneous fat across different populations: effect of regional adiposity and the comorbidities of obesity.The Journal of clinical endocrinology and metabolismMore Details

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



    PPI interactions

    There were totally 10 unique genes interacted with CSF1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PIK3R2 Reconstituted Complex1334406|1334406 No
    CBL Affinity Capture-Western17353186 No
    UBC Affinity Capture-Western17353186 No
    HLA-B in vitro15494511 No
    CSF1 in vitro1733926,8422357 CHD related
    CSF1R Reconstituted Complex8355686|2408759,8355686 No
    SLA2 Reconstituted Complex17353186 No
    TNF in vivo8336080 CHD related
    SOCS1 in vitro;in vivo;yeast 2-hybrid11297560 CHD related
    GAB3 in vivo11739737 No


    Involved FDA drugs

    There was no drug associated with CSF1