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: B2M

    Description: beta-2-microglobulin

    Entrez Gene ID: 567

    SwissProt Acc Number: P61769

    RefSeq: NM_004048

    It was suspected to be CHD related:

    .."In PAD patients, circulating B2M is elevated and correlates with the severity of disease independent of other risk factors. "..

    From PMID: 17724262, in Journal Circulation , 2007


    References

    There were 6 potential papers with B2M and CHD.

    PMIDTitleJournalsDetails
    23518194 Novel filtration markers as predictors of all-cause and cardiovascular mortality in US adults.American journal of kidney diseases : the official journal of the National KidneyMore Details
    22305758 "Novel markers of kidney function as predictors of ESRD, cardiovascular disease, and mortality in the general population."American journal of kidney diseases : the official journal of the National KidneyMore Details
    23006766 The LO-BaFL method and ALS microarray expression analysis.BMC bioinformaticsMore Details
    21546482 Beta 2 microglobulin and the risk for cardiovascular events in patients with asymptomatic carotid atherosclerosis.Stroke; a journal of cerebral circulationMore Details
    20667078 Novel proteins associated with risk for coronary heart disease or stroke among postmenopausal women identified by in-depth plasma proteome profiling.Genome medicineMore Details
    17724262 Beta2-microglobulin as a biomarker in peripheral arterial disease: proteomic profiling and clinical studies.CirculationMore Details

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



    PPI interactions

    There were totally 25 unique genes interacted with B2M. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    BAG6 Two-hybrid16169070 No
    A2M Reconstituted Complex10731476|10731476 No
    TAPBP Affinity Capture-Western17055437 No
    B2M Reconstituted Complex18543331|12023961 CHD related
    HFE Affinity Capture-Western20618438 CHD related
    CALR in vivo8769474 No
    CD8A in vitro11914379 No
    BAT3 yeast 2-hybrid16169070 CHD related
    PRSS23 Two-hybrid16169070 No
    HLA-E Co-crystal Structure9605335|9605335,10064069 CHD related
    CD1D Affinity Capture-Western10221650|11257307,10221650 No
    GRB2 Two-hybrid18624398 CHD related
    UBC Affinity Capture-MS18781797|21139048 No
    KIAA0101 Affinity Capture-MS21628590 No
    TAP1 Affinity Capture-MS17055437 CHD related
    HLA-B Co-crystal Structure17057332|11738047,2450918 No
    HLA-A in vitro;in vivo93026,11502003,1448153 No
    HLA-C in vitro2450918 No
    HLA-G in vivo9228302 No
    HLA-F in vivo11169396 No
    CD1B in vitro12118248 No
    CD1A in vitro12833155 No
    CD1E in vivo10948205 No
    FCGRT in vitro12006623,10933786 No
    LILRB1 in vitro12897781 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB027403-Indolebutyric Acid
    experimentalDB04464N-Formylmethionine