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: CD44

    Description: CD44 molecule (Indian blood group)

    Entrez Gene ID: 960

    SwissProt Acc Number: P16070

    RefSeq: NM_000610

    It was suspected to be CHD related:

    .."The expression of HAS1, HAS2, CD44, and FGF-2 was considerably up-regulated at days 1 and 6 and returned to basal levels after 42 days."..

    From PMID: 18196276, in Journal Cell Tissue Res , 2008


    References

    There were 11 potential papers with CD44 and CHD.

    PMIDTitleJournalsDetails
    24019856 Bioengineering silicon quantum dot theranostics using a network analysis of metabolomic and proteomic data in cardiac ischemia.TheranosticsMore Details
    22711477 Osteopontin promotes inflammation in patients with acute coronary syndrome through its activity on IL-17 producing cells.European journal of immunologyMore Details
    21493893 Malignant tumor formation after transplantation of short-term cultured bone marrow mesenchymal stem cells in experimental myocardial infarction and diabetic neuropathy.Circulation researchMore Details
    19286938 Myocardial oxygenation and functional recovery in infarct rat hearts transplanted with mesenchymal stem cells.American journal of physiology. Heart and circulatory physiologyMore Details
    18196276 Parallel up-regulation of FGF-2 and hyaluronan during development of cardiac hypertrophy in rat.Cell and tissue researchMore Details
    17429297 Adipose tissue stromal cells transplantation in rats of acute myocardial infarction.Coronary artery diseaseMore Details
    16889848 Transplantation of mesenchymal stem cells from human bone marrow improves damaged heart function in rats.International journal of cardiologyMore Details
    16620830 Augmented levels of CD44 in macrophages from atherosclerotic subjects: a possible IL-6-CD44 feedback loop?AtherosclerosisMore Details
    15621483 Upregulation of endothelial adhesion molecules in hearts with congestive and ischemic cardiomyopathy: immunohistochemical evaluation of inflammatory endothelial cell activation.European journal of cardio-thoracic surgery : official journal of the EuropeanMore Details
    15302784 Extracellular matrix changes in stented human coronary arteries.CirculationMore Details
    15023889 CD44 regulates arteriogenesis in mice and is differentially expressed in patients with poor and good collateralization.CirculationMore Details

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



    PPI interactions

    There were totally 51 unique genes interacted with CD44. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    LCK Affinity Capture-Western8576267|9573028|9573028 No
    ERBB4 Affinity Capture-Western11825873 No
    TIAM1 Reconstituted Complex10636882 No
    TGFBR1 Reconstituted Complex12145287 CHD related
    VAV2 Affinity Capture-Western11606575 No
    FN1 Affinity Capture-Western1730778|1730778 CHD related
    EGFR Affinity Capture-Western12093135 CHD related
    ERBB2 Affinity Capture-Western12093135 CHD related
    HBEGF Reconstituted Complex7532176 No
    EZR Reconstituted Complex12032545 No
    VCAN Reconstituted Complex10950950 CHD related
    SRC Affinity Capture-Western11084024|11084024|21701559 CHD related
    PTPRC Co-fractionation9573028 CHD related
    FYN Co-fractionation9573028|9573028 No
    MSN Reconstituted Complex9472040 No
    NF2 Affinity Capture-Western17891137 No
    PRKCZ Affinity Capture-Western22610405 No
    ITGB1 Co-localization21701559 CHD related
    FLOT2 Co-localization21701559 No
    CAV1 Co-localization21701559 CHD related
    EP300 Affinity Capture-Western21701559 CHD related
    STAT3 Affinity Capture-Western21701559 CHD related
    PKN1 in vivo15123640 No
    ARHGEF12 in vivo16565089 No
    GARS in vivo;yeast 2-hybrid15452148 No
    MADCAM1 in vitro2474557 No
    CD44 in vivo11825873 CHD related
    ARHGEF1 Affinity Capture-Western12748184|12748184 No
    COL14A1 Co-purification8986622|8986622 No
    IGFBP3 Reconstituted Complex12127836|12127836 CHD related
    MMP7 Affinity Capture-Western11825873|11825873 CHD related
    UBC Affinity Capture-MS21987572|21139048|21906983 No
    ELAVL1 Affinity Capture-RNA19322201 No
    VHL Affinity Capture-MS22234250 No
    SLC3A2 Co-fractionation22939629 No
    SRGN in vivo9334256 No
    CD4 in vitro7539755 CHD related
    TGFBR2 in vivo12145287 CHD related
    DMP1 in vitro11825898 No
    ANK1 in vitro;in vivo15051494,7505012 CHD related
    HMMR in vitro12939665 No
    COL1A1 in vitro1730778 CHD related
    COL1A2 in vitro1730778 CHD related
    MMP1 in vitro11381077 CHD related
    MMP9 in vivo10652271,17912438 CHD related
    CSK in vitro;in vivo11084024 No
    EPB41 in vitro12901833 No
    SELE in vitro;in vivo11402070 CHD related
    FGF2 in vivo7532176 CHD related
    CD74 in vivo8343954 No
    SPP1 in vitro10657301,12377945 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB08818Hyaluronan"Used to treat knee pain in patients with joint inflammation (osteoarthritis). It is usually used in patients who have not responded to other treatments such as acetaminophen, exercise, or physical therapy. Sodium hyaluronate may also be used in plastic surgery to reduce wrinkles on the face or as a filler in other parts of the body. May be used in ophthalmology to assist in the extraction of cataracts, the implantation of intraocular lenses, corneal transplants, glaucoma filtration, retinal attachment and in the treatment of dry eyes. Finally, Sodium hyaluronate is also used to coat the bladder lining in treating interstitial cystitis."R01AX09;S01KA01;D03AX05;M09AX01