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: S100B

    Description: S100 calcium binding protein B

    Entrez Gene ID: 6285

    SwissProt Acc Number: P04271

    RefSeq: NM_006272

    It was suspected to be CHD related:

    ..These results suggest that interaction of RAGE and its ligand S100B after myocardial infarction may play a role in myocyte apoptosis by activating ERK1/2 and p53 signaling...

    From PMID: 19910580, in Journal Circ Res. , 2010


    References

    There were 4 potential papers with S100B and CHD.

    PMIDTitleJournalsDetails
    21663912 "Association of increased S100B, S100A6 and S100P in serum levels with acute coronary syndrome and also with the severity of myocardial infarction in cardiac tissue of rat models with ischemia-reperfusion injury."AtherosclerosisMore Details
    19910580 S100B interaction with the receptor for advanced glycation end products (RAGE): a novel receptor-mediated mechanism for myocyte apoptosis postinfarction.Circulation researchMore Details
    20381659 Evaluation of methods to predict early long-term neurobehavioral outcome after coronary artery bypass grafting.The American journal of cardiologyMore Details
    18539754 AGE/RAGE produces endothelial dysfunction in coronary arterioles in type 2 diabetic mice.American journal of physiology. Heart and circulatory physiologyMore Details

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



    PPI interactions

    There were totally 23 unique genes interacted with S100B. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    TP53 Affinity Capture-Western15178678 CHD related
    IQGAP1 Affinity Capture-Western12377780 No
    S100B Two-hybrid10913138|10913138|9925766|9519411|9335118,9519411 CHD related
    S100A11 Two-hybrid10913138|10913138 No
    S100A6 Two-hybrid10913138|10913138|9925766|9925766|9925766,10913138 CHD related
    CAPZA1 Reconstituted Complex12470955 No
    MAPT Reconstituted Complex11264299|2833519|2833519,11264299 No
    VAV1 Affinity Capture-Western10394361 No
    AHNAK Reconstituted Complex11312263|11312263|11312263 No
    NDRG1 Affinity Capture-Western12493777 No
    STK38 Reconstituted Complex9774336|9774336 No
    DES in vitro10510252 No
    GFAP in vitro10510252 CHD related
    S100A1 Two-hybrid16189514 CHD related
    ANXA6 Reconstituted Complex9883272 No
    PGM1 Far Western8894274 No
    MDM2 Reconstituted Complex20591429 CHD related
    CALM1 Reconstituted Complex15840729 No
    GUCY2D in vivo15556616 No
    AGER in vivo10399917 CHD related
    CACYBP in vitro;in vivo12042313 CHD related
    TNIP1 in vitro;yeast 2-hybrid9923610 No
    SUGT1 in vitro12746458 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00768OlopatadineFor the treatment of ocular itching associated with allergic conjunctivitis.S01GX09;R01AC08
    experimentalDB01373Calcium"Calcium plays a vital role in the anatomy, physiology and biochemistry of organisms and of the cell, particularly in signal transduction pathways. It is vital in cell signaling, muscular contractions, bone health, and signalling cascades."D11AX03;V03AF04;C05BX01;B02BC08;B01AC08;R01AX01;N02BA15;V03AF03;G04BA03;B05XA07;A01AD11;A12AA03;A11HA31;V08AC10;A12AA11;D03AX04;A12AA06;A11GA01;J04AA03;A12AA12;A12AA30;A06AC08;A12AA02;A12AA05;A12AA09;N07BB02;A07XA03;A12AA07;A12AA10;V03AE01;A02AC01;A12AA04;A02AC02;A12AA08;A12AA01;A12AA20
    experimentalDB04464N-Formylmethionine
    experimentalDB06941(Z)-2-[2-(4-methylpiperazin-1-yl)benzyl]diazenecarbothioamide
    experimentalDB070042-[(5-hex-1-yn-1-ylfuran-2-yl)carbonyl]-N-methylhydrazinecarbothioamide