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: CDC42

    Description: "cell division cycle 42 (GTP binding protein, 25kDa)"

    Entrez Gene ID: 998

    SwissProt Acc Number: P60953

    RefSeq: NM_001039802

    It was suspected to be CHD related:

    ..The altered melusin pathways and CDC42 parallel the cardiac function progression during cardiac remodeling post-MI...

    From PMID: 21546274, in Journal Cardiovasc Pathol , 2012


    References

    There were 2 potential papers with CDC42 and CHD.

    PMIDTitleJournalsDetails
    21546274 Altered melusin pathways involved in cardiac remodeling following acute myocardial infarction.Cardiovascular pathology : the official journal of the Society for CardiovascularMore Details
    14660654 The apolipoprotein(a) component of lipoprotein(a) stimulates actin stress fiber formation and loss of cell-cell contact in cultured endothelial cells.The Journal of biological chemistryMore Details

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



    PPI interactions

    There were totally 155 unique genes interacted with CDC42. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CDC42EP1 Two-hybrid16189514|20936779|16189514 No
    FNBP1L Affinity Capture-Western15260990 No
    ARHGAP29 Two-hybrid14749388 No
    KAT5 Two-hybrid16169070 No
    C14orf1 Two-hybrid16169070|16169070 No
    PDE6D Two-hybrid16169070|16169070 No
    UBR1 Two-hybrid16169070|16169070 No
    LRIF1 Two-hybrid16169070 No
    TP53 Two-hybrid16169070|16169070 CHD related
    EEF1G Two-hybrid16169070|16169070 No
    UNC119 Two-hybrid16169070|16169070 No
    Kin Two-hybrid9535835 No
    Net1 Two-hybrid9535835 No
    Diap3 Two-hybrid9535835 No
    Rock1 Two-hybrid9535835 No
    CDC42EP3 Two-hybrid9535835|20936779|10490598 No
    VAV1 Affinity Capture-Western11287617 No
    MAP3K10 Two-hybrid9427749 No
    ARHGAP1 Two-hybrid9427749|10551883|10684602 No
    MAP3K11 Two-hybrid9427749|10799501 No
    RAC1 Two-hybrid9427749 CHD related
    CDC42SE1 Two-hybrid10816584|20936779|10816584,12421766 No
    CDC42SE2 Two-hybrid10816584 No
    CDC42 Co-crystal Structure10211824 CHD related
    IQGAP2 Reconstituted Complex8756646 No
    PARD6B Two-hybrid11162552|10934474|20936779|14676191,11260256,10934474 No
    MAP3K4 Reconstituted Complex9079650 No
    ERRFI1 Affinity Capture-Western10749885|10749885 No
    PAK6 Reconstituted Complex11773441|20936779 No
    IQGAP1 Reconstituted Complex8798539|8798539|8670801|9182573|9535855 No
    WAS Reconstituted Complex10713100|20936779|10360579|10684602|8625410,10724160,15361624,12235133,10068673,12769846,9742969,10360578,10802735 No
    MCF2 Reconstituted Complex10854437 No
    DOCK9 Reconstituted Complex12172552 No
    CDC42EP5 Reconstituted Complex11035016 No
    CDC42EP2 Reconstituted Complex11035016|20936779 No
    PLEKHG2 Reconstituted Complex11839748 No
    FGD1 Reconstituted Complex8969170 No
    ARHGEF25 Reconstituted Complex12547822 No
    PLD1 Reconstituted Complex10747870|10747870 No
    ARRB1 Two-hybrid20936779 No
    ARRB2 Two-hybrid20936779 No
    CSN2 Two-hybrid20936779 No
    DIAPH2 Two-hybrid20936779 No
    COX1 Two-hybrid20936779 No
    MYO6 Two-hybrid20936779 No
    MYO9A Two-hybrid20936779|16169070 No
    PAK3 Two-hybrid20936779 No
    RAP1GDS1 Two-hybrid20936779 No
    RPL22 Two-hybrid20936779 No
    S100A9 Two-hybrid20936779 CHD related
    ST13 Two-hybrid20936779 No
    UBC Two-hybrid20936779 No
    VRK2 Two-hybrid20936779 No
    ZNF175 Two-hybrid20936779 No
    CDC42BPA Two-hybrid20936779 No
    MCM3AP Two-hybrid20936779 No
    HERC2 Two-hybrid20936779 No
    RPL23 Two-hybrid20936779 No
    CDC42BPB Two-hybrid20936779 No
    ARHGEF11 Two-hybrid20936779 No
    SYNE1 Two-hybrid20936779 No
    CDC42EP4 Two-hybrid20936779 No
    FMNL2 Two-hybrid20936779 No
    SH3D19 Two-hybrid20936779 No
    KIAA2026 Two-hybrid20936779 No
    MUC12 Two-hybrid20936779 No
    CBL Affinity Capture-Western14505571|14505571|16356860 No
    ARHGEF7 Affinity Capture-Western14505571|14505571|15649357,16983070 No
    CBLL1 Reconstituted Complex18057010|18057010 No
    CDH1 Reconstituted Complex18057010|18057010 No
    A2M Two-hybrid18624398 No
    AHSG Two-hybrid18624398 CHD related
    APOH Two-hybrid18624398 CHD related
    CPN1 Two-hybrid18624398 No
    ETFA Two-hybrid18624398 No
    CFHR4 Two-hybrid18624398 No
    LGALS1 Two-hybrid18624398 No
    ZNF234 Two-hybrid18624398 No
    USP6 Reconstituted Complex12612085 No
    BCAR1 Affinity Capture-Western17038317 No
    LRRK2 Affinity Capture-Western21048939|21048939 No
    ARHGEF6 Affinity Capture-Western15306850|15649357 No
    FGD3 Reconstituted Complex18363964 No
    TGFBR1 Affinity Capture-Western15761153 CHD related
    TGFBR2 Affinity Capture-Western15761153 CHD related
    RAP1A Co-fractionation22939629 No
    C1orf103 yeast 2-hybrid16169070 No
    FNBP1 yeast 2-hybrid12421766 No
    LCK in vitro16293614 No
    DOCK8 Two-hybrid15304341|15304341 No
    TRIP10 Two-hybrid9210375|10713100|9210375|12456510 No
    ARHGDIA Affinity Capture-MS17353931|9490022|10676816,11149925 No
    PAK4 Affinity Capture-MS17353931|11756552|9822598 CHD related
    CDC42BPG Reconstituted Complex15194684|15194684 No
    ARHGAP27 Biochemical Activity15147912 No
    DEF6 Reconstituted Complex15023524|15023524 No
    MCF2L Affinity Capture-Western14701795|11889037|11889037 No
    BNIPL Two-hybrid12901880 No
    ARHGAP32 Biochemical Activity12857875|12819203|12446789 No
    PAK1 Reconstituted Complex12650940|16678097|9705280,7744004,8107774,10802735 CHD related
    BNIP2 Reconstituted Complex10799524|10799524|10954711|10954711,10799524,10551883 No
    BAIAP2 Far Western12504591|11696321|11130076|11696321 No
    PAK2 Protein-peptide10320322|20696164|10320322,16204230 No
    CSPG4 Affinity Capture-Western10587647|10587647 No
    GOPC Reconstituted Complex11162552 No
    NCF2 Reconstituted Complex9642115|9642115,7738010 No
    GDI1 Reconstituted Complex11583574|11583574|11583574 No
    TNK2 Affinity Capture-Western11394904|20086093|15123659|11394904,10802735 No
    PAK7 Affinity Capture-Western11756552|12032833,11756552 No
    ARHGAP26 Biochemical Activity11432776 No
    ARHGAP10 Biochemical Activity11432776 No
    ARHGAP17 Biochemical Activity11431473 No
    ARHGAP44 Biochemical Activity11431473 No
    PARD6A Two-hybrid10934474|10873802|10873802|11260256|11260256|14676191|10873802,12606577 No
    OPHN1 Biochemical Activity9582072|11998687,9582072 No
    CLIP1 Affinity Capture-Western12110184 No
    WASL Reconstituted Complex10781580|10724160,9422512,11943145 No
    ARHGDIG Reconstituted Complex9113980|9113980 No
    PARD6G Reconstituted Complex11260256|14676191|11260256 No
    ITSN1 Affinity Capture-Western11584276|11584276|12006984|12006984,11584276,15824104 No
    CNTNAP1 Reconstituted Complex9535855 No
    BCR Reconstituted Complex9535855 CHD related
    TNF Affinity Capture-MS15485837 CHD related
    CDKN1A Reconstituted Complex18057010 CHD related
    MARK4 Affinity Capture-MS14676191|14676191 No
    GRB2 Two-hybrid21900206 CHD related
    ABCA1 Affinity Capture-Western16443932 CHD related
    ELAVL1 Affinity Capture-RNA19322201 No
    SH3RF3 Affinity Capture-Western20696164 No
    PIK3R1 in vitro;in vivo9381982,7629060,8034624 CHD related
    EIF2AK2 in vitro7738010 No
    PRKCA in vivo11284700 CHD related
    PRKCG in vivo14676191 No
    PRKCZ in vivo10733591 No
    FLNA in vitro10051605 No
    PRKCI in vivo10934474,14676191 No
    KTN1 in vitro;yeast 2-hybrid9535835 No
    CASP3 in vitro;in vivo11278572 CHD related
    STAU1 in vitro15121898 No
    CASP7 in vitro;in vivo11278572 CHD related
    METAP2 in vitro7738010 No
    RAC2 in vitro9748241 No
    ARHGDIB in vivo9799233 No
    ACTR3 in vitro9860974 No
    WASF1 in vitro;in vivo12181570,15834156 No
    WASF2 in vitro;in vivo12181570 No
    PARD3 in vitro10934474 No
    SRGAP1 in vivo11672528 No
    RHOJ in vitro;yeast 2-hybrid10967094 No
    TBC1D3F in vivo12612085 No
    RPS6KB1 in vitro11438723 CHD related
    DOCK7 in vitro12432077 No
    OCRL in vitro12915445 No
    PGGT1B in vitro15451670 No
    ANXA2 in vitro;in vivo17254974 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB02623Aminophosphonic Acid-Guanylate Ester
    experimentalDB04315Guanosine-5'-Diphosphate