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: BCL2

    Description: B-cell CLL/lymphoma 2

    Entrez Gene ID: 596

    SwissProt Acc Number: P10415

    RefSeq: NM_000633

    It was suspected to be CHD related:

    ..These findings establish a novel extracellular cytoprotective activity of BCL2 BH4-domain proteins as potent cytoprotective DAMPs...

    From PMID: 20161703, in Journal PLoS One , 2010


    References

    There were 3 potential papers with BCL2 and CHD.

    PMIDTitleJournalsDetails
    20117381 Growth differentiation factor 5 regulates cardiac repair after myocardial infarction.Journal of the American College of CardiologyMore Details
    20559783 Mitochondrial pruning by Nix and BNip3: an essential function for cardiac-expressed death factors.Journal of cardiovascular translational researchMore Details
    20161703 Extracellular BCL2 proteins are danger-associated molecular patterns that reduce tissue damage in murine models of ischemia-reperfusion injury.PloS oneMore Details

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



    PPI interactions

    There were totally 105 unique genes interacted with BCL2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    BECN1 Two-hybrid9765397|9765397|20889974|21543763|20010695|21358617 No
    BIK Protein-peptide15694340|9488477 No
    HRK Protein-peptide15694340 No
    BID Protein-peptide15694340 CHD related
    PMAIP1 Protein-peptide15694340 No
    ITPR1 Affinity Capture-Western15613488|15613488 No
    BAX Affinity Capture-Western15231068|14980220|14980220|20865015|22262057 CHD related
    SERPINB8 Affinity Capture-Western15231068 No
    MYC Affinity Capture-Western15210690|15210690|15210690 CHD related
    SOD1 Affinity Capture-Western15233914|15233914|15233914 CHD related
    BAK1 Affinity Capture-Western14980220|11728179 No
    RRAS Two-hybrid8232588|8232588 No
    RAD9A Two-hybrid10620799|10620799|18794804 No
    IRS1 Affinity Capture-Western10679027 CHD related
    IRS2 Affinity Capture-Western10679027 CHD related
    CDK1 Affinity Capture-Western11774038|11326318 CHD related
    PIN1 Affinity Capture-Western11326318 No
    PPP2R5A Affinity Capture-Western11929874 No
    CASP8 Affinity Capture-Western11406564 CHD related
    FKBP8 Affinity Capture-Western12510191|17379601 No
    PPP3CA Affinity Capture-Western9109491|9109491,7593193 CHD related
    DYNLL1 Affinity Capture-Western10198631 No
    BNIP3 Two-hybrid7954800|10625696 CHD related
    BNIP3L Affinity Capture-Western10467396 No
    UBC Affinity Capture-Western16980304|20889974|20865015|20865015 No
    HSP90AA1 Affinity Capture-Western21543763 CHD related
    ITLN1 Dosage Rescue22647378 No
    MEX3D Two-hybrid14769789 No
    HNRNPD Two-hybrid14769789 No
    BRCA1 FRET21444675 CHD related
    AMBRA1 Affinity Capture-Western21358617 No
    IKBKB Affinity Capture-Western22262057 CHD related
    CHUK Affinity Capture-Western22262057 CHD related
    HIF1A Affinity Capture-Western20668552 CHD related
    ATP2A2 in vivo9788433 CHD related
    CDK2 in vivo15619620 No
    PRKACA in vitro11158204,7929424,9115213 CHD related
    MAPK3 in vitro10677502 CHD related
    MAPK14 in vivo11495898 CHD related
    CYCS in vivo10622714 No
    BCL2 in vitro;in vivo;yeast 2-hybrid15302859,9111042,9463381 CHD related
    BNIPL Two-hybrid12901880|12901880|12901880 No
    BNIP2 Two-hybrid12901880|12901880,7954800 No
    SMN1 Two-hybrid9389483|9389483|9389483 No
    TP53BP2 Two-hybrid8668206|8668206|8668206 No
    RTN4 Two-hybrid11126360|11126360|11126360 No
    Bcl2l11 Protein-peptide15694340|10198631 No
    BBC3 Affinity Capture-Western15694340|11463392|11463392,16697956 CHD related
    BAD Affinity Capture-Western15694340|7834748|7834748|7834748,11483855,9463381,16697956,19168699 CHD related
    CASP3 Biochemical Activity11752215|11948397,9395403 CHD related
    BCL2L1 Protein-peptide12137781|11583631 CHD related
    EPHB2 Biochemical Activity15225643 No
    PPP2R4 Biochemical Activity15225643 No
    NR4A1 Reconstituted Complex14980220|14980220 CHD related
    SPNS1 Affinity Capture-Western12815463|12815463 No
    CAPN2 Biochemical Activity12000759|12000759 CHD related
    TP53AIP1 Affinity Capture-Western12019168|12019168 No
    BCL2L10 Affinity Capture-Western11278245|11278245 No
    RAF1 Reconstituted Complex8929532|8929532,8910675 CHD related
    TOMM20 Reconstituted Complex9119086|9119086 No
    BLK Reconstituted Complex9525867|9525867 CHD related
    BCAP31 Reconstituted Complex9334338|9334338|9334338 No
    PSEN1 Two-hybrid10521466 No
    ITM2B Affinity Capture-Western12082633|12082633 No
    BMF Affinity Capture-Western11546872|11546872,16697956 No
    HSPA1A Affinity Capture-Western10354271 CHD related
    TMBIM6 Affinity Capture-Western9660918 No
    MOAP1 Affinity Capture-Western11060313|11060313 No
    PPP2CA Biochemical Activity9852076|9852076 CHD related
    AVEN Two-hybrid10949025|10949025 No
    CASP2 Phenotypic Suppression11832478 No
    BNIP1 Reconstituted Complex10217402|10217402 No
    PARP1 Reconstituted Complex11790116|11790116 CHD related
    BAG1 Reconstituted Complex9305631|9305631 No
    BLID Affinity Capture-Western20400521 No
    PARK2 Reconstituted Complex20889974|20889974 No
    KEAP1 Biochemical Activity20865015|20865015|20865015|20865015 No
    CUL3 Affinity Capture-Western20865015 No
    RBX1 Affinity Capture-Western20865015 No
    TP53 Affinity Capture-Western21624955|21597459|12667443 CHD related
    gag-pol Biochemical Activity8790371 No
    CISD2 Affinity Capture-Western20010695 No
    PPP1CA Affinity Capture-Western17274640|11390485 No
    PPP1CB Affinity Capture-Western17274640 No
    PPP1CC Affinity Capture-Western17274640 No
    ATG12 Affinity Capture-Western22152474 No
    BFAR Affinity Capture-Western10716992|10716992 No
    PML Affinity Capture-Western15231068 No
    CRYAB Affinity Capture-Western20841355 No
    MAPK8 Biochemical Activity15733859|10567572,12039864,15225643 CHD related
    CPT1A in vitro;in vivo;yeast 2-hybrid9070836 No
    NLRP1 in vitro;in vivo17418785 No
    NMT2 in vivo16530191 No
    NRAS in vivo10490827 No
    MAPK1 in vivo15225643,10567572,12039864 CHD related
    PRKCA in vivo9738012 CHD related
    HRAS in vivo10490827 No
    KRAS in vivo10490827 No
    SF1 in vitro8668206 No
    PKMYT1 in vivo11326318 No
    MAPK11 in vitro11495898 No
    BAG3 in vitro;in vivo11513873 No
    BAG4 in vitro11527400 No
    BCL2L14 in vivo11054413 No
    BCLAF1 in vitro;yeast 2-hybrid10330179 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB01229Paclitaxel"Used in the treatment of Kaposi's sarcoma and cancer of the lung, ovarian, and breast."L01CD01
    approvedDB01248Docetaxel"For the treatment of patients with locally advanced or metastatic breast cancer after failure of prior chemotherapy. Also used as a single agent in the treatment of patients with locally advanced or metastatic non-small cell lung cancer after failure of prior platinum-based chemotherapy. Lastly, for use, in combination with prednisone, in the treatment of patients with androgen independent (hormone refractory) metastatic prostate cancer."L01CD02
    approvedDB01367RasagilineFor the treatment of the signs and symptoms of idiopathic Parkinsons disease as initial monotherapy and as adjunct therapy to levodopa.N04BD02