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: CASP1

    Description: "caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase)"

    Entrez Gene ID: 834

    SwissProt Acc Number: P29466

    RefSeq: NM_001223

    It was suspected to be CHD related:

    ..These results indicate that caspase-1 levels are predictive of future cardiovascular death in patients with coronary artery disease. ..

    From PMID: 16778130, in Journal Circ Res , 2006


    References

    There were 4 potential papers with CASP1 and CHD.

    PMIDTitleJournalsDetails
    21052690 The 5352 A allele of the pro-inflammatory caspase-1 gene predicts late-acquired stent malapposition in STEMI patients treated with sirolimus stents.Heart and vesselsMore Details
    20184726 Caspase-1 genetic variation is not associated with Alzheimer's disease risk.BMC medical geneticsMore Details
    16778130 "Haplotypes of the caspase-1 gene, plasma caspase-1 levels, and cardiovascular risk."Circulation researchMore Details
    15364800 Different quantitative apoptotic traits in coronary atherosclerotic plaques from patients with stable angina pectoris and acute coronary syndromes.CirculationMore Details

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



    PPI interactions

    There were totally 48 unique genes interacted with CASP1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    NLRC4 Affinity Capture-Western15107016 No
    NOD2 Affinity Capture-Western15107016 CHD related
    NA Affinity Capture-Western15107016 No
    CASP1 Affinity Capture-Western11432859|9190289,12459189,7721861 CHD related
    BCAP31 Biochemical Activity9334338 No
    RIPK2 Affinity Capture-Western9705938 No
    IL37 Biochemical Activity12096920 No
    IL18 Biochemical Activity12096920|9334240 CHD related
    EGFR Biochemical Activity11226410|11226410 CHD related
    TIRAP Biochemical Activity20048342 No
    TRAF2 Affinity Capture-Western22195745 No
    UBC Affinity Capture-Western22195745 No
    TFAP2A in vitro;in vivo11438643 No
    CAST in vitro9705209 CHD related
    CDC2L2 in vitro;in vivo9115219 No
    AR in vitro9535906 CHD related
    ATN1 in vitro9535906 No
    CDK11B in vitro9632733 No
    IL1A in vivo18329368 CHD related
    FGF2 in vivo18329368 CHD related
    HTT in vitro9535906 No
    PSEN1 in vitro;in vivo10069390 No
    IL1B in vitro;in vivo7797510,1919001 CHD related
    LMNA in vitro;in vivo8978814,11953316 CHD related
    MAPT in vitro;in vivo12888622 No
    PARP1 in vitro;in vivo7642516 CHD related
    BCL2L1 in vitro9435230 CHD related
    PSEN2 in vitro;in vivo9990034,9219695,10069390 No
    BID in vivo9727491,11085743 CHD related
    NEDD4 in vitro;in vivo9593687 No
    PLA2G4A in vitro9875225 CHD related
    COP Affinity Capture-Western11432859 No
    NOD1 Affinity Capture-Western10329646|10329646,12459189 CHD related
    CASP10 Biochemical Activity8962078 No
    CASP8 Biochemical Activity8962078 CHD related
    CASP4 Reconstituted Complex10477277 No
    CASP14 Affinity Capture-Western9792675|9792675 No
    CEBPB Affinity Capture-Western11684016 No
    BIRC3 Affinity Capture-Western22195745 No
    NLRP1 in vivo17418785 No
    NFE2L2 in vivo;yeast 2-hybrid10510468 CHD related
    PARK2 in vitro12692130 No
    PAK1 in vitro;in vivo15561713 CHD related
    PYCARD in vitro;in vivo11967258,12019269,12191486 CHD related
    ATXN3 in vitro9535906 No
    CARD8 in vitro;in vivo11821383 No
    CARD16 in vivo11432859,11536016 No
    CARD17 in vitro;in vivo15383541 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB01017Minocycline"For the treatment of infections caused by susceptible strains of microorganisms, such as Rocky Mountain spotted fever, typhus fever and the typhus group, Q fever, rickettsial pox and tick fevers caused by Rickettsiae, upper respiratory tract infections caused by <i>Streptococcus pneumoniae</i> and for the treatment of asymptomatic carriers of <i>Neisseria meningitidis</i>."A01AB23;J01AA08
    experimentalDB07733"1-METHYL-3-TRIFLUOROMETHYL-1H-THIENO[2,3-C]PYRAZOLE-5-CARBOXYLIC ACID (2-MERCAPTO-ETHYL)-AMIDE"
    experimentalDB077443-[2-(2-BENZYLOXYCARBONYLAMINO-3-METHYL-BUTYRYLAMINO)-PROPIONYLAMINO]-4-OXO-PENTANOIC ACID
    experimentalDB079163-{6-[(8-HYDROXY-QUINOLINE-2-CARBONYL)-AMINO]-2-THIOPHEN-2-YL-HEXANOYLAMINO}-4-OXO-BUTYRI ACID