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: ROCK1

    Description: "Rho-associated, coiled-coil containing protein kinase 1"

    Entrez Gene ID: 6093

    SwissProt Acc Number: Q13464

    RefSeq: NM_005406

    It was suspected to be CHD related:

    ..This review will focus on the potential role of ROCKs in cellular functions and discuss the prospects of ROCK inhibitors as emerging therapy for cardiovascular diseases...

    From PMID: 15889972, in Journal Expert Rev Cardiovasc Ther , 2005


    References

    There were 3 potential papers with ROCK1 and CHD.

    PMIDTitleJournalsDetails
    21929346 Rho kinase as a therapeutic target in cardiovascular disease.Future cardiologyMore Details
    18374165 A method for measuring Rho kinase activity in tissues and cells.Methods in enzymologyMore Details
    17482681 Development of Rho-kinase inhibitors for cardiovascular medicine.Trends in pharmacological sciencesMore Details

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



    PPI interactions

    There were totally 31 unique genes interacted with ROCK1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CDC25A Biochemical Activity14657354|14657354 No
    GAB1 Co-crystal Structure12748184 No
    LIMK2 Biochemical Activity10436159|11018042,11340065 No
    RHOC in vivo8816443 No
    RDX in vitro9456324 No
    ROCK1 in vitro16249185 CHD related
    VIM in vitro;in vivo9565595 CHD related
    MSN in vitro9516463,9856983 No
    LIMK1 in vitro;in vivo10436159,10652353,11340065,10559936 No
    PPP1R12A in vitro;in vivo9354661,12600888,10601309,11931630,12220642,12563012 No
    DPYSL2 in vitro;in vivo12482610,10818093 No
    EZR in vivo11387207,10970850 No
    DES in vitro;in vivo10574968 No
    ARHGAP24 in vivo16862148 No
    ADD1 in vivo10209029 CHD related
    GFAP in vitro;in vivo9099667,2155236,7822264,2114109 CHD related
    PFN2 Affinity Capture-Western14517206 No
    RHOA Reconstituted Complex12773565|12773565|12773565|8798490 CHD related
    RND3 Reconstituted Complex12773565|12773565 No
    CFL1 Affinity Capture-Western10436159 No
    HNRNPA1 Affinity Capture-MS17643375 No
    UBC Affinity Capture-MS21139048|21906983 No
    ITSN2 Two-hybrid22558309 No
    ARRB1 Affinity Capture-MS17620599 No
    TSG101 Two-hybrid17853893|17853893|17853893 No
    CDC34 in vitro16123592 No
    CASP3 in vitro;in vivo11283607 CHD related
    CRMP1 in vivo12482610 No
    IRS1 in vitro;in vivo11739394 CHD related
    PTK2 in vitro15247219 No
    SMAD2 yeast 2-hybrid15231748 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB04707HYDROXYFASUDIL
    experimentalDB07876(S)-2-METHYL-1-[(4-METHYL-5-ISOQUINOLINE)SULFONYL]-HOMOPIPERAZINE
    experimentalDB08162"5-(1,4-DIAZEPAN-1-SULFONYL)ISOQUINOLINE"
    experimentalDB08756(R)-TRANS-4-(1-AMINOETHYL)-N-(4-PYRIDYL) CYCLOHEXANECARBOXAMIDE