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: CFTR

    Description: "cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)"

    Entrez Gene ID: 1080

    SwissProt Acc Number: P13569

    RefSeq: NM_000492

    It was suspected to be CHD related:

    ..These results provide compelling evidence for a critical role for CFTR Cl(-) channels in IPC- and POC-mediated cardioprotection against I/R-induced myocardial injury...

    From PMID: 21642951, in Journal Acta Pharmacol Sin , 2011


    References

    There were 2 potential papers with CFTR and CHD.

    PMIDTitleJournalsDetails
    21642951 Characterization of a critical role for CFTR chloride channels in cardioprotection against ischemia/reperfusion injury.Acta pharmacologica SinicaMore Details
    18342019 Influence of PDZK1 on lipoprotein metabolism and atherosclerosis.Biochimica et biophysica actaMore Details

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



    PPI interactions

    There were totally 50 unique genes interacted with CFTR. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    GOPC Two-hybrid11707463|11707463 No
    KCNJ1 Affinity Capture-Western14604981 No
    PDZD3 Reconstituted Complex12615054|1553237 No
    SLC9A3R1 Reconstituted Complex12615054|9613608|9671706|9677412|12403779 No
    HSPA8 Affinity Capture-Western10075921|15611333|17272822|17272822 CHD related
    DNAJB1 Affinity Capture-Western10075921 No
    DNAJA1 Affinity Capture-Western10075921 No
    SNAP23 Affinity Capture-Western12209004|12209004 No
    CLCN3 Reconstituted Complex12471024 No
    SLC9A3R2 Affinity Capture-Western10893422|10893422 No
    EZR Affinity Capture-Western10893422|10893422 No
    SLC4A8 Affinity Capture-Western12403779 No
    Pdzk1 Affinity Capture-MS11051556|11051556 No
    CFTR Affinity Capture-Western11051556|11707463,11051556,10893422,12471024 CHD related
    UBC Affinity Capture-Western18216283|19307599|20525683|19617352|19269966|19828134|20147297|19398555|17272822|16954204|16901789|19098309 No
    AMFR Affinity Capture-Western18216283|19828134 No
    VCP Affinity Capture-Western16621797|19828134|17272822|17272822|16954204 No
    CBL Affinity Capture-Western20525683 No
    NEDD4 Affinity Capture-Western19617352 No
    JKAMP Affinity Capture-Western19269966 No
    RNF5 Affinity Capture-Western19269966 No
    RAB5A Affinity Capture-Western19398555 No
    RAB11A Affinity Capture-Western19398555 No
    cse1l Affinity Capture-Western20933420 No
    HSPA4 Affinity Capture-MS17272822|17272822|18556464|19098309|18716059 No
    DERL1 Affinity Capture-Western16954204 No
    AHSA1 Affinity Capture-Western18556464 No
    NHS Reconstituted Complex14595111 No
    CANX Affinity Capture-Western18716059|12208510,16546175 No
    SLC9A6 in vivo11707463 No
    PRKAR2A in vivo10799517 No
    STX1A Reconstituted Complex9384384|9384384 No
    PRKCE Affinity Capture-Western11956211 CHD related
    Prkaa1 Two-hybrid10862786 No
    PDZK1 Reconstituted Complex12471024|12471024|11051556|11051556,12471024,12615054,15553237 CHD related
    DNAJC5 Affinity Capture-Western12039948|12039948 No
    STUB1 Biochemical Activity15611333|19056735|21898230|11146634 No
    HDAC6 Affinity Capture-Western14675537|22069321 No
    HSP90AA1 Reconstituted Complex10982807 CHD related
    USP10 Affinity Capture-Western20215869|19398555 No
    COMMD1 Affinity Capture-Western21483833|21483833 No
    UBE3A Co-localization19233847 No
    PSMA3 Co-purification16390870 No
    PRKACA Biochemical Activity17272822|1377674 CHD related
    Prkaa2 Biochemical Activity16844684 No
    BCAP31 Affinity Capture-Western18555783 No
    PRKCA in vitro1377674 CHD related
    SLC4A7 in vitro;in vivo12403779 No
    PRKG1 in vitro1377674 CHD related
    PPP2R1B in vivo;yeast 2-hybrid15936019 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00887Bumetanide"For the treatment of edema associated with congestive heart failure, hepatic and renal disease including the nephrotic syndrome."C03CA02
    approvedDB01016GlyburideIndicated as an adjunct to diet to lower the blood glucose in patients with NIDDM whose hyperglycemia cannot be satisfactorily controlled by diet alone.A10BB01
    experimentalDB03431Adenosine-5'-Diphosphate
    experimentalDB04395Phosphoaminophosphonic Acid-Adenylate Ester
    experimentalDB04522Phosphonoserine
    approvedDB08820IvacaftorFor the treatment of cystic fibrosis (CF) in patients age 6 years and older who have a G551D mutation in the CFTR gene.