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: PPARGC1A

    Description: "peroxisome proliferator-activated receptor gamma, coactivator 1 alpha"

    Entrez Gene ID: 10891

    SwissProt Acc Number: Q9UBK2

    RefSeq: NM_013261

    It was suspected to be CHD related:

    ..The results indicate that the PPARGC1A Gly482Ser polymorphism may contribute to the risk of CAD in the Chinese population investigated...

    From PMID: 18565194, in Journal Clin Exp Pharmacol Physiol. , 2008


    References

    There were 3 potential papers with PPARGC1A and CHD.

    PMIDTitleJournalsDetails
    21894159 "PGC1alpha gene Gly482Ser polymorphism predicts improved metabolic, inflammatory and vascular outcomes following bariatric surgery."International journal of obesity (2005)More Details
    20512451 "Association of the CYBA, PPARGC1A, PPARG3, and PPARD gene variants with coronary artery disease and metabolic risk factors of coronary atherosclerosis in a Russian population."Heart and vesselsMore Details
    18565194 Association between PPARGC1A gene polymorphisms and coronary artery disease in a Chinese population.Clinical and experimental pharmacology & physiologyMore Details

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



    PPI interactions

    There were totally 55 unique genes interacted with PPARGC1A. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    NR1H4 Reconstituted Complex14729567|14729567|14729567 No
    MED1 Affinity Capture-Western14636573|14636573|14636573 No
    MED16 Affinity Capture-Western14636573 No
    MED17 Affinity Capture-Western14636573|14636573 No
    MED21 Affinity Capture-Western14636573 No
    MED12 Affinity Capture-Western14636573|14636573 No
    MED14 Affinity Capture-Western14636573|14636573 No
    MED20 Affinity Capture-Western14636573 No
    HCFC1 Affinity Capture-Western11733490|11733490 No
    ESR1 Reconstituted Complex10748020|10748020 CHD related
    THRB Reconstituted Complex11751919|11751919 No
    SRSF5 Affinity Capture-Western10983978 No
    SRSF6 Affinity Capture-Western10983978 No
    SRSF4 Affinity Capture-Western10983978 No
    PPARA Reconstituted Complex10669761|10669761 CHD related
    NR3C1 Two-hybrid10713165|10713165 CHD related
    CREBBP Reconstituted Complex10558993|10558993 No
    UBC Affinity Capture-Western18198341|22099309|18198341 No
    EP300 Affinity Capture-MS17050673 CHD related
    IQGAP1 Affinity Capture-MS17050673 No
    LRPPRC Affinity Capture-MS17050673|17050673 No
    SIRT1 Co-localization19553684|15744310 CHD related
    MYOD1 Co-localization19553684 No
    NR1I2 Reconstituted Complex15322103 No
    SF1 Affinity Capture-Western20133449 No
    NR5A2 Affinity Capture-Western20133449 No
    RNF34 Affinity Capture-Western22064484 No
    RNF2 Affinity Capture-Western22099309 No
    USF2 in vitro;in vivo12611894 No
    SFRS5 in vitro10983978 No
    SFRS4 in vitro10983978 No
    SFRS6 in vitro10983978 No
    NCL in vivo10983978 No
    PPARG Reconstituted Complex14636573|19631645 CHD related
    NRF1 Reconstituted Complex10412986|10412986 CHD related
    SRSF2 Affinity Capture-Western10983978 No
    RXRA Affinity Capture-Western11714715|11714715 CHD related
    NCOA1 Affinity Capture-Western10558993|10558993 No
    Esrrg Phenotypic Enhancement12470660|12470660 No
    FBXW7 Affinity Capture-Western18198341|18198341 No
    GSK3B Biochemical Activity18198341 CHD related
    HNF4A Reconstituted Complex18552123|15322103|17636037|20926756|15826954,15744310 No
    NCOA6 Reconstituted Complex18552123 No
    ESRRA Co-crystal Structure15337744|12181319 No
    MYEF2 Affinity Capture-Western15111488 No
    BCL6 Affinity Capture-MS16147992 No
    ESR2 Two-hybrid15604093|15784253,15604093 CHD related
    CREBZF Affinity Capture-Western21994947|21994947 No
    TP53 Affinity Capture-Western22099309|22099309 CHD related
    PIAS1 Affinity Capture-Western22969086 No
    PARK7 Phenotypic Enhancement18689799 No
    SFPQ Affinity Capture-Western18689799 No
    MAPK14 in vitro;in vivo11741533 CHD related
    MYBBP1A in vitro14744933 No
    NR1I3 yeast 2-hybrid15572376 No


    Involved FDA drugs

    There was no drug associated with PPARGC1A