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: LDHA

    Description: lactate dehydrogenase A

    Entrez Gene ID: 3939

    SwissProt Acc Number: P00338

    RefSeq: NM_001135239

    It was supported literatures to be a novel CHD related gene:

    ..Lactate dehydrogenase (LDH) is a crucial regulator of energy metabolism in many organs including the heart. ..

    From PMID: 21362345, in Journal Chin Med J (Engl) , 2011


    References

    There were 1 potential papers with LDHA and CHD.

    PMIDTitleJournalsDetails
    18618261 Adaptive match filter based method for time vs. amplitude characterization of microvolt ECG T-wave alternans.Annals of biomedical engineeringMore Details

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



    PPI interactions

    There were totally 29 unique genes interacted with LDHA. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    KCNJ11 Affinity Capture-Western12145195 No
    ABCC9 Affinity Capture-Western12145195 No
    MDH1 Co-fractionation22939629 No
    LDHB Co-fractionation22939629 CHD related
    LDHA in vitro11276087 CHD related
    KAT5 Affinity Capture-MS20946988 No
    KAT2A Affinity Capture-MS20946988 No
    UBC Affinity Capture-MS16196087|20639865|18781797|21987572|21139048|21890473|21906983|22536838|21853274|22505724 No
    Mapk13 Affinity Capture-MS19135240 No
    YWHAQ Affinity Capture-MS15161933 No
    HDAC5 Affinity Capture-MS21081666 No
    PCNA Reconstituted Complex20849852 CHD related
    PSMA3 Affinity Capture-MS22079093 No
    PCK1 Affinity Capture-MS21726808 No
    KIAA0101 Affinity Capture-MS21628590 No
    NDRG1 Affinity Capture-MS17220478|17220478 No
    SUMO2 Affinity Capture-MS21252943 No
    ISG15 Affinity Capture-MS16009940 No
    TERF1 Two-hybrid21044950 No
    TINF2 Two-hybrid21044950 No
    ACD Two-hybrid21044950 No
    POT1 Two-hybrid21044950 No
    CUL3 Affinity Capture-MS21145461 No
    CUL5 Affinity Capture-MS21145461 No
    CDK2 Affinity Capture-MS21319273 No
    CAND1 Affinity Capture-MS21145461 No
    AKT1 Affinity Capture-MS16027165 CHD related
    HNRNPD in vitro;in vivo12107167 No
    XRN1 yeast 2-hybrid15231747 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approved;nutraceuticalDB00157NADH"Some evidence suggests that NADH might be useful in treating Parkinson's disease, chronic fatigue syndrome, Alzheimer's disease and cardiovascular disease."
    experimentalDB01907Nicotinamide-Adenine-Dinucleotide
    experimentalDB02483Etheno-Nad
    experimentalDB02701NicotinamideA11HA01
    experimentalDB03940Oxamic Acid