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: LDHB

    Description: lactate dehydrogenase B

    Entrez Gene ID: 3945

    SwissProt Acc Number: P07195

    RefSeq: NM_002300

    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 0 potential papers with LDHB and CHD.

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



    PPI interactions

    There were totally 19 unique genes interacted with LDHB. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    LDHB Co-crystal Structure11276087|11276087 CHD related
    H2AFX Affinity Capture-MS20000738 No
    UBC Affinity Capture-MS16196087|20639865|18781797|21987572|21963094|21139048|21890473|21906983|22053931|21853274|22505724 No
    Mapk13 Affinity Capture-MS19135240 No
    EBNA-LP Affinity Capture-MS18457437 No
    SUMO1 Affinity Capture-MS19596686 No
    KIAA0101 Affinity Capture-MS21628590 No
    SUMO4 Affinity Capture-MS16236267|16236267 CHD related
    CKS1B Affinity Capture-MS19786724 No
    CKS2 Affinity Capture-MS19786724 No
    TERF1 Two-hybrid21044950 No
    POT1 Two-hybrid21044950 No
    CUL3 Affinity Capture-MS21145461 No
    CUL4B Affinity Capture-MS21145461 No
    CDK2 Affinity Capture-MS21319273 No
    COPS5 Affinity Capture-MS21145461 No
    SUMO3 Affinity Capture-MS15576338 No
    FBXO6 Affinity Capture-MS22268729 No
    LDHA Co-fractionation22939629 CHD related


    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
    experimentalDB02401"4-Hydroxy-1,2,5-Oxadiazole-3-Carboxylic Acid"
    experimentalDB03940Oxamic Acid