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: HLA-DRB1

    Description: "major histocompatibility complex, class II, DR beta 1"

    Entrez Gene ID: 3123

    SwissProt Acc Number: P01912

    RefSeq: NM_002124

    It was suspected to be CHD related:

    .."The results are in concordance with previous data on non-STEMI patients, implying that a HLA-DRB1*01--related haplotype increases the risk of CAD,possibly though increased inflammation."..

    From PMID: 22310063, in Journal Atherosclerosis. , 2012


    References

    There were 8 potential papers with HLA-DRB1 and CHD.

    PMIDTitleJournalsDetails
    23505291 Gene-centric analysis identifies variants associated with interleukin-6 levels and shared pathways with other inflammation markers.Circulation. Cardiovascular geneticsMore Details
    22122841 HLA-DRB1*12:02:01 plays a protective role against coronary artery disease in women of southern Han Chinese descent.Human immunologyMore Details
    20842443 "Association between HLA-DRB1, HLA-DRQB1 alleles, and CD4(+)CD28(null) T cells in a Chinese population with coronary heart disease."Molecular biology reportsMore Details
    18064508 Polymorphisms of human leukocyte antigen genes in korean children with Kawasaki disease.Pediatric cardiologyMore Details
    18384488 Lymphotoxin alpha LTA+496C allele is a risk factor for periodontitis in patients with coronary artery disease.Tissue antigensMore Details
    17989341 Association of Chlamydia pneumoniae infection with HLA-B*35 in patients with coronary artery disease.Clinical and vaccine immunology : CVIMore Details
    17212707 Human MHC region harbors both susceptibility and protective haplotypes for coronary artery disease.Tissue antigensMore Details
    17207714 Genetic variations of HLA-DRB1 and susceptibility to Kawasaki disease in Taiwanese children.Human immunologyMore Details

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



    PPI interactions

    There were totally 17 unique genes interacted with HLA-DRB1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    UBC Affinity Capture-Western16785530|18022694 No
    VCP Affinity Capture-Western18022694 No
    PKM2 Affinity Capture-MS20458337 No
    HSP90AA1 Affinity Capture-MS20458337 CHD related
    HSPA8 Affinity Capture-MS20458337 CHD related
    ANXA11 Affinity Capture-MS20458337 No
    HSP90AB1 Affinity Capture-MS20458337 CHD related
    ATP1B1 Affinity Capture-MS20458337 No
    YWHAE Affinity Capture-MS20458337 No
    MS4A1 Affinity Capture-MS20458337 No
    MAGEA3 Protein-peptide12393675 No
    TRB@ in vitro11877480 No
    HLA-DRA in vitro9354468 No
    HLA-DMA Reconstituted Complex9371817 No
    TRA@ Co-crystal Structure11877480 No
    TRIM21 Two-hybrid18022694 No
    CTAG1B in vitro11782380 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB05259Glatiramer AcetateFor reduction of the frequency of relapses in patients with Relapsing-Remitting Multiple Sclerosis.L03AX13