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: MTHFD1L

    Description: methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like

    Entrez Gene ID: 25902

    SwissProt Acc Number: Q6UB35

    RefSeq: NM_015440

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

    .."The Ch9p21 SNPs rs1333049 (OR 1.17; 95% confidence limits 1.11-1.24) and rs10757274 (OR 1.17; 1.09-1.26), MIA3 rs17465637 (OR 1.10; 1.04-1.15), Ch2q36 rs2943634 (OR 1.08; 1.03-1.14), APC rs383830 (OR 1.10; 1.02, 1.18), MTHFD1L rs6922269 (OR 1.10; 1.03, 1.16), CXCL12 rs501120 (OR 1.12; 1.04, 1.20), and SMAD3 rs17228212 (OR 1.11; 1.05, 1.17) were all associated with CHD risk, but not with the CHD biomarkers and risk factors measured.//Nine loci were statistically associated with incident CHD events in white participants: 9p21 (rs10757278; P=4.7 10(-41)), 16q23.1 (rs2549513; P=0.0004), 6p24.1 (rs499818; P=0.0002), 2q36.3 (rs2943634; P=6.7 10(-6)), MTHFD1L (rs6922269, P=5.1 10(-10)), APOE (rs429358; P=2.7 10(-18)), ZNF627 (rs4804611; P=5.0 10(-8)), CXCL12 (rs501120; P=1.4 10(-6)) and LPL (rs268; P=2.7 10(-17)). "..

    From PMID: 21804106, in Journal Eur Heart J. , 2012


    References

    There were 7 potential papers with MTHFD1L and CHD.

    PMIDTitleJournalsDetails
    21804106 "Comparative analysis of genome-wide association studies signals for lipids, diabetes, and coronary heart disease: Cardiovascular Biomarker Genetics Collaboration."European heart journalMore Details
    21860704 Implications of discoveries from genome-wide association studies in current cardiovascular practice.World journal of cardiologyMore Details
    21463265 Association of SNP rs17465637 on chromosome 1q41 and rs599839 on 1p13.3 with myocardial infarction in an American caucasian population.Annals of human geneticsMore Details
    22042884 Association of genetic variants and incident coronary heart disease in multiethnic cohorts: the PAGE study.Circulation. Cardiovascular geneticsMore Details
    21957892 Investigation of 95 variants identified in a genome-wide study for association with mortality after acute coronary syndrome.BMC medical geneticsMore Details
    22216278 Large scale association analysis identifies three susceptibility loci for coronary artery disease.PloS oneMore Details
    19777576 A common variant in MTHFD1L is associated with neural tube defects and mRNA splicing efficiency.Human mutationMore Details

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



    PPI interactions

    There were totally 9 unique genes interacted with MTHFD1L. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CASP4 Affinity Capture-MS17353931 No
    MAGED1 Affinity Capture-MS17353931 No
    WRAP73 Affinity Capture-MS17353931 No
    HGS Reconstituted Complex19019082 No
    USP50 Affinity Capture-MS19615732 No
    UBC Affinity Capture-MS21139048 No
    SIRT7 Affinity Capture-MS22586326 No
    CUL3 Affinity Capture-MS21145461 No
    COPS5 Affinity Capture-MS21145461 No


    Involved FDA drugs

    There was no drug associated with MTHFD1L