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: MTAP

    Description: methylthioadenosine phosphorylase

    Entrez Gene ID: 4507

    SwissProt Acc Number: Q13126

    RefSeq: NM_002451

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

    .."we find that in human vascular endothelial cells the enhancer interval containing the CAD locus physically interacts with the?CDKN2A/B?locus, the?MTAP?gene and an interval downstream of?IFNA21"..

    From PMID: 21307941, in Journal Nature. , 2011


    References

    There were 8 potential papers with MTAP and CHD.

    PMIDTitleJournalsDetails
    23462334 Association between rs10118757(A/G) in methylthioadenosine phosphorylase gene and coronary artery disease in Chinese Hans.GeneMore Details
    22952318 Effect of 9p21.3 coronary artery disease locus neighboring genes on atherosclerosis in mice.CirculationMore Details
    21307941 9p21 DNA variants associated with coronary artery disease impair interferon-gamma signalling response.NatureMore Details
    20637465 "Expression of Chr9p21 genes CDKN2B (p15(INK4b)), CDKN2A (p16(INK4a), p14(ARF)) and MTAP in human atherosclerotic plaque."AtherosclerosisMore Details
    20056914 ANRIL expression is associated with atherosclerosis risk at chromosome 9p21."Arteriosclerosis, thrombosis, and vascular biology"More Details
    19427650 MTAP gene is associated with ischemic stroke in Chinese Hans.Journal of the neurological sciencesMore Details
    19343170 INK4/ARF transcript expression is associated with chromosome 9p21 variants linked to atherosclerosis.PloS oneMore Details
    19888323 Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants.PloS oneMore Details

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



    PPI interactions

    There were totally 3 unique genes interacted with MTAP. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    UBC Affinity Capture-MS15852347|21139048|21890473|21906983 No
    ELAVL1 Affinity Capture-RNA19322201 No
    MYLIP in vitro;yeast 2-hybrid12826659 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approved;nutraceuticalDB00173Adenine"For nutritional supplementation, also for treating dietary shortage or imbalance"
    experimentalDB02158"(1s)-1-(9-Deazaadenin-9-Yl)-1,4,5-Trideoxy-1,4-Imino-5-Methylthio-D-Ribitol"
    experimentalDB02281Formycin
    experimentalDB022825'-Deoxy-5'-Methylthioadenosine
    experimentalDB029335'-Deoxy-5'-(Methylthio)-Tubercidin