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 (

    Website using assistance : Leihong Wu (

    Basic Information

    Gene Name: PTGDS

    Description: prostaglandin D2 synthase 21kDa (brain)

    Entrez Gene ID: 5730

    SwissProt Acc Number: P41222

    RefSeq: NM_000954

    It was suspected to be CHD related:

    .."Levels of the prostaglandin D2 synthase (PTGDS) gene, recently associated with the progression of atherosclerosis, were significantly different in the three pairwise comparisons (EAT>MAT>SAT)."..

    From PMID: 21603615, in Journal PLoS One , 2011


    There were 1 potential papers with PTGDS and CHD.

    21603615 "The transcriptome of human epicardial, mediastinal and subcutaneous adipose tissues in men with coronary artery disease."PloS oneMore Details

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

    PPI interactions

    There were totally 10 unique genes interacted with PTGDS. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PTGER1 in vivo8253813 No
    EGFR PCA20029029 CHD related
    CACNA1A Two-hybrid21078624 No
    SHBG Two-hybrid15862967 CHD related
    ATXN1 Two-hybrid16713569 No
    PTGER2 in vivo8163486 No
    PTGFR in vivo8300593 No
    CAPN1 yeast 2-hybrid12358155 No
    HK2 in vitro;in vivo;yeast 2-hybrid11068878 No
    HK3 in vitro;in vivo;yeast 2-hybrid11068878 No

    Involved FDA drugs

    There was no drug associated with PTGDS