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: CDKAL1

    Description: CDK5 regulatory subunit associated protein 1-like 1

    Entrez Gene ID: 54901

    SwissProt Acc Number: Q5VV42

    RefSeq: NM_017774

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

    .."This approach replicated HNRNPA3P1-CXCL12 association with CAD and identified new significant associations of CDKAL1, ST6GAL1, and PTPRD with CAD. "..

    From PMID: 22216278, in Journal PLoS One , 2011


    References

    There were 3 potential papers with CDKAL1 and CHD.

    PMIDTitleJournalsDetails
    23104008 Bayesian refinement of association signals for 14 loci in 3 common diseases.Nature geneticsMore Details
    22216278 Large scale association analysis identifies three susceptibility loci for coronary artery disease.PloS oneMore Details
    20616309 Coronary artery calcification and its relationship to validated genetic variants for diabetes mellitus assessed in the Heinz Nixdorf recall cohort."Arteriosclerosis, thrombosis, and vascular biology"More Details

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



    PPI interactions

    There were totally 2 unique genes interacted with CDKAL1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    UBC Affinity Capture-MS21890473|21906983|22505724 No
    ELAVL1 Affinity Capture-RNA19322201 No


    Involved FDA drugs

    There was no drug associated with CDKAL1