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: ALMS1

    Description: Alstrom syndrome 1

    Entrez Gene ID: 7840

    SwissProt Acc Number: Q8TCU4

    RefSeq: NM_015120

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

    .."Confirmation of significant mutations in the ALMS1 gene should lead to advice to screen the subject for cardiomyopathy, and metabolic disorders."..

    From PMID: 19515241, in Journal Orphanet J Rare Dis , 2009


    References

    There were 3 potential papers with ALMS1 and CHD.

    PMIDTitleJournalsDetails
    24122612 Identification of a Glutamic Acid Repeat Polymorphism of ALMS1 as a Novel Genetic Risk Marker for Early-Onset Myocardial Infarction by Genome-Wide Linkage Analysis.Circulation. Cardiovascular geneticsMore Details
    21897446 Coronary artery disease in Alstrom syndrome.European journal of human genetics : EJHGMore Details
    19515241 Cardiac magnetic resonance imaging in Alstrom syndrome.Orphanet journal of rare diseasesMore Details

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



    PPI interactions

    There were totally 2 unique genes interacted with ALMS1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    UBC Affinity Capture-MS21139048|21906983|22505724 No
    MEGF10 yeast 2-hybrid12421765 No


    Involved FDA drugs

    There was no drug associated with ALMS1