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: PHACTR1

    Description: phosphatase and actin regulator 1

    Entrez Gene ID: 221692

    SwissProt Acc Number: Q9C0D0

    RefSeq: NM_030948

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

    .."We also replicated four loci previously identified in European populations (in or near PHACTR1, TCF21, CDKN2A-CDKN2B and C12orf51). These findings provide new insights into pathways contributing to the susceptibility for coronary artery disease in the Chinese Han population."..

    From PMID: 22751097, in Journal Nat Genet , 2012


    References

    There were 8 potential papers with PHACTR1 and CHD.

    PMIDTitleJournalsDetails
    24005217 From genotype to phenotype in human atherosclerosis--recent findings.Current opinion in lipidologyMore Details
    23561647 Genome-wide association study of coronary and aortic calcification implicates risk loci for coronary artery disease and myocardial infarction.AtherosclerosisMore Details
    23394302 Risk loci for coronary artery calcification replicated at 9p21 and 6q24 in the Heinz Nixdorf Recall Study.BMC medical geneticsMore Details
    23870195 "Genetics of coronary artery calcification among African Americans, a meta-analysis."BMC medical geneticsMore Details
    22751097 Genome-wide association study in Han Chinese identifies four new susceptibility loci for coronary artery disease.Nature geneticsMore Details
    22745674 Genome-wide association study in a Lebanese cohort confirms PHACTR1 as a major determinant of coronary artery stenosis.PloS oneMore Details
    22144573 Genome-wide association study for coronary artery calcification with follow-up in myocardial infarction.CirculationMore Details
    22152955 Genetic susceptibility to coronary heart disease in type 2 diabetes: 3 independent studies.Journal of the American College of CardiologyMore Details

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



    PPI interactions

    There were totally 2 unique genes interacted with PHACTR1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    ACTA1 Affinity Capture-Western15107502|15107502 CHD related
    PPP1CA Affinity Capture-Western15107502|15107502 No


    Involved FDA drugs

    There was no drug associated with PHACTR1