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.

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  • 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.

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  • 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)




    "Rapid triplex asymmetric real-time PCR hybridization probe assay for the joint genotyping of F2, F5 and F12."
  • Author:"Martinez-Serra, J;Gutierrez, A;Amat, J C;Galmes, B;Vila, A;Julia, M;Lopez, H;Bautista, A M;Truyols, C;Ros, T;Navarro, M;Canaro, M;Diaz, M;Besalduch, J"

  • Published Year:2009

  • Journal:Clinical biochemistry

  • Abstract:"INTRODUCTION: The Factor 5 Leiden mutation and the G20210A variant of Factor 2 are two important risk factors for hereditary thromboembolism. Several reports have demonstrated that homozygous carriers for C46T mutation of the Factor 12 gene is associated with a significant increased risk for the development of coronary disease as well as cerebral and peripheral venous thrombosis. DESIGN AND METHODS: We develop a rapid and feasible asymmetric multiplex real-time PCR-based method using fluorescence resonance emission transfer (FRET) probes followed by a melting temperature (T(m)) curve assay for the simultaneous clinical diagnosis of F2, F5 and F12 mutations in a 10 microl closed tube. This new tool uses three different fluorescence channels in a LightCycler 2.0 for the robust genotyping of each one of the mutations included in the reaction. RESULTS: Assay evaluation performed on 67 DNA samples previously genotyped with reference methods resulted in full concordance of results for the three mutations tested. Higher asymmetric ratio of primer pair concentration significantly increased the efficiency of the melting peak assay used for the mutation genotyping without modifying the Crossing Point (CP) obtained from the amplification curves. CONCLUSIONS: To our knowledge this is the first triplex real-time PCR FRET-based assay reported in bibliography that allows a rapid and simultaneous genotyping of these three thrombosis risk factors. This new and rapid tool may contribute to the better understanding of the interrelations or contributions of these gene mutations to different thrombotic or coronary disease-related events."

  • 10.1016/j.clinbiochem.2009.04.013

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