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)




    Newly identified loci that influence lipid concentrations and risk of coronary artery disease.
  • Author:"Willer, Cristen J;Sanna, Serena;Jackson, Anne U;Scuteri, Angelo;Bonnycastle, Lori L;Clarke, Robert;Heath, Simon C;Timpson, Nicholas J;Najjar, Samer S;Stringham, Heather M;Strait, James;Duren, William L;Maschio, Andrea;Busonero, Fabio;Mulas, Antonella;Albai, Giuseppe;Swift, Amy J;Morken, Mario A;Narisu, Narisu;Bennett, Derrick;Parish, Sarah;Shen, Haiqing;Galan, Pilar;Meneton, Pierre;Hercberg, Serge;Zelenika, Diana;Chen, Wei-Min;Li, Yun;Scott, Laura J;Scheet, Paul A;Sundvall, Jouko;Watanabe, Richard M;Nagaraja, Ramaiah;Ebrahim, Shah;Lawlor, Debbie A;Ben-Shlomo, Yoav;Davey-Smith, George;Shuldiner, Alan R;Collins, Rory;Bergman, Richard N;Uda, Manuela;Tuomilehto, Jaakko;Cao, Antonio;Collins, Francis S;Lakatta, Edward;Lathrop, G Mark;Boehnke, Michael;Schlessinger, David;Mohlke, Karen L;Abecasis, Goncalo R"

  • Published Year:2008

  • Journal:Nature genetics

  • Abstract:"To identify genetic variants influencing plasma lipid concentrations, we first used genotype imputation and meta-analysis to combine three genome-wide scans totaling 8,816 individuals and comprising 6,068 individuals specific to our study (1,874 individuals from the FUSION study of type 2 diabetes and 4,184 individuals from the SardiNIA study of aging-associated variables) and 2,758 individuals from the Diabetes Genetics Initiative, reported in a companion study in this issue. We subsequently examined promising signals in 11,569 additional individuals. Overall, we identify strongly associated variants in eleven loci previously implicated in lipid metabolism (ABCA1, the APOA5-APOA4-APOC3-APOA1 and APOE-APOC clusters, APOB, CETP, GCKR, LDLR, LPL, LIPC, LIPG and PCSK9) and also in several newly identified loci (near MVK-MMAB and GALNT2, with variants primarily associated with high-density lipoprotein (HDL) cholesterol; near SORT1, with variants primarily associated with low-density lipoprotein (LDL) cholesterol; near TRIB1, MLXIPL and ANGPTL3, with variants primarily associated with triglycerides; and a locus encompassing several genes near NCAN, with variants strongly associated with both triglycerides and LDL cholesterol). Notably, the 11 independent variants associated with increased LDL cholesterol concentrations in our study also showed increased frequency in a sample of coronary artery disease cases versus controls."

  • 10.1038/ng.76

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