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)




    Genome-wide association study for circulating levels of PAI-1 provides novel insights into its regulation.
  • Author:"Huang, Jie;Sabater-Lleal, Maria;Asselbergs, Folkert W;Tregouet, David;Shin, So-Youn;Ding, Jingzhong;Baumert, Jens;Oudot-Mellakh, Tiphaine;Folkersen, Lasse;Johnson, Andrew D;Smith, Nicholas L;Williams, Scott M;Ikram, Mohammad A;Kleber, Marcus E;Becker, Diane M;Truong, Vinh;Mychaleckyj, Josyf C;Tang, Weihong;Yang, Qiong;Sennblad, Bengt;Moore, Jason H;Williams, Frances M K;Dehghan, Abbas;Silbernagel, Gunther;Schrijvers, Elisabeth M C;Smith, Shelly;Karakas, Mahir;Tofler, Geoffrey H;Silveira, Angela;Navis, Gerjan J;Lohman, Kurt;Chen, Ming-Huei;Peters, Annette;Goel, Anuj;Hopewell, Jemma C;Chambers, John C;Saleheen, Danish;Lundmark, Per;Psaty, Bruce M;Strawbridge, Rona J;Boehm, Bernhard O;Carter, Angela M;Meisinger, Christa;Peden, John F;Bis, Joshua C;McKnight, Barbara;Ohrvik, John;Taylor, Kent;Franzosi, Maria Grazia;Seedorf, Udo;Collins, Rory;Franco-Cereceda, Anders;Syvanen, Ann-Christine;Goodall, Alison H;Yanek, Lisa R;Cushman, Mary;Muller-Nurasyid, Martina;Folsom, Aaron R;Basu, Saonli;Matijevic, Nena;van Gilst, Wiek H;Kooner, Jaspal S;Hofman, Albert;Danesh, John;Clarke, Robert;Meigs, James B;Kathiresan, Sekar;Reilly, Muredach P;Klopp, Norman;Harris, Tamara B;Winkelmann, Bernhard R;Grant, Peter J;Hillege, Hans L;Watkins, Hugh;Spector, Timothy D;Becker, Lewis C;Tracy, Russell P;Marz, Winfried;Uitterlinden, Andre G;Eriksson, Per;Cambien, Francois;Morange, Pierre-Emmanuel;Koenig, Wolfgang;Soranzo, Nicole;van der Harst, Pim;Liu, Yongmei;O'Donnell, Christopher J;Hamsten, Anders"

  • Published Year:2012

  • Journal:Blood

  • Abstract:"We conducted a genome-wide association study to identify novel associations between genetic variants and circulating plasminogen activator inhibitor-1 (PAI-1) concentration, and examined functional implications of variants and genes that were discovered. A discovery meta-analysis was performed in 19 599 subjects, followed by replication analysis of genome-wide significant (P < 5 x 10(-8)) single nucleotide polymorphisms (SNPs) in 10 796 independent samples. We further examined associations with type 2 diabetes and coronary artery disease, assessed the functional significance of the SNPs for gene expression in human tissues, and conducted RNA-silencing experiments for one novel association. We confirmed the association of the 4G/5G proxy SNP rs2227631 in the promoter region of SERPINE1 (7q22.1) and discovered genome-wide significant associations at 3 additional loci: chromosome 7q22.1 close to SERPINE1 (rs6976053, discovery P = 3.4 x 10(-10)); chromosome 11p15.2 within ARNTL (rs6486122, discovery P = 3.0 x 10(-8)); and chromosome 3p25.2 within PPARG (rs11128603, discovery P = 2.9 x 10(-8)). Replication was achieved for the 7q22.1 and 11p15.2 loci. There was nominal association with type 2 diabetes and coronary artery disease at ARNTL (P < .05). Functional studies identified MUC3 as a candidate gene for the second association signal on 7q22.1. In summary, SNPs in SERPINE1 and ARNTL and an SNP associated with the expression of MUC3 were robustly associated with circulating levels of PAI-1."

  • 10.1182/blood-2012-06-436188

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