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)




    Loci influencing blood pressure identified using a cardiovascular gene-centric array.
  • Author:"Ganesh, Santhi K;Tragante, Vinicius;Guo, Wei;Guo, Yiran;Lanktree, Matthew B;Smith, Erin N;Johnson, Toby;Castillo, Berta Almoguera;Barnard, John;Baumert, Jens;Chang, Yen-Pei Christy;Elbers, Clara C;Farrall, Martin;Fischer, Mary E;Franceschini, Nora;Gaunt, Tom R;Gho, Johannes M I H;Gieger, Christian;Gong, Yan;Isaacs, Aaron;Kleber, Marcus E;Mateo Leach, Irene;McDonough, Caitrin W;Meijs, Matthijs F L;Mellander, Olle;Molony, Cliona M;Nolte, Ilja M;Padmanabhan, Sandosh;Price, Tom S;Rajagopalan, Ramakrishnan;Shaffer, Jonathan;Shah, Sonia;Shen, Haiqing;Soranzo, Nicole;van der Most, Peter J;Van Iperen, Erik P A;Van Setten, Jessica;Vonk, Judith M;Zhang, Li;Beitelshees, Amber L;Berenson, Gerald S;Bhatt, Deepak L;Boer, Jolanda M A;Boerwinkle, Eric;Burkley, Ben;Burt, Amber;Chakravarti, Aravinda;Chen, Wei;Cooper-Dehoff, Rhonda M;Curtis, Sean P;Dreisbach, Albert;Duggan, David;Ehret, Georg B;Fabsitz, Richard R;Fornage, Myriam;Fox, Ervin;Furlong, Clement E;Gansevoort, Ron T;Hofker, Marten H;Hovingh, G Kees;Kirkland, Susan A;Kottke-Marchant, Kandice;Kutlar, Abdullah;Lacroix, Andrea Z;Langaee, Taimour Y;Li, Yun R;Lin, Honghuang;Liu, Kiang;Maiwald, Steffi;Malik, Rainer;Murugesan, Gurunathan;Newton-Cheh, Christopher;O'Connell, Jeffery R;Onland-Moret, N Charlotte;Ouwehand, Willem H;Palmas, Walter;Penninx, Brenda W;Pepine, Carl J;Pettinger, Mary;Polak, Joseph F;Ramachandran, Vasan S;Ranchalis, Jane;Redline, Susan;Ridker, Paul M;Rose, Lynda M;Scharnag, Hubert;Schork, Nicholas J;Shimbo, Daichi;Shuldiner, Alan R;Srinivasan, Sathanur R;Stolk, Ronald P;Taylor, Herman A;Thorand, Barbara;Trip, Mieke D;van Duijn, Cornelia M;Verschuren, W Monique;Wijmenga, Cisca;Winkelmann, Bernhard R;Wyatt, Sharon;Young, J Hunter;Boehm, Bernhard O;Caulfield, Mark J;Chasman, Daniel I;Davidson, Karina W;Doevendans, Pieter A;Fitzgerald, Garret A;Gums, John G;Hakonarson, Hakon;Hillege, Hans L;Illig, Thomas;Jarvik, Gail P;Johnson, Julie A;Kastelein, John J P;Koenig, Wolfgang;Marz, Winfried;Mitchell, Braxton D;Murray, Sarah S;Oldehinkel, Albertine J;Rader, Daniel J;Reilly, Muredach P;Reiner, Alex P;Schadt, Eric E;Silverstein, Roy L;Snieder, Harold;Stanton, Alice V;Uitterlinden, Andre G;van der Harst, Pim;van der Schouw, Yvonne T;Samani, Nilesh J;Johnson, Andrew D;Munroe, Patricia B;de Bakker, Paul I W;Zhu, Xiaofeng;Levy, Daniel;Keating, Brendan J;Asselbergs, Folkert W"

  • Published Year:2013

  • Journal:Human molecular genetics

  • Abstract:"Blood pressure (BP) is a heritable determinant of risk for cardiovascular disease (CVD). To investigate genetic associations with systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP) and pulse pressure (PP), we genotyped approximately 50 000 single-nucleotide polymorphisms (SNPs) that capture variation in approximately 2100 candidate genes for cardiovascular phenotypes in 61 619 individuals of European ancestry from cohort studies in the USA and Europe. We identified novel associations between rs347591 and SBP (chromosome 3p25.3, in an intron of HRH1) and between rs2169137 and DBP (chromosome1q32.1 in an intron of MDM4) and between rs2014408 and SBP (chromosome 11p15 in an intron of SOX6), previously reported to be associated with MAP. We also confirmed 10 previously known loci associated with SBP, DBP, MAP or PP (ADRB1, ATP2B1, SH2B3/ATXN2, CSK, CYP17A1, FURIN, HFE, LSP1, MTHFR, SOX6) at array-wide significance (P < 2.4 x 10(-6)). We then replicated these associations in an independent set of 65 886 individuals of European ancestry. The findings from expression QTL (eQTL) analysis showed associations of SNPs in the MDM4 region with MDM4 expression. We did not find any evidence of association of the two novel SNPs in MDM4 and HRH1 with sequelae of high BP including coronary artery disease (CAD), left ventricular hypertrophy (LVH) or stroke. In summary, we identified two novel loci associated with BP and confirmed multiple previously reported associations. Our findings extend our understanding of genes involved in BP regulation, some of which may eventually provide new targets for therapeutic intervention."

  • 10.1093/hmg/dds555

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