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)




    A method for measuring Rho kinase activity in tissues and cells.
  • Author:"Liu, Ping-Yen;Liao, James K"

  • Published Year:2008

  • Journal:Methods in enzymology

  • Abstract:"The Rho-associated kinases (ROCKs) can regulate cell shape and function by modulating the actin cytoskeleton. ROCKs are serine-threonine protein kinases that can phosphorylate adducin, ezrin-radixin-moesin proteins, LIM kinase, and myosin light chain phosphatase. In the cardiovascular system, the RhoA/ROCK pathway has been implicated in angiogenesis, atherosclerosis, cerebral and coronary vasospasm, cerebral ischemia, hypertension, myocardial hypertrophy, and neointima formation after vascular injury. ROCKs consist of two isoforms: ROCK1 and ROCK2. They share overall 65% homology in their amino acid sequence and 92% homology in their amino kinase domains. However, these two isoforms have different subcellular localizations and exert biologically different functions. In particular, ROCK1 appears to be more important for immunological functions, whereas ROCK2 is more important for endothelial and vascular smooth muscle function. Thus, the ability to measure ROCK activity in tissues and cells would be important for understanding mechanisms underlying cardiovascular disease. This chapter describes a method for measuring ROCK activity in peripheral blood, tissues, and cells."

  • 10.1016/S0076-6879(07)00414-4

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