Canonical labels for protein spots of proteomics maps

详细信息    查看全文

• 作者：Milan Randi? (1)
  Rok Orel (2)
  
• 关键词：Canonical labels ; Proteomics maps ; Chaos game
• 刊名：Journal of Mathematical Chemistry
• 出版年：2014
• 出版时间：January 2014
• 年：2014
• 卷：52
• 期：1
• 页码：198-212
• 全文大小：333 KB
• 作者单位：Milan Randi? (1)
  Rok Orel (2)
  
  1. National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
  2. XLAB, Pot za Brdom 100, Ljubljana, Slovenia
  
• ISSN：1572-8897

文摘

We consider the problem of canonical labeling for a class of maps, which include proteomics maps, which consist of a set of vertices or protein spots. If this problem is solved and followed, different laboratories studying proteomics maps will arrive at the same numbering of spots, which would facilitate comparisons of data from different sources. In addition, the proposed canonical numberings of protein spots would allow compiling a catalog of proteomics maps just as canonical labeling allows making catalogs graphs, or molecules, and other canonically labeled systems, which would make search for similar sets of maps very efficient. We approach the problem by modifying the algorithm of Jeffrey for graphical representation of DNA based on the chaos game. Graphical representation of DNA as a chaos game map has an important property in that this representation allows one to assign sequential labels to spots in a DNA map. We have modified the approach for sequential labeling of chaos game map representations to graphical representation of any tabular data, such as listing of (x, y) coordinates of protein spots of proteomics maps.