Chinese Bulletin of Botany ›› 2009, Vol. 44 ›› Issue (02): 159-166.DOI: 10.3969/j.issn.1674-3466.2009.02.003

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Transitive Functional Annotation by Shortest-path Analysis of Gene Expression Data Under Abscisic-acid and Environmental Stresses in Rice

Xiaopeng Zhang1 , Zhixing Huang2 , Jie Zhou3, Naihua Xiu2 , Yang Zhong3, Fan Chen1   

  1. 1 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100190, China; 2 Department of Applied Mathematics, Beijing Jiaotong University, Beijing 100044, China; 3 School of Life Sciences, Fudan University, Shanghai 200433, China
  • Received:2008-06-23 Revised:2008-06-30 Online:2009-03-01 Published:2009-03-01
  • Contact: Fan Chen


Current methods for the functional analysis of microarray gene expression data make the implicit assumption that genes with similar expression profiles have similar functions. However genes involved in the same biological pathway could be associated because of their temporal and spatial relationship but not always because of the high expression similarity. Here we explored the possible application of shortest-path analysis on expression of rice genes under abscisic-acid, drought, cold and salinity stress by rice cDNA microarray. We constructed the shortest path among the selected genes with low expression similarity using software we developed and found functional relationships among rice genes and predicted the function of unknown genes. The data were explored to understand the network of gene expression and response to environmental stress in rice.

Key words: gene annotation, microarray, shortest path, transitive co-expression