RT Journal
A1 Ma, Ligeng
A1 Chen, Chen
A1 Liu, Xigang
A1 Jiao, Yuling
A1 Su, Ning
A1 Li, Lin
A1 Wang, Xiangfeng
A1 Cao, Mengliang
A1 Sun, Ning
A1 Zhang, Xiuqing
A1 Bao, Jingyue
A1 Li, Jian
A1 Pedersen, Soren
A1 Bolund, Lars
A1 Zhao, Hongyu
A1 Yuan, Longping
A1 Wong, Gane Ka-Shu
A1 Wang, Jun
A1 Deng, Xing Wang
A1 Wang, Jian
T1 A microarray analysis of the rice transcriptome and its comparison to Arabidopsis
JF Genome Research 
JO Genome Research 
YR 2005 
FD September 01 
VO 15 
IS 9 
SP 1274 
OP 1283 
DO 10.1101/gr.3657405 
UL http://genome.cshlp.org/content/15/9/1274.abstract 
AB Arabidopsis and rice are the only two model plants whose finished phase genome sequence has been completed. Here we report the construction of an oligomer microarray based on the presently known and predicted gene models in the rice genome. This microarray was used to analyze the transcriptional activity of the gene models in representative rice organ types. Expression of 86% of the 41,754 known and predicted gene models was detected. A significant fraction of these expressed gene models are organized into chromosomal regions, about 100 kb in length, that exhibit a coexpression pattern. Compared with similar genome-wide surveys of the Arabidopsis transcriptome, our results indicate that similar proportions of the two genomes are expressed in their corresponding organ types. A large percentage of the rice gene models that lack significant Arabidopsis homologs are expressed. Furthermore, the expression patterns of rice and Arabidopsis best-matched homologous genes in distinct functional groups indicate dramatic differences in their degree of conservation between the two species. Thus, this initial comparative analysis reveals some basic similarities and differences between the Arabidopsis and rice transcriptomes.