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A microarray analysis of the rice transcriptome and its comparison to Arabidopsis
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| Zeitschriftentitel: | Genome Research |
|---|---|
| Personen und Körperschaften: | , , , , , , , , , , , , , , , , , , , |
| In: | Genome Research, 15, 2005, 9, S. 1274-1283 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Cold Spring Harbor Laboratory
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| Schlagwörter: |
| author_facet |
Ma, Ligeng Chen, Chen Liu, Xigang Jiao, Yuling Su, Ning Li, Lin Wang, Xiangfeng Cao, Mengliang Sun, Ning Zhang, Xiuqing Bao, Jingyue Li, Jian Pedersen, Soren Bolund, Lars Zhao, Hongyu Yuan, Longping Wong, Gane Ka-Shu Wang, Jun Deng, Xing Wang Wang, Jian Ma, Ligeng Chen, Chen Liu, Xigang Jiao, Yuling Su, Ning Li, Lin Wang, Xiangfeng Cao, Mengliang Sun, Ning Zhang, Xiuqing Bao, Jingyue Li, Jian Pedersen, Soren Bolund, Lars Zhao, Hongyu Yuan, Longping Wong, Gane Ka-Shu Wang, Jun Deng, Xing Wang Wang, Jian |
|---|---|
| author |
Ma, Ligeng Chen, Chen Liu, Xigang Jiao, Yuling Su, Ning Li, Lin Wang, Xiangfeng Cao, Mengliang Sun, Ning Zhang, Xiuqing Bao, Jingyue Li, Jian Pedersen, Soren Bolund, Lars Zhao, Hongyu Yuan, Longping Wong, Gane Ka-Shu Wang, Jun Deng, Xing Wang Wang, Jian |
| spellingShingle |
Ma, Ligeng Chen, Chen Liu, Xigang Jiao, Yuling Su, Ning Li, Lin Wang, Xiangfeng Cao, Mengliang Sun, Ning Zhang, Xiuqing Bao, Jingyue Li, Jian Pedersen, Soren Bolund, Lars Zhao, Hongyu Yuan, Longping Wong, Gane Ka-Shu Wang, Jun Deng, Xing Wang Wang, Jian Genome Research A microarray analysis of the rice transcriptome and its comparison to Arabidopsis Genetics (clinical) Genetics |
| author_sort |
ma, ligeng |
| spelling |
Ma, Ligeng Chen, Chen Liu, Xigang Jiao, Yuling Su, Ning Li, Lin Wang, Xiangfeng Cao, Mengliang Sun, Ning Zhang, Xiuqing Bao, Jingyue Li, Jian Pedersen, Soren Bolund, Lars Zhao, Hongyu Yuan, Longping Wong, Gane Ka-Shu Wang, Jun Deng, Xing Wang Wang, Jian 1088-9051 Cold Spring Harbor Laboratory Genetics (clinical) Genetics http://dx.doi.org/10.1101/gr.3657405 <jats:p><jats:italic>Arabidopsis</jats:italic> 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 <jats:italic>Arabidopsis</jats:italic> 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 <jats:italic>Arabidopsis</jats:italic> homologs are expressed. Furthermore, the expression patterns of rice and <jats:italic>Arabidopsis</jats:italic> 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 <jats:italic>Arabidopsis</jats:italic> and rice transcriptomes.</jats:p> A microarray analysis of the rice transcriptome and its comparison to <i>Arabidopsis</i> Genome Research |
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Cold Spring Harbor Laboratory, 2005 |
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| title |
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis |
| title_unstemmed |
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis |
| title_full |
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis |
| title_fullStr |
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis |
| title_full_unstemmed |
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis |
| title_short |
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis |
| title_sort |
a microarray analysis of the rice transcriptome and its comparison to <i>arabidopsis</i> |
| topic |
Genetics (clinical) Genetics |
| url |
http://dx.doi.org/10.1101/gr.3657405 |
| publishDate |
2005 |
| physical |
1274-1283 |
| description |
<jats:p><jats:italic>Arabidopsis</jats:italic> 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 <jats:italic>Arabidopsis</jats:italic> 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 <jats:italic>Arabidopsis</jats:italic> homologs are expressed. Furthermore, the expression patterns of rice and <jats:italic>Arabidopsis</jats:italic> 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 <jats:italic>Arabidopsis</jats:italic> and rice transcriptomes.</jats:p> |
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| author | Ma, Ligeng, Chen, Chen, Liu, Xigang, Jiao, Yuling, Su, Ning, Li, Lin, Wang, Xiangfeng, Cao, Mengliang, Sun, Ning, Zhang, Xiuqing, Bao, Jingyue, Li, Jian, Pedersen, Soren, Bolund, Lars, Zhao, Hongyu, Yuan, Longping, Wong, Gane Ka-Shu, Wang, Jun, Deng, Xing Wang, Wang, Jian |
| author_facet | Ma, Ligeng, Chen, Chen, Liu, Xigang, Jiao, Yuling, Su, Ning, Li, Lin, Wang, Xiangfeng, Cao, Mengliang, Sun, Ning, Zhang, Xiuqing, Bao, Jingyue, Li, Jian, Pedersen, Soren, Bolund, Lars, Zhao, Hongyu, Yuan, Longping, Wong, Gane Ka-Shu, Wang, Jun, Deng, Xing Wang, Wang, Jian, Ma, Ligeng, Chen, Chen, Liu, Xigang, Jiao, Yuling, Su, Ning, Li, Lin, Wang, Xiangfeng, Cao, Mengliang, Sun, Ning, Zhang, Xiuqing, Bao, Jingyue, Li, Jian, Pedersen, Soren, Bolund, Lars, Zhao, Hongyu, Yuan, Longping, Wong, Gane Ka-Shu, Wang, Jun, Deng, Xing Wang, Wang, Jian |
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| description | <jats:p><jats:italic>Arabidopsis</jats:italic> 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 <jats:italic>Arabidopsis</jats:italic> 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 <jats:italic>Arabidopsis</jats:italic> homologs are expressed. Furthermore, the expression patterns of rice and <jats:italic>Arabidopsis</jats:italic> 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 <jats:italic>Arabidopsis</jats:italic> and rice transcriptomes.</jats:p> |
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| spelling | Ma, Ligeng Chen, Chen Liu, Xigang Jiao, Yuling Su, Ning Li, Lin Wang, Xiangfeng Cao, Mengliang Sun, Ning Zhang, Xiuqing Bao, Jingyue Li, Jian Pedersen, Soren Bolund, Lars Zhao, Hongyu Yuan, Longping Wong, Gane Ka-Shu Wang, Jun Deng, Xing Wang Wang, Jian 1088-9051 Cold Spring Harbor Laboratory Genetics (clinical) Genetics http://dx.doi.org/10.1101/gr.3657405 <jats:p><jats:italic>Arabidopsis</jats:italic> 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 <jats:italic>Arabidopsis</jats:italic> 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 <jats:italic>Arabidopsis</jats:italic> homologs are expressed. Furthermore, the expression patterns of rice and <jats:italic>Arabidopsis</jats:italic> 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 <jats:italic>Arabidopsis</jats:italic> and rice transcriptomes.</jats:p> A microarray analysis of the rice transcriptome and its comparison to <i>Arabidopsis</i> Genome Research |
| spellingShingle | Ma, Ligeng, Chen, Chen, Liu, Xigang, Jiao, Yuling, Su, Ning, Li, Lin, Wang, Xiangfeng, Cao, Mengliang, Sun, Ning, Zhang, Xiuqing, Bao, Jingyue, Li, Jian, Pedersen, Soren, Bolund, Lars, Zhao, Hongyu, Yuan, Longping, Wong, Gane Ka-Shu, Wang, Jun, Deng, Xing Wang, Wang, Jian, Genome Research, A microarray analysis of the rice transcriptome and its comparison to Arabidopsis, Genetics (clinical), Genetics |
| title | A microarray analysis of the rice transcriptome and its comparison to Arabidopsis |
| title_full | A microarray analysis of the rice transcriptome and its comparison to Arabidopsis |
| title_fullStr | A microarray analysis of the rice transcriptome and its comparison to Arabidopsis |
| title_full_unstemmed | A microarray analysis of the rice transcriptome and its comparison to Arabidopsis |
| title_short | A microarray analysis of the rice transcriptome and its comparison to Arabidopsis |
| title_sort | a microarray analysis of the rice transcriptome and its comparison to <i>arabidopsis</i> |
| title_unstemmed | A microarray analysis of the rice transcriptome and its comparison to Arabidopsis |
| topic | Genetics (clinical), Genetics |
| url | http://dx.doi.org/10.1101/gr.3657405 |