Additional file 24: Table S14. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Additional file 19: Figure S9. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Expression types of global DE genes among the three strains. (PDF 344Â kb) (PDF 333Â kb

Additional file 6: Figure S3. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Scatter plots of Ď values for highly expressed genes in respective japonica or indica tissues. (PDF...

Additional file 21: Figure S10. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Commonly detected changed-tissues jiDE genes between the NM and NZ combinations. (PDF 385Â kb) (PDF ...

Additional file 25: Figure S11. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Relationship between explained variation by detected eQTLs and Zhenshan97 Ď. (PDF 455Â kb) (PDF 442...

Additional file 22: Table S12. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Commonly detected changed-tissues jiDE genes between the NM and NZ combinations. (XLSX 53Â kb) (XLSX...

Additional file 26: Table S15. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Description of the number of unique transcripts and unique probes. (DOCX 111Â kb) (DOCX 105Â kb

Additional file 17: Table S9. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

GO enrichment analysis of tissue specific changed-tissues jiDE genes of the NM combination. (XLSX 49...

Additional file 20: Table S11. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Expression types of global DE genes among the three strains. (XLSX 49Â kb) (XLSX 45Â kb

Additional file 18: Table S10. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

GO enrichment analysis of tissue specific changed-tissues jiDE genes of the NZ combination. (XLSX 45...

Additional file 15: Table S7. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

GO enrichment analysis of global jiDE genes of the NM combination. (XLSX 57Â kb) (XLSX 52Â kb

Additional file 4: Table S2. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Number of highly expressed genes and SNEP detected jiDE genes in each tissue in the two japonica and...

Additional file 13: Table S5. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Expression of transposable element (TE) related genes. (XLSX 45Â kb) (XLSX 44Â kb

Additional file 16: Table S8. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

GO enrichment analysis of global jiDE genes of the NZ combination. (XLSX 53Â kb) (XLSX 49Â kb

Additional file 11: Figure S7. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Ratio distribution of changed-tissues jiDE genes of the NM combination. (PDF 762Â kb) (PDF 741Â kb

Additional file 5: Table S3. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Highly expressed genes and the two types of jiDE genes of the two japonica-indica combinations in th...

Additional file 19: Figure S9. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Expression types of global DE genes among the three strains. (PDF 344Â kb) (PDF 333Â kb

Additional file 6: Figure S3. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Scatter plots of Ď values for highly expressed genes in respective japonica or indica tissues. (PDF...

Additional file 21: Figure S10. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Commonly detected changed-tissues jiDE genes between the NM and NZ combinations. (PDF 385Â kb) (PDF ...

Additional file 25: Figure S11. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Relationship between explained variation by detected eQTLs and Zhenshan97 Ď. (PDF 455Â kb) (PDF 442...

Additional file 22: Table S12. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Commonly detected changed-tissues jiDE genes between the NM and NZ combinations. (XLSX 53Â kb) (XLSX...

Additional file 26: Table S15. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Description of the number of unique transcripts and unique probes. (DOCX 111Â kb) (DOCX 105Â kb

Additional file 17: Table S9. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

GO enrichment analysis of tissue specific changed-tissues jiDE genes of the NM combination. (XLSX 49...

Additional file 20: Table S11. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Expression types of global DE genes among the three strains. (XLSX 49Â kb) (XLSX 45Â kb

Additional file 18: Table S10. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

GO enrichment analysis of tissue specific changed-tissues jiDE genes of the NZ combination. (XLSX 45...

Additional file 15: Table S7. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

GO enrichment analysis of global jiDE genes of the NM combination. (XLSX 57Â kb) (XLSX 52Â kb

Additional file 4: Table S2. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Number of highly expressed genes and SNEP detected jiDE genes in each tissue in the two japonica and...

Additional file 13: Table S5. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Expression of transposable element (TE) related genes. (XLSX 45Â kb) (XLSX 44Â kb

Additional file 16: Table S8. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

GO enrichment analysis of global jiDE genes of the NZ combination. (XLSX 53Â kb) (XLSX 49Â kb

Additional file 11: Figure S7. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Ratio distribution of changed-tissues jiDE genes of the NM combination. (PDF 762Â kb) (PDF 741Â kb

Additional file 5: Table S3. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Highly expressed genes and the two types of jiDE genes of the two japonica-indica combinations in th...

Additional file 19: Figure S9. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Expression types of global DE genes among the three strains. (PDF 344Â kb) (PDF 333Â kb

Additional file 6: Figure S3. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Scatter plots of Ď values for highly expressed genes in respective japonica or indica tissues. (PDF...

Additional file 21: Figure S10. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Commonly detected changed-tissues jiDE genes between the NM and NZ combinations. (PDF 385Â kb) (PDF ...

Additional file 24: Table S14. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Abstract

Extracted data

Additional file 24: Table S14. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Abstract

Extracted data

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