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. 2013 Oct 11;5(11):2032–2050. doi: 10.1093/gbe/evt152

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© The Author(s) 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Fig. 1.— — The effects of SNPs on gene functions and GSEA. (A) GO term analysis of genes with large-effect SNPs by comparing with all annotated rice non-TE genes. Green and pink columns indicate the percentages of this GO term in SNP-affected proteins and total annotated rice proteins in the release 7 of MSU rice genome annotation database (http://rice.plantbiology.msu.edu/ [last accessed October 28, 2013]; Ouyang et al. 2007; Kawahara et al. 2013), respectively. (B) GO term analysis of genes with nonsynonymous substitutions by SNPs. Green and blue columns indicate the percentages of this GO term in SNP-affected proteins and total annotated rice proteins, respectively. Only GO terms with statistically significant differences at P < 0.05 were listed in (A) and (B). “P,” “F,” and “C” in (A) and (B) indicate the GO categories biological process, molecular function, and cellular component, respectively. GO term annotation in (A) and (B) refers to the following: GO:0006464 (protein modification process), GO:0043412 (macromolecule modification), GO:0030246 (carbohydrate binding), GO:0005515 (protein binding), GO:0000166 (nucleotide binding), GO:0005886 (plasma membrane), GO:0023052 (signaling), GO:0009875 (pollen–pistil interaction), GO:0007165 (signal transduction), GO:0050789 (regulation of biological process), GO:0050794 (regulation of cellular process), GO:0023046 (signaling process), GO:0023060 (signal transmission), GO:0065007 (biological regulation), GO:0051704 (multiorganism process), GO:0009856 (pollination), GO:0016265 (death), GO:0008219 (cell death), GO:0006950 (response to stress), GO:0007154 (cell communication), GO:0016301 (kinase activity), GO:0016772 (transferase activity, transferring phosphorus-containing groups), GO:0016740 (transferase activity), GO:0004872 (receptor activity), GO:0016818 (hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides), GO:0019825 (oxygen binding), GO:0016817 (hydrolase activity, acting on acid anhydrides), GO:0003774 (motor activity), GO:0003824 (catalytic activity), GO:0016462 (pyrophosphatase activity), GO:0017111 (nucleoside-triphosphatase activity), GO:0060089 (molecular transducer activity), GO:0016787 (hydrolase activity), and GO:0004871 (signal transducer activity).