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Additional file 6: of OsNOA1 functions in a threshold-dependent manner to regulate chloroplast proteins in rice at lower temperatures
Figure S5. Comparison of the quantile-quantile (Q-Q) plot of the same data sets in both sets of biological replicates as described in Additional file 2: Figure S1. The top four panels (A-D) represent the log2 ratios for 127/126, 129/126, 130/126 and 131/126 respectively in biological set 1. The bottom four panels (E-H) represent the equivalent of A-D but for biological set 2. The Q-Q plot is a graph of the input (observed) data values plotted against the theoretical (fitted) distribution quantiles. The approximately linear plots for each of the data sets confirm the data consistency between two sets of biological replicates. (TIFF 314 kb
Additional file 3: of OsNOA1 functions in a threshold-dependent manner to regulate chloroplast proteins in rice at lower temperatures
Figure S2. Comparison of the probability density function of the relative expression data (Treated/WT) for all proteins quantified for each of the individual transgenic line in both sets of biological replicates. Each set of data was simultaneously fit to 50 standard data distribution models using the EasyFit software suit (MathWave Technologies, http://www.mathwave.com ). The data were judged to be best fit by the Burr distribution, using the Kolmogrov/Sminov, Aderson/Darling and Chi-Squared tests for goodness of fit. The four top panels (A-D) represent the log2 ratios for 127-tag (RNAi-20 at 22 °C)/126-tag (WT 22 °C), for 129-tag (Ox-45 at 22 °C)/126-tag (WT 22 °C), for 130-tag (WT 30 °C)/126-tag (WT 22 °C), and for 131-tag (RNAi-20 30 °C)/126-tag (WT 22 °C), respectively, in biological set 1. The bottom four panels (E-H) represent the equivalent of A-D, but for biological set 2. Each data set was found to be consistent and normally distributed, as shown in this graph. (TIFF 482 kb
Additional file 1: of OsNOA1 functions in a threshold-dependent manner to regulate chloroplast proteins in rice at lower temperatures
Table S1. Complete list of all identified proteins. Complete list of all identified proteins (4176 proteins) were organized by protein accession numbers. (XLS 4120 kb
Additional file 5: of OsNOA1 functions in a threshold-dependent manner to regulate chloroplast proteins in rice at lower temperatures
Figure S4. Comparison of the probability-probability (P-P) plot of the same data sets in both sets of biological replicates as described in Additional file 2: Figure S1. The top four panels (A-D) represent the log2 ratios for 127/126, 129/126, 130/126 and 131/126 respectively in biological set 1. The bottom four panels (E-H) represent the equivalent of A-D but for biological set 2. The P-P plot is a graph of the empirical CDF values plotted against the theoretical CDF values, and used to determine how well a specific distribution fits to the observed data. The approximately linear plots for each of the data sets confirmed the correct theoretical distribution model and data consistency between two sets of biological replicates. (TIFF 339 kb
Additional file 4: of OsNOA1 functions in a threshold-dependent manner to regulate chloroplast proteins in rice at lower temperatures
Figure S3. Comparison of the cumulative distribution function (CDF) of the relative expression data (Treated/WT) for all proteins quantified for each of the individual treatments in both sets of biological replicates. The top four panels (A-D) represent the log2 ratios for 127-tag (RNAi-20 at 22 °C)/126-tag (WT 22 °C), for 129-tag (Ox-45 at 22 °C)/126-tag (WT 22 °C), for 130-tag (WT 30 °C)/126-tag (WT 22 °C), and for 131-tag (RNAi-20 30 °C)/126-tag (WT 22 °C) in biological set 1. The bottom four panels (E-H) represent the equivalent of A-D, but for biological set 2. Consistent distribution for each data set between the two sets of biological replicates was demonstrated. (TIFF 336 kb
Additional file 9: of OsNOA1 functions in a threshold-dependent manner to regulate chloroplast proteins in rice at lower temperatures
Table S4. A comparison of proteomics data with previously published microarray data. Transcripts matched to down-regulated proteins in the silenced line at 22 °C were listed in this table (mentioned in Table S2). (XLS 86 kb
Additional file 10: of OsNOA1 functions in a threshold-dependent manner to regulate chloroplast proteins in rice at lower temperatures
Table S5. Predicted functional partners of OsNOA1. 44 potential interaction partners of OsNOA1 predicted by STRING database were listed in this table. (XLS 22 kb
Additional file 8: of OsNOA1 functions in a threshold-dependent manner to regulate chloroplast proteins in rice at lower temperatures
Table S3. Up-regulated protein species in the silenced line at 22 °C and corresponding ratios at 30 °C. A total of 241 up-regulated proteins in the silenced line at 22 °C were organized by functional groups. Corresponding ratios of these proteins in line Ox-45 were also included in the table. (XLS 65 kb
Additional file 7: of OsNOA1 functions in a threshold-dependent manner to regulate chloroplast proteins in rice at lower temperatures
Table S2. Down-regulated protein species in the silenced line at 22 °C and corresponding ratios at 30 °C. A total of 256 down-regulated proteins in the silenced line at 22 °C were organized by localization and functional groups. Ratios of these proteins in silenced line grown at 30 °C as well as corresponding ratios in line Ox-45 grown at 22 °C were also included in the table. (XLS 90 kb
Additional file 2: of OsNOA1 functions in a threshold-dependent manner to regulate chloroplast proteins in rice at lower temperatures
Figure S1. Venn diagrams of differentially expressed identified protein species in duplicated sets of biological samples. For comparison of RNAi-20 vs. WT, the maximum RSDs for up-regulated (A) and down-regulated (B) protein species were 17% (A) and 29% (B) with average RSDs = 6% and 10%, respectively. For comparison of Ox-45 vs. WT, the maximum RSDs for up-regulated (C) and down-regulated (D) protein species were 25% and 43% each, with average RSDs = of 9% and 17% respectively. (TIFF 1721 kb