IC4R014-RNA-Seq-2013-23322175 - Revision history

Liman: /* Research Findings */

2016-07-13T16:46:53Z

‎Research Findings

Liman: /* Research Findings */

2016-07-13T16:45:43Z

‎Research Findings

Liman: /* Research Findings */

2016-07-13T16:45:28Z

‎Research Findings

Liman: /* Research Findings */

2016-07-13T16:44:53Z

‎Research Findings

Liman: /* Research Findings */

2016-07-13T16:43:05Z

‎Research Findings

Liman: /* Research Findings */

2016-07-13T16:39:51Z

‎Research Findings

Liman: /* Research Findings */

2016-07-13T16:36:35Z

‎Research Findings

Liman: /* Research Findings */

2016-07-13T16:25:30Z

‎Research Findings

Liman: /* Research Findings */

2016-07-13T16:15:28Z

‎Research Findings

Liman: /* Research Findings */

2016-07-13T16:04:23Z

‎Research Findings

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 [[File:IC4R014-RNA-Seq-2013-23322175-f1.png |center |thumb |400px |'''Figure 1. Venn diagram showing the genes expressed in each of the three stages of rice endosperm development.''']]
+<br>
 * From the analysis of differentially expressed genes (DEG) between samples ,the researchers could also identify the change in gene expression between three stages (Table 1). They identified 10,371 DEGs in three comparisons (R1-v-R2, R2-v-R3 and R1-v-R3). The overall trend in all the comparisons was downregulation of gene expression. Only a minority of genes were up-regulated during rice endosperm development.
 [[File:IC4R014-RNA-Seq-2013-23322175-t1.png |center |thumb |800px |'''Table 1. All 10,371 DEGs divided according to the folds of RPKM value between two stages in rice endosperm development''']]
+<br>
 * To identify clusters with functional enrichment, the researchers performed hierarchical clustering of the expression patterns of all DEGs and found that there was a similarity relationship in gene expression among three stages (Fig. 2). The hierarchical clustering analysis indicates that the majority of genes were downregulated in all three comparisons, and that a minority of genes were up-regulated.
 [[File:IC4R014-RNA-Seq-2013-23322175-f2.png |center |thumb |800px |'''Figure 2. Hierarchical cluster analysis of gene expression based on log ratio RPKM data.''']]
+<br>
 * Through the GO analysis, all genes were separated into three major parts (i.e., biological process, molecular function, and cellular component). Using BLAST2GO (version 2.3.5), a total of 157,650 GO terms were associated with all 23,836 genes and classified into 41 functional subcategory annotations (Fig. 3).The GO annotation assignment determined that the genes expressed in this study encode diverse structural, regulatory and metabolic proteins.
 [[File:IC4R014-RNA-Seq-2013-23322175-f3.png |center |thumb |800px |'''Figure 3. GO classifications of genes.'''The results are summarized in three main categories: biological process, molecular function and cellular component by GO analysis. a GO classifications of all genes between three stages. b GO classifications of all 10,371 DEGs among three contrasts. c GO analysis of the up-regulated and down-regulated genes in R1-v-R2. d GO analysis of the up-regulated and downregulated genes in R2-v-R3 (*P\0.05)]]
+<br>
 * To reveal the molecular mechanisms of events involving TFs in rice endosperm development, the researchers used the Rice TF database to search for TFs. In total, 1,118 putative TF genes of 55 TF families were identified in 23,836 genes from RNA-Seq analysis. This provided a deeper understanding of the role of TFs during rice endosperm development.

@@ Line 16: / Line 16: @@
 * By comparison with the rice genome and trimming, all 35.9 high-quality million clean reads were assembled into 23,836 genes. Among the three stages, the number of genes found were 21,596 (R1), 20,910 (R2) and 19,459 (R3), providing massive data for endosperm development analysis. From these numbers, there is an apparent decline in quantity during endosperm development. A Venn diagram shows the overlapping relationship between the three stages (Fig. 1).
-[[File:IC4R014-RNA-Seq-2013-23322175-f1.png |center |thumb |200px |'''Figure 1. Venn diagram showing the genes expressed in each of the three stages of rice endosperm development.''']]
+[[File:IC4R014-RNA-Seq-2013-23322175-f1.png |center |thumb |400px |'''Figure 1. Venn diagram showing the genes expressed in each of the three stages of rice endosperm development.''']]
 * From the analysis of differentially expressed genes (DEG) between samples ,the researchers could also identify the change in gene expression between three stages (Table 1). They identified 10,371 DEGs in three comparisons (R1-v-R2, R2-v-R3 and R1-v-R3). The overall trend in all the comparisons was downregulation of gene expression. Only a minority of genes were up-regulated during rice endosperm development.

@@ Line 16: / Line 16: @@
 * By comparison with the rice genome and trimming, all 35.9 high-quality million clean reads were assembled into 23,836 genes. Among the three stages, the number of genes found were 21,596 (R1), 20,910 (R2) and 19,459 (R3), providing massive data for endosperm development analysis. From these numbers, there is an apparent decline in quantity during endosperm development. A Venn diagram shows the overlapping relationship between the three stages (Fig. 1).
-[[File:IC4R014-RNA-Seq-2013-23322175-f1.png |center |thumb |500px |'''Figure 1. Venn diagram showing the genes expressed in each of the three stages of rice endosperm development.''']]
+[[File:IC4R014-RNA-Seq-2013-23322175-f1.png |center |thumb |200px |'''Figure 1. Venn diagram showing the genes expressed in each of the three stages of rice endosperm development.''']]
 * From the analysis of differentially expressed genes (DEG) between samples ,the researchers could also identify the change in gene expression between three stages (Table 1). They identified 10,371 DEGs in three comparisons (R1-v-R2, R2-v-R3 and R1-v-R3). The overall trend in all the comparisons was downregulation of gene expression. Only a minority of genes were up-regulated during rice endosperm development.
@@ Line 28: / Line 28: @@
 * Through the GO analysis, all genes were separated into three major parts (i.e., biological process, molecular function, and cellular component). Using BLAST2GO (version 2.3.5), a total of 157,650 GO terms were associated with all 23,836 genes and classified into 41 functional subcategory annotations (Fig. 3).The GO annotation assignment determined that the genes expressed in this study encode diverse structural, regulatory and metabolic proteins.
-[[File:IC4R014-RNA-Seq-2013-23322175-f2.png |center |thumb |800px |'''Figure 3. GO classifications of genes.'''The results are summarized in three main categories: biological process, molecular function and cellular component by GO analysis. a GO classifications of all genes between three stages. b GO classifications of all 10,371 DEGs among three contrasts. c GO analysis of the up-regulated and down-regulated genes in R1-v-R2. d GO analysis of the up-regulated and downregulated genes in R2-v-R3 (*P\0.05)]]
+[[File:IC4R014-RNA-Seq-2013-23322175-f3.png |center |thumb |800px |'''Figure 3. GO classifications of genes.'''The results are summarized in three main categories: biological process, molecular function and cellular component by GO analysis. a GO classifications of all genes between three stages. b GO classifications of all 10,371 DEGs among three contrasts. c GO analysis of the up-regulated and down-regulated genes in R1-v-R2. d GO analysis of the up-regulated and downregulated genes in R2-v-R3 (*P\0.05)]]
 * To reveal the molecular mechanisms of events involving TFs in rice endosperm development, the researchers used the Rice TF database to search for TFs. In total, 1,118 putative TF genes of 55 TF families were identified in 23,836 genes from RNA-Seq analysis. This provided a deeper understanding of the role of TFs during rice endosperm development.

@@ Line 16: / Line 16: @@
 * By comparison with the rice genome and trimming, all 35.9 high-quality million clean reads were assembled into 23,836 genes. Among the three stages, the number of genes found were 21,596 (R1), 20,910 (R2) and 19,459 (R3), providing massive data for endosperm development analysis. From these numbers, there is an apparent decline in quantity during endosperm development. A Venn diagram shows the overlapping relationship between the three stages (Fig. 1).
-[[File:IC4R014-RNA-Seq-2013-23322175-f1.png |center |thumb |800px |'''Figure 1. Venn diagram showing the genes expressed in each of the three stages of rice endosperm development.''']]
+[[File:IC4R014-RNA-Seq-2013-23322175-f1.png |center |thumb |500px |'''Figure 1. Venn diagram showing the genes expressed in each of the three stages of rice endosperm development.''']]
 * From the analysis of differentially expressed genes (DEG) between samples ,the researchers could also identify the change in gene expression between three stages (Table 1). They identified 10,371 DEGs in three comparisons (R1-v-R2, R2-v-R3 and R1-v-R3). The overall trend in all the comparisons was downregulation of gene expression. Only a minority of genes were up-regulated during rice endosperm development.

← Older revision		Revision as of 16:43, 13 July 2016
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	[[File:IC4R014-RNA-Seq-2013-23322175-f2.png \|center \|thumb \|800px \|'''Figure 3. GO classifications of genes.'''The results are summarized in three main categories: biological process, molecular function and cellular component by GO analysis. a GO classifications of all genes between three stages. b GO classifications of all 10,371 DEGs among three contrasts. c GO analysis of the up-regulated and down-regulated genes in R1-v-R2. d GO analysis of the up-regulated and downregulated genes in R2-v-R3 (*P\0.05)]]		[[File:IC4R014-RNA-Seq-2013-23322175-f2.png \|center \|thumb \|800px \|'''Figure 3. GO classifications of genes.'''The results are summarized in three main categories: biological process, molecular function and cellular component by GO analysis. a GO classifications of all genes between three stages. b GO classifications of all 10,371 DEGs among three contrasts. c GO analysis of the up-regulated and down-regulated genes in R1-v-R2. d GO analysis of the up-regulated and downregulated genes in R2-v-R3 (*P\0.05)]]
		+
		+	* To reveal the molecular mechanisms of events involving TFs in rice endosperm development, the researchers used the Rice TF database to search for TFs. In total, 1,118 putative TF genes of 55 TF families were identified in 23,836 genes from RNA-Seq analysis. This provided a deeper understanding of the role of TFs during rice endosperm development.

	==Labs working on this Project==		==Labs working on this Project==

@@ Line 12: / Line 12: @@
 ==Research Findings==
-* A large number of genes related to ribosomes, the spliceosome and oxidative phosphorylation were found to be expressed in the early and middle stages. Plant hormone, galactose metabolism and carbon fixation related genes showed a significant increase in expression at the middle stage, whereas genes for defense against disease or response to stress as well as genes for starch/sucrose metabolism were strongly expressed during the later stages of endosperm development.
+* A large number of genes related to ribosomes, the spliceosome and oxidative phosphorylation were found to be expressed in the early and middle stages of rice endosperm development. Plant hormone, galactose metabolism and carbon fixation related genes showed a significant increase in expression at the middle stage, whereas genes for defense against disease or response to stress as well as genes for starch/sucrose metabolism were strongly expressed during the later stages of endosperm development.
 * By comparison with the rice genome and trimming, all 35.9 high-quality million clean reads were assembled into 23,836 genes. Among the three stages, the number of genes found were 21,596 (R1), 20,910 (R2) and 19,459 (R3), providing massive data for endosperm development analysis. From these numbers, there is an apparent decline in quantity during endosperm development. A Venn diagram shows the overlapping relationship between the three stages (Fig. 1).
@@ Line 29: / Line 29: @@
 [[File:IC4R014-RNA-Seq-2013-23322175-f2.png |center |thumb |800px |'''Figure 3. GO classifications of genes.'''The results are summarized in three main categories: biological process, molecular function and cellular component by GO analysis. a GO classifications of all genes between three stages. b GO classifications of all 10,371 DEGs among three contrasts. c GO analysis of the up-regulated and down-regulated genes in R1-v-R2. d GO analysis of the up-regulated and downregulated genes in R2-v-R3 (*P\0.05)]]
 ==Labs working on this Project==

← Older revision		Revision as of 16:36, 13 July 2016
Line 12:		Line 12:

	==Research Findings==		==Research Findings==
		+	* A large number of genes related to ribosomes, the spliceosome and oxidative phosphorylation were found to be expressed in the early and middle stages. Plant hormone, galactose metabolism and carbon fixation related genes showed a significant increase in expression at the middle stage, whereas genes for defense against disease or response to stress as well as genes for starch/sucrose metabolism were strongly expressed during the later stages of endosperm development.
		+
	* By comparison with the rice genome and trimming, all 35.9 high-quality million clean reads were assembled into 23,836 genes. Among the three stages, the number of genes found were 21,596 (R1), 20,910 (R2) and 19,459 (R3), providing massive data for endosperm development analysis. From these numbers, there is an apparent decline in quantity during endosperm development. A Venn diagram shows the overlapping relationship between the three stages (Fig. 1).		* By comparison with the rice genome and trimming, all 35.9 high-quality million clean reads were assembled into 23,836 genes. Among the three stages, the number of genes found were 21,596 (R1), 20,910 (R2) and 19,459 (R3), providing massive data for endosperm development analysis. From these numbers, there is an apparent decline in quantity during endosperm development. A Venn diagram shows the overlapping relationship between the three stages (Fig. 1).

← Older revision		Revision as of 16:25, 13 July 2016
Line 27:		Line 27:

	[[File:IC4R014-RNA-Seq-2013-23322175-f2.png \|center \|thumb \|800px \|'''Figure 3. GO classifications of genes.'''The results are summarized in three main categories: biological process, molecular function and cellular component by GO analysis. a GO classifications of all genes between three stages. b GO classifications of all 10,371 DEGs among three contrasts. c GO analysis of the up-regulated and down-regulated genes in R1-v-R2. d GO analysis of the up-regulated and downregulated genes in R2-v-R3 (*P\0.05)]]		[[File:IC4R014-RNA-Seq-2013-23322175-f2.png \|center \|thumb \|800px \|'''Figure 3. GO classifications of genes.'''The results are summarized in three main categories: biological process, molecular function and cellular component by GO analysis. a GO classifications of all genes between three stages. b GO classifications of all 10,371 DEGs among three contrasts. c GO analysis of the up-regulated and down-regulated genes in R1-v-R2. d GO analysis of the up-regulated and downregulated genes in R2-v-R3 (*P\0.05)]]
		+
		+
		+	* To perform functional classification and pathway assignment of genes during rice endosperm development, all DEGs were analyzed against the KEGG (Kyoto Encyclopedia of Genes and Genomes) and the MapMan tool. By mapping to the reference canonical pathways, all DEGs were assigned to 123 KEGG pathways. On the basis of RPKM, the researchers found four significant expression types among all pathways.

	==Labs working on this Project==		==Labs working on this Project==

← Older revision		Revision as of 16:15, 13 July 2016
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	[[File:IC4R014-RNA-Seq-2013-23322175-f2.png \|center \|thumb \|800px \|'''Figure 2. Hierarchical cluster analysis of gene expression based on log ratio RPKM data.''']]		[[File:IC4R014-RNA-Seq-2013-23322175-f2.png \|center \|thumb \|800px \|'''Figure 2. Hierarchical cluster analysis of gene expression based on log ratio RPKM data.''']]
		+
		+	* Through the GO analysis, all genes were separated into three major parts (i.e., biological process, molecular function, and cellular component). Using BLAST2GO (version 2.3.5), a total of 157,650 GO terms were associated with all 23,836 genes and classified into 41 functional subcategory annotations (Fig. 3).The GO annotation assignment determined that the genes expressed in this study encode diverse structural, regulatory and metabolic proteins.
		+
		+	[[File:IC4R014-RNA-Seq-2013-23322175-f2.png \|center \|thumb \|800px \|'''Figure 3. GO classifications of genes.'''The results are summarized in three main categories: biological process, molecular function and cellular component by GO analysis. a GO classifications of all genes between three stages. b GO classifications of all 10,371 DEGs among three contrasts. c GO analysis of the up-regulated and down-regulated genes in R1-v-R2. d GO analysis of the up-regulated and downregulated genes in R2-v-R3 (*P\0.05)]]

	==Labs working on this Project==		==Labs working on this Project==