Ratio-Based Analysis of Differential mRNA Processing and Expression of a Polyadenylation Factor Mutant pcfs4 Using Arabidopsis Tiling Microarray
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{"title"=>"Ratio-based analysis of differential mRNA processing and expression of a polyadenylation factor mutant pcfs4 using arabidopsis tiling microarray", "type"=>"journal", "authors"=>[{"first_name"=>"Jianti", "last_name"=>"Zheng", "scopus_author_id"=>"16029996900"}, {"first_name"=>"Denghui", "last_name"=>"Xing", "scopus_author_id"=>"24333548000"}, {"first_name"=>"Xiaohui", "last_name"=>"Wu", "scopus_author_id"=>"55715137900"}, {"first_name"=>"Yingjia", "last_name"=>"Shen", "scopus_author_id"=>"16029587500"}, {"first_name"=>"Diana M.", "last_name"=>"Kroll", "scopus_author_id"=>"41461520500"}, {"first_name"=>"Guoli", "last_name"=>"Ji", "scopus_author_id"=>"16028704900"}, {"first_name"=>"Qingshun Quinn", "last_name"=>"Li", "scopus_author_id"=>"7405857786"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-79952128134", "pui"=>"361354805", "doi"=>"10.1371/journal.pone.0014719", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "sgr"=>"79952128134", "pmid"=>"21364912"}, "id"=>"b9b9bfd5-0330-38f8-a0e9-d0f3fec17c5d", "abstract"=>"BACKGROUND: Alternative polyadenylation as a mechanism in gene expression regulation has been widely recognized in recent years. Arabidopsis polyadenylation factor PCFS4 was shown to function in leaf development and in flowering time control. The function of PCFS4 in controlling flowering time was correlated with the alternative polyadenylation of FCA, a flowering time regulator. However, genetic evidence suggested additional targets of PCFS4 that may mediate its function in both flowering time and leaf development.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: To identify further targets, we investigated the whole transcriptome of a PCFS4 mutant using Affymetrix Arabidopsis genomic tiling 1.0R array and developed a data analysis pipeline, termed RADPRE (Ratio-based Analysis of Differential mRNA Processing and Expression). In RADPRE, ratios of normalized probe intensities between wild type Columbia and a pcfs4 mutant were first generated. By doing so, one of the major problems of tiling array data--variations caused by differential probe affinity--was significantly alleviated. With the probe ratios as inputs, a hierarchy of statistical tests was carried out to identify differentially processed genes (DPG) and differentially expressed genes (DEG). The false discovery rate (FDR) of this analysis was estimated by using the balanced random combinations of Col/pcfs4 and pcfs4/Col ratios as inputs. Gene Ontology (GO) analysis of the DPGs and DEGs revealed potential new roles of PCFS4 in stress responses besides flowering time regulation.\\n\\nCONCLUSION/SIGNIFICANCE: We identified 68 DPGs and 114 DEGs with FDR at 1% and 2%, respectively. Most of the 68 DPGs were subjected to alternative polyadenylation, splicing or transcription initiation. Quantitative PCR analysis of a set of DPGs confirmed that most of these genes were truly differentially processed in pcfs4 mutant plants. The enriched GO term \"regulation of flower development\" among PCFS4 targets further indicated the efficacy of the RADPRE pipeline. This simple but effective program is available upon request.", "link"=>"http://www.mendeley.com/research/ratiobased-analysis-differential-mrna-processing-expression-polyadenylation-factor-mutant-pcfs4-usin", "reader_count"=>23, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Student > Doctoral Student"=>1, "Researcher"=>8, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>1, "Other"=>1, "Student > Master"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Student > Doctoral Student"=>1, "Researcher"=>8, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>1, "Other"=>1, "Student > Master"=>1}, "reader_count_by_subject_area"=>{"Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>20, "Physics and Astronomy"=>1}, "reader_count_by_subdiscipline"=>{"Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>20}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"United Kingdom"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/795138"], "description"=>"<p>The across-array variations were significantly reduced after normalization.</p>", "links"=>[], "tags"=>["plots", "log-transformed", "vsn-normalized", "rma-normalized"], "article_id"=>465504, "categories"=>["Genetics", "Medicine", "Virology", "Computational Biology", "Developmental Biology", "Molecular Biology"], "users"=>["Jianti Zheng", "Denghui Xing", "Xiaohui Wu", "Yingjia Shen", "Diana M. Kroll", "Guoli Ji", "Qingshun Quinn Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014719.g002", "stats"=>{"downloads"=>2, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Box_plots_of_log_transformed_raw_data_left_panel_VSN_normalized_middle_panel_and_RMA_normalized_right_panel_data_/465504", "title"=>"Box plots of log-transformed raw data (left panel), VSN-normalized (middle panel) and RMA-normalized (right panel) data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-02-25 01:31:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/795356"], "description"=>"<p>The latter was largely normal.</p>", "links"=>[], "tags"=>["ratios", "log-transformed"], "article_id"=>465723, "categories"=>["Genetics", "Medicine", "Virology", "Computational Biology", "Developmental Biology", "Molecular Biology"], "users"=>["Jianti Zheng", "Denghui Xing", "Xiaohui Wu", "Yingjia Shen", "Diana M. Kroll", "Guoli Ji", "Qingshun Quinn Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014719.g004", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_density_distribution_of_ratios_upper_panel_or_log_transformed_ratios_lower_panel_/465723", "title"=>"The density distribution of ratios (upper-panel) or log-transformed ratios (lower-panel).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-02-25 01:35:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/795024"], "description"=>"<p><b>A</b>) Preprocessing of data including background correction, across-array normalization, probe filtering and trimming, ratio generation, and log-transformation. <b>B</b>) To identify transcripts with at least one of its exon ratio means not equal to one, a one-sample two-tails T-test was applied to every exon of an annotated transcript with the null hypothesis that the ratio mean of the exon was equal to one. <b>C</b>) For those transcripts identified from the T-test in (B), a one-way ANOVA and F-test was performed for each transcript with its exons as the “level” parameter. Every transcript with the ratio means of all its exons being equal would be a putative DEG target. Otherwise, the transcript would be a direct DPG target. <b>D</b>) A further one-sample two-tails T-test was applied to every one of the putative DEG targets from (C) to test whether the ratio mean of the whole transcript was equal to one. If the ratio mean was not equal to one, the transcript would be a DEG target.</p>", "links"=>[], "tags"=>["flow-chart", "radpre"], "article_id"=>465388, "categories"=>["Genetics", "Medicine", "Virology", "Computational Biology", "Developmental Biology", "Molecular Biology"], "users"=>["Jianti Zheng", "Denghui Xing", "Xiaohui Wu", "Yingjia Shen", "Diana M. Kroll", "Guoli Ji", "Qingshun Quinn Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014719.g001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_flow_chart_of_RADPRE_analysis_pipeline_/465388", "title"=>"A flow-chart of RADPRE analysis pipeline.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-02-25 01:29:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/795574"], "description"=>"<p>Each data point represented the average of three replicates. The dotted vertical lines separate annotation units of the gene with or without difference between wild type (WT) and <i>pcfs4</i> mutant. The corresponding gene structure was presented under each plot with boxes denoting the exons and lines denoting the introns.</p>", "links"=>[], "tags"=>["dpgs", "pcfs4", "explained", "splicing", "transcription", "shown"], "article_id"=>465929, "categories"=>["Genetics", "Medicine", "Virology", "Computational Biology", "Developmental Biology", "Molecular Biology"], "users"=>["Jianti Zheng", "Denghui Xing", "Xiaohui Wu", "Yingjia Shen", "Diana M. Kroll", "Guoli Ji", "Qingshun Quinn Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014719.g006", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_DPGs_of_PCFS4_could_be_explained_by_3_simple_models_alternative_polyadenylation_alternative_splicing_and_alternative_transcription_initiation_as_shown_by_A_At4g38160_2_B_At5g46490_2_and_C_At5g52910_1_respectively_/465929", "title"=>"The DPGs of PCFS4 could be explained by 3 simple models: alternative polyadenylation, alternative splicing and alternative transcription initiation, as shown by A) At4g38160.2, B) At5g46490.2, and C) At5g52910.1, respectively.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-02-25 01:38:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/795755"], "description"=>"<p>Note: T-test and F-test, as depicted in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014719#pone-0014719-g001\" target=\"_blank\">Figure 1b and c</a>; the p-value for the T-test on the whole transcript level (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014719#pone-0014719-g001\" target=\"_blank\">Figure 1d</a>) was set at 0.05 (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014719#s2\" target=\"_blank\">Results</a> section).</p>", "links"=>[], "tags"=>["differentially", "processed", "genes"], "article_id"=>466121, "categories"=>["Genetics", "Medicine", "Virology", "Computational Biology", "Developmental Biology", "Molecular Biology"], "users"=>["Jianti Zheng", "Denghui Xing", "Xiaohui Wu", "Yingjia Shen", "Diana M. Kroll", "Guoli Ji", "Qingshun Quinn Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014719.t001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_false_discovery_rate_FDR_of_Differentially_Processed_Genes_DPGs_and_Differentially_Expressed_Genes_DEGs_/466121", "title"=>"The false discovery rate (FDR) of Differentially Processed Genes (DPGs) and Differentially Expressed Genes (DEGs).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-02-25 01:42:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/795442"], "description"=>"<p>The gene structure was shown on the top of the graph with filled boxes denoting exons, lines denoting introns, and the short lines under the exons denoting the tiling array probes. The gene could generate two transcripts, a long (LT) and a short (ST), with LT derived from a distal poly(A) site and containing exon 3 (hatched box), and ST from a proximal poly(A) site within intron 2. The thickness of the box represents the relative abundance of the transcripts. The relative abundance of two transcripts was altered between WT and MU due to the shift of the poly(A) site usage between WT and MU. The measured abundance of each exon was based on its corresponding probes, which reflected the sum of two transcripts. The measured abundance of exon 1 and 2 was the same between WT and MU, but that of exon 3 was different. Therefore, the ratio of exon 1 and 2 between WT and MU was equal to 1, but different from the ratio of exon 3. In that case, the poly(A) site choice was not affected by the mutant and the relative abundance of the two transcripts would be the same between WT and MU. The ratio of the measured abundance between WT and MU would be equal for all three exons.</p>", "links"=>[], "tags"=>["dpg", "ratios", "exons", "col", "mutant"], "article_id"=>465800, "categories"=>["Genetics", "Medicine", "Virology", "Computational Biology", "Developmental Biology", "Molecular Biology"], "users"=>["Jianti Zheng", "Denghui Xing", "Xiaohui Wu", "Yingjia Shen", "Diana M. Kroll", "Guoli Ji", "Qingshun Quinn Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014719.g005", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematics_of_how_a_DPG_gene_could_be_identified_based_on_the_ratios_of_its_exons_between_wild_type_Col_WT_and_the_pcfs4_mutant_MU_/465800", "title"=>"Schematics of how a DPG gene could be identified based on the ratios of its exons between wild type Col (WT) and the <i>pcfs4</i> mutant (MU).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-02-25 01:36:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/795255"], "description"=>"<p><b>A</b>) A plot of the probe intensities normalized against the average of all the probes across the annotation unit. The probe intensities fluctuated dramatically among probes, yet were highly correlated between wild type (WT) and mutant (<i>pcfs4</i>). <b>B</b>) The correlation coefficients of all exons with more than three probes were first calculated and then box-plotted. The median correlation coefficient was around 0.67 with the majority between 0.34 and 0.86. <b>C</b>) A plot of probe intensity ratios across the annotation unit. With the ratios, the variation among the probes was significantly reduced compared to the variation of intensities in (A). <b>D</b>) The variations of probe intensities or ratios across every exon with more than three probes were measured with standard deviation and then box-plotted. With ratios (<i>pcfs4</i>/WT), the median Standard Deviation (Std) was around 0.40, in contrast to the median Std of probe intensities of WT or <i>pcfs4</i>, 0.67 and 0.69.</p>", "links"=>[], "tags"=>["probe", "annotation", "was", "alleviated", "generating", "wt"], "article_id"=>465614, "categories"=>["Genetics", "Medicine", "Virology", "Computational Biology", "Developmental Biology", "Molecular Biology"], "users"=>["Jianti Zheng", "Denghui Xing", "Xiaohui Wu", "Yingjia Shen", "Diana M. Kroll", "Guoli Ji", "Qingshun Quinn Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014719.g003", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_variation_of_probe_intensity_across_the_same_annotation_unit_was_significantly_alleviated_by_generating_a_ratio_between_WT_and_the_pcfs4_mutant_/465614", "title"=>"The variation of probe intensity across the same annotation unit was significantly alleviated by generating a ratio between WT and the <i>pcfs4</i> mutant.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-02-25 01:33:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/795659"], "description"=>"<p>The average log fold change of <i>pcfs4</i>/WT is shown for two parts of each gene with a capped vertical line representing the standard error. The filled and open boxes represent the two parts of each gene being tested. The gene part showing a larger difference between wild type and mutant based on the tiling array data is represented by the filled box while the part showing less (or no) difference is represented by the open box. The double asterisk “**” denotes the genes showing significant difference (p = 0.05) for the ratios of two parts of each gene by qPCR. The single asterisk “*” denotes the genes whose one or both parts showed significant difference (p = 0.05) between wild type and the <i>pcfs4</i> mutant, but whose ratio of two parts showed no significant difference. The first 7 genes were from the DPG list with the FDR of 1% and they were a part of the total 17 genes from the DPG list with the FDR of 2%.</p>", "links"=>[], "tags"=>["pcr", "confirmation", "dpg", "targets"], "article_id"=>466028, "categories"=>["Genetics", "Medicine", "Virology", "Computational Biology", "Developmental Biology", "Molecular Biology"], "users"=>["Jianti Zheng", "Denghui Xing", "Xiaohui Wu", "Yingjia Shen", "Diana M. Kroll", "Guoli Ji", "Qingshun Quinn Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014719.g007", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Quantitative_PCR_confirmation_of_the_DPG_targets_of_PCFS4_/466028", "title"=>"Quantitative PCR confirmation of the DPG targets of PCFS4.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-02-25 01:40:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/397711", "https://ndownloader.figshare.com/files/397754", "https://ndownloader.figshare.com/files/397787", "https://ndownloader.figshare.com/files/397864", "https://ndownloader.figshare.com/files/397935", "https://ndownloader.figshare.com/files/397984", "https://ndownloader.figshare.com/files/398040"], "description"=>"<div><h3>Background</h3><p>Alternative polyadenylation as a mechanism in gene expression regulation has been widely recognized in recent years. Arabidopsis polyadenylation factor PCFS4 was shown to function in leaf development and in flowering time control. The function of PCFS4 in controlling flowering time was correlated with the alternative polyadenylation of <em>FCA</em>, a flowering time regulator. However, genetic evidence suggested additional targets of PCFS4 that may mediate its function in both flowering time and leaf development.</p><h3>Methodology/Principal Findings</h3><p>To identify further targets, we investigated the whole transcriptome of a <em>PCFS4</em> mutant using Affymetrix Arabidopsis genomic tiling 1.0R array and developed a data analysis pipeline, termed RADPRE (Ratio-based Analysis of Differential mRNA Processing and Expression). In RADPRE, ratios of normalized probe intensities between wild type Columbia and a <em>pcfs4</em> mutant were first generated. By doing so, one of the major problems of tiling array data—variations caused by differential probe affinity—was significantly alleviated. With the probe ratios as inputs, a hierarchy of statistical tests was carried out to identify differentially processed genes (DPG) and differentially expressed genes (DEG). The false discovery rate (FDR) of this analysis was estimated by using the balanced random combinations of Col/<em>pcfs4</em> and <em>pcfs4</em>/Col ratios as inputs. Gene Ontology (GO) analysis of the DPGs and DEGs revealed potential new roles of PCFS4 in stress responses besides flowering time regulation.</p><h3>Conclusion/Significance</h3><p>We identified 68 DPGs and 114 DEGs with FDR at 1% and 2%, respectively. Most of the 68 DPGs were subjected to alternative polyadenylation, splicing or transcription initiation. Quantitative PCR analysis of a set of DPGs confirmed that most of these genes were truly differentially processed in <em>pcfs4</em> mutant plants. The enriched GO term “regulation of flower development” among PCFS4 targets further indicated the efficacy of the RADPRE pipeline. This simple but effective program is available upon request.</p></div>", "links"=>[], "tags"=>["ratio-based", "differential", "mrna", "polyadenylation", "mutant", "arabidopsis", "tiling", "microarray"], "article_id"=>138559, "categories"=>["Genetics", "Medicine", "Cancer", "Biological Sciences", "Developmental Biology", "Molecular Biology"], "users"=>["Jianti Zheng", "Denghui Xing", "Xiaohui Wu", "Yingjia Shen", "Diana M. Kroll", "Guoli Ji", "Qingshun Quinn Li"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0014719.s001", "https://dx.doi.org/10.1371/journal.pone.0014719.s002", "https://dx.doi.org/10.1371/journal.pone.0014719.s003", "https://dx.doi.org/10.1371/journal.pone.0014719.s004", "https://dx.doi.org/10.1371/journal.pone.0014719.s005", "https://dx.doi.org/10.1371/journal.pone.0014719.s006", "https://dx.doi.org/10.1371/journal.pone.0014719.s007"], "stats"=>{"downloads"=>8, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Ratio_Based_Analysis_of_Differential_mRNA_Processing_and_Expression_of_a_Polyadenylation_Factor_Mutant_pcfs4_Using_Arabidopsis_Tiling_Microarray/138559", "title"=>"Ratio-Based Analysis of Differential mRNA Processing and Expression of a Polyadenylation Factor Mutant <em>pcfs4</em> Using Arabidopsis Tiling Microarray", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-02-25 02:22:39"}

PMC Usage Stats | Further Information

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