Dataset Information

Identification of global transcriptional dynamics.

ABSTRACT: One of the challenges in exploiting high throughput measurement techniques such as microarrays is the conversion of the vast amounts of data obtained into relevant knowledge. Of particular importance is the identification of the intrinsic response of a transcriptional experiment and the characterization of the underlying dynamics.The proposed algorithm seeks to provide the researcher a summary as to various aspects relating to the dynamic progression of a biological system, rather than that of individual genes. The approach is based on the identification of smaller number of expression motifs that define the transcriptional state of the system which quantifies the deviation of the cellular response from a control state in the presence of an external perturbation. The approach is demonstrated with a number of data sets including a synthetic base case and four animal studies. The synthetic dataset will be used to establish the response of the algorithm on a "null" dataset, whereas the four different experimental datasets represent a spectrum of possible time course experiments in terms of the degree of perturbation associated with the experiment as well as representing a wide range of temporal sampling strategies. This wide range of experimental datasets will thus allow us to explore the performance of the proposed algorithm and determine its ability identify relevant information.In this work, we present a computational approach which operates on high throughput temporal gene expression data to assess the information content of the experiment, identify dynamic markers of important processes associated with the experimental perturbation, and summarize in a concise manner the evolution of the system over time with respect to the experimental perturbation.

SUBMITTER: Yang EH

PROVIDER: S-EPMC2705787 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature

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Identification of global transcriptional dynamics.

Yang Eric H EH Almon Richard R RR Dubois Debra C DC Jusko Willian J WJ Androulakis Ioannis P IP

PloS one 20090710 7

<h4>Background</h4>One of the challenges in exploiting high throughput measurement techniques such as microarrays is the conversion of the vast amounts of data obtained into relevant knowledge. Of particular importance is the identification of the intrinsic response of a transcriptional experiment and the characterization of the underlying dynamics.<h4>Methodology and findings</h4>The proposed algorithm seeks to provide the researcher a summary as to various aspects relating to the dynamic progr ...[more]

PMID: 19593450

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Project description:BackgroundAedes albopictus is a vector of increasing public health concern due to its rapid global range expansion and ability to transmit Dengue virus, Chikungunya virus and a wide range of additional arboviruses. Traditional vector control strategies have been largely ineffective against Ae. albopictus and novel approaches are urgently needed. Photoperiodic diapause is a crucial ecological adaptation in a wide range of temperate insects. Therefore, targeting the molecular regulation of photoperiodic diapause or diapause-associated physiological processes could provide the basis of novel approaches to vector control.Methodology/principal findingsWe investigated the global transcriptional profiles of diapause induction in Ae. albopictus by performing paired-end RNA-Seq of biologically replicated libraries. We sequenced RNA from whole bodies of adult females reared under diapause-inducing and non-diapause-inducing photoperiods either with or without a blood meal. We constructed a comprehensive transcriptome assembly that incorporated previous assemblies and represents over 14,000 annotated dipteran gene models. Mapping of sequence reads to the transcriptome identified differential expression of 2,251 genes in response to diapause-inducing short-day photoperiods. In non-blood-fed females, potential regulatory elements of diapause induction were transcriptionally up-regulated, including two of the canonical circadian clock genes, timeless and cryptochrome 1. In blood-fed females, genes in metabolic pathways related to energy production and offspring provisioning were differentially expressed under diapause-inducing conditions, including the oxidative phosphorylation pathway and lipid metabolism genes.Conclusions/significanceThis study is the first to utilize powerful RNA-Seq technologies to elucidate the transcriptional basis of diapause induction in any insect. We identified candidate genes and pathways regulating diapause induction, including a conserved set of genes that are differentially expressed as part of the diapause program in a diverse group of insects. These genes provide candidates whose diapause-associated function can be further interrogated using functional genomics approaches in Ae. albopictus and other insects.

Project description:BACKGROUND: The paper mulberry (Broussonetia papyifera) is one of the multifunctional tree species in agroforestry system and is also commonly utilized in traditional medicine in China and other Asian countries. To identify the transcription factors (TFs) and comprehensively understand their regulatory roles in the growth of the paper mulberry, a global transcriptomics TF prediction and the differential expression analysis among root, shoot and leaf were performed by using RNA-seq. RESULTS: Results indicate that there is 1, 337 TFs encoded by the paper mulberry and they belong to the 55 well-characterized TF families. Based on the phylogenetic analysis, the TFs exist extensively in all organisms are more conservative than those exclusively exist in plant and the paper mulberry has the closest relationship with the mulberry. According to the results of differential expression analysis, there are 627 TFs which exhibit the differential expression profiles in root, shoot and leaf. ARR-Bs, ARFs, NACs and bHLHs together with other root-specific and highly expressed TFs might account for the developed lateral root and unconspicuous taproot in the paper mulberry. Meanwhile, five TCPs highly expressed in shoot of the paper mulberry might negatively regulate the expression of 12 LBDs in shoot. Besides, LBDs, which could directly or indirectly cooperate with ARFs, bHLHs and NACs, seem to be the center knot involving in the regulation of the shoot development in the paper mulberry. CONCLUSIONS: Our study provides the comprehensive transcriptomics identification of TFs in the paper mulberry without genome reference. A large number of lateral organ growth regulation related TFs exhibiting the tissue differential expression may entitle the paper mulberry the developed lateral roots, more branches and rapid growth. It will increase our knowledge of the structure and composition of TFs in tree plant and it will substantially contribute to the improving of this tree.

Dataset Information

Identification of global transcriptional dynamics.

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Identification of global transcriptional dynamics.

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