RNA-Seq Analysis of Spatiotemporal Gene Expression Patterns During Fruit Development Revealed Reference Genes for Transcript Normalization in Plums

2015 ◽  
Vol 33 (6) ◽  
pp. 1634-1649 ◽  
Author(s):  
Ho-Youn Kim ◽  
Prasenjit Saha ◽  
Macarena Farcuh ◽  
Bosheng Li ◽  
Avi Sadka ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fruit Development ◽  
Reference Genes ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Rna Seq

scholarly journals An Actinidia chinensis (kiwifruit) eFP browser and network analysis of transcription factors

2020 ◽  
Author(s):  
Lara Brian ◽  
Ben Warren ◽  
Peter McAtee ◽  
Jessica Rodrigues ◽  
Niels Nieuwenhuizen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Network Analysis ◽  
Fruit Development ◽  
Transcriptional Control ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Actinidia Chinensis ◽  
Knox Gene ◽  
Hub Genes ◽  
Flower And Fruit Development

Abstract BackgroundTranscriptomic studies combined with a well annotated genome have laid the foundations for new understanding of molecular processes. Tools which visualise gene expression patterns have further added to these resources. The manual annotation of the Actinidia chinensis (kiwifruit) genome has resulted in a high quality set of 33,044 genes. Here we investigate gene expression patterns in diverse tissues, visualised in an Electronic Fluorescent Pictograph (eFP) browser, to study the relationship of transcription factor (TF) expression using network analysis. ResultsSixty-one samples covering diverse tissues at different developmental time points were selected for RNAseq analysis and an eFP browser was generated to visualise this dataset. 2,839 TFs representing 57 different classes were identified and named. Network analysis of the TF expression patterns separated TFs into 14 different modules. Two modules consisting of 237 TFs were correlated with floral bud and flower development, a further two modules containing 160 TFs were associated with fruit development and maturation. A single module of 480 TFs was associated with ethylene-induced fruit ripening. Three “hub” genes correlated with flower and fruit development consisted of a HAF-like gene central to gynoecium development, an ERF and a DOF gene. Maturing and ripening hub genes included a KNOX gene that was associated with seed maturation, and a GRAS-like TF.ConclusionsThis study provides an insight into the complexity of the transcriptional control of flower and fruit development, as well as providing a new resource to the plant community. The eFP browser is provided in an accessible format that allows researchers to download and work internally.

scholarly journals Raw sequence to target gene prediction: An integrated inference pipeline for ChIP-seq and RNA-seq datasets

2017 ◽  
Author(s):  
Nisar Wani ◽  
Khalid Raza
Keyword(s):  
Gene Expression ◽  
Target Gene ◽  
Target Genes ◽  
Gene Prediction ◽  
Expression Patterns ◽  
Dna Binding Proteins ◽  
Gene Expression Patterns ◽  
Rna Seq ◽  
Cellular Processes ◽  
Regulatory Effects

AbstractGene expression patterns determine the manner whereby organisms regulate various cellular processes and therefore their organ functions.These patterns do not emerge on their own, but as a result of diverse regulatory factors such as, DNA binding proteins known as transcription factors (TF), chromatin structure and various other environmental factors. TFs play a pivotal role in gene regulation by binding to different locations on the genome and influencing the expression of their target genes. Therefore, predicting target genes and their regulation becomes an important task for understanding mechanisms that control cellular processes governing both healthy and diseased cells.In this paper, we propose an integrated inference pipeline for predicting target genes and their regulatory effects for a specific TF using next-generation data analysis tools.

scholarly journals Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

2020 ◽  
Author(s):  
Timothy J. Durham ◽  
Riza M. Daza ◽  
Louis Gevirtzman ◽  
Darren A. Cusanovich ◽  
William Stafford Noble ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Expression Patterns ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Gene Expression Patterns ◽  
Rna Seq ◽  
Cell Type ◽  
Tissue Specific ◽  
C Elegans

AbstractRecently developed single cell technologies allow researchers to characterize cell states at ever greater resolution and scale. C. elegans is a particularly tractable system for studying development, and recent single cell RNA-seq studies characterized the gene expression patterns for nearly every cell type in the embryo and at the second larval stage (L2). Gene expression patterns are useful for learning about gene function and give insight into the biochemical state of different cell types; however, in order to understand these cell types, we must also determine how these gene expression levels are regulated. We present the first single cell ATAC-seq study in C. elegans. We collected data in L2 larvae to match the available single cell RNA-seq data set, and we identify tissue-specific chromatin accessibility patterns that align well with existing data, including the L2 single cell RNA-seq results. Using a novel implementation of the latent Dirichlet allocation algorithm, we leverage the single-cell resolution of the sci-ATAC-seq data to identify accessible loci at the level of individual cell types, providing new maps of putative cell type-specific gene regulatory sites, with promise for better understanding of cellular differentiation and gene regulation in the worm.

Differences in gene expression patterns, revealed by RNA-seq analysis, between various Sanfilippo and Morquio disease subtypes

Gene ◽  
2021 ◽  
pp. 146090
Author(s):  
Karolina Wiśniewska ◽  
Lidia Gaffke ◽  
Karolina Krzelowska ◽  
Grzegorz Węgrzyn ◽  
Karolina Pierzynowska
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Rna Seq ◽  
Morquio Disease ◽  
Disease Subtypes

scholarly journals A gene expression atlas for kiwifruit (Actinidia chinensis) and network analysis of transcription factors

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Lara Brian ◽  
Ben Warren ◽  
Peter McAtee ◽  
Jessica Rodrigues ◽  
Niels Nieuwenhuizen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Network Analysis ◽  
Fruit Development ◽  
Transcriptional Control ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Actinidia Chinensis ◽  
Knox Gene ◽  
Hub Genes ◽  
Flower And Fruit Development

Abstract Background Transcriptomic studies combined with a well annotated genome have laid the foundations for new understanding of molecular processes. Tools which visualise gene expression patterns have further added to these resources. The manual annotation of the Actinidia chinensis (kiwifruit) genome has resulted in a high quality set of 33,044 genes. Here we investigate gene expression patterns in diverse tissues, visualised in an Electronic Fluorescent Pictograph (eFP) browser, to study the relationship of transcription factor (TF) expression using network analysis. Results Sixty-one samples covering diverse tissues at different developmental time points were selected for RNA-seq analysis and an eFP browser was generated to visualise this dataset. 2839 TFs representing 57 different classes were identified and named. Network analysis of the TF expression patterns separated TFs into 14 different modules. Two modules consisting of 237 TFs were correlated with floral bud and flower development, a further two modules containing 160 TFs were associated with fruit development and maturation. A single module of 480 TFs was associated with ethylene-induced fruit ripening. Three “hub” genes correlated with flower and fruit development consisted of a HAF-like gene central to gynoecium development, an ERF and a DOF gene. Maturing and ripening hub genes included a KNOX gene that was associated with seed maturation, and a GRAS-like TF. Conclusions This study provides an insight into the complexity of the transcriptional control of flower and fruit development, as well as providing a new resource to the plant community. The Actinidia eFP browser is provided in an accessible format that allows researchers to download and work internally.

scholarly journals Pseudo-Location: A novel predictor for predicting pseudo-temporal gene expression patterns using spatial functional regression

2020 ◽  
Author(s):  
Kyungmin Ahn ◽  
Hironobu Fujiwara
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Functional Regression ◽  
Rna Seq ◽  
Temporal Gene Expression ◽  
Early Stages ◽  
The Future

Statement of withdrawalThe authors have withdrawn version 1 of this manuscript because a draft manuscript, which was still in the early stages of preparation and required major revisions including the replacement of the source RNA-seq datasets, was erroneously submitted. The authors do not wish this version to be cited as reference for this study. We will post a revised manuscript in the future. If you have any questions, please contact the corresponding author.

scholarly journals Mapping gastrointestinal gene expression patterns in wild primates and humans via fecal RNA-seq

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Ashok Kumar Sharma ◽  
Barbora Pafčo ◽  
Klára Vlčková ◽  
Barbora Červená ◽  
Jakub Kreisinger ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Rna Seq
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