Development of SSR markers based on transcriptome data and association mapping analysis for fruit shell thickness associated traits in oil palm (Elaeis guineensis Jacq.)
Sign Up to like & getrecommendations! Published in 2020 at "3 Biotech"
DOI: 10.1007/s13205-020-02269-3
Abstract: Present study mainly aimed to ascertain the distribution characteristics of gene-based microsatellite loci and to develop polymorphic SSR markers from the already available transcriptome data of Elaeis guineensis Jacq, an important oil crop. From this… read more here.
Keywords: ssr markers; transcriptome data; oil; oil palm ... See more keywords
MATHT: A web server for comprehensive transcriptome data analysis.
Sign Up to like & getrecommendations! Published in 2018 at "Journal of theoretical biology"
DOI: 10.1016/j.jtbi.2018.07.021
Abstract: The current software/algorithms for high-throughput sequence data analysis are not user-friendly. We developed MATHT, the Multifaceted Analysis Tool for Human Transcriptome, which is a free web server available at www.biocloudservice.com, to provide more comprehensive and… read more here.
Keywords: matht web; data analysis; analysis; web server ... See more keywords
Robust classification of single-cell transcriptome data by nonnegative matrix factorization
Sign Up to like & getrecommendations! Published in 2017 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btw607
Abstract: Motivation: Single-cell transcriptome data provide unprecedented resolution to study heterogeneity in cell populations and present a challenge for unsupervised classification. Popular methods, like principal component analysis (PCA), often suffer from the high level of noise… read more here.
Keywords: single cell; classification; cell transcriptome; transcriptome data ... See more keywords
Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data.
Sign Up to like & getrecommendations! Published in 2020 at "Genome research"
DOI: 10.1101/gr.267047.120
Abstract: Single-cell DNA methylation data has become increasingly abundant and has uncovered many genes with a positive correlation between expression and promoter methylation, challenging the common dogma based on bulk data. However, computational tools for analyzing… read more here.
Keywords: single cell; methylation; expression; transcriptome data ... See more keywords
Normalization of Large-Scale Transcriptome Data Using Heuristic Methods
Sign Up to like & getrecommendations! Published in 2023 at "Bioinformatics and Biology Insights"
DOI: 10.1177/11779322231160397
Abstract: In this study, we introduce an artificial intelligent method for addressing the batch effect of a transcriptome data. The method has several clear advantages in comparison with the alternative methods presently in use. Batch effect… read more here.
Keywords: batch; batch effect; transcriptome data; distribution ... See more keywords
Profiling transcription factor activity dynamics using intronic reads in time-series transcriptome data
Sign Up to like & getrecommendations! Published in 2022 at "PLoS Computational Biology"
DOI: 10.1371/journal.pcbi.1009762
Abstract: Activities of transcription factors (TFs) are temporally modulated to regulate dynamic cellular processes, including development, homeostasis, and disease. Recent developments of bioinformatic tools have enabled the analysis of TF activities using transcriptome data. However, because… read more here.
Keywords: transcriptome data; intronic reads; time series;
DEclust: A statistical approach for obtaining differential expression profiles of multiple conditions
Sign Up to like & getrecommendations! Published in 2017 at "PLoS ONE"
DOI: 10.1371/journal.pone.0188285
Abstract: High-throughput RNA sequencing technology is widely used to comprehensively detect and quantify cellular gene expression. Thus, numerous analytical methods have been proposed for identifying differentially expressed genes (DEGs) between paired samples such as tumor and… read more here.
Keywords: multiple conditions; statistical approach; differential expression; declust statistical ... See more keywords
Transcriptome profiling of subepithelial PDGFRα cells in colonic mucosa reveals several cell-selective markers
Sign Up to like & getrecommendations! Published in 2022 at "PLoS ONE"
DOI: 10.1371/journal.pone.0261743
Abstract: Subepithelial platelet-derived growth factor receptor alpha (PDGFRα)+ cells found in the colonic mucosal tissue come in close contact with epithelial cells, immune cells, neurons, capillaries, and lymphatic networks. Mucosal subepithelial PDGFRα+ cells (MuPαC) are important… read more here.
Keywords: pdgfr cells; mup; pdgfr; subepithelial pdgfr ... See more keywords
Characterization of Immune-Related Genes and Immune Infiltration Features in Epilepsy by Multi-Transcriptome Data
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Inflammation Research"
DOI: 10.2147/jir.s360743
Abstract: Background Epilepsy encompasses a group of heterogeneous brain diseases that afflict about 1% of the world’s population. Accumulating evidence shows that the immune system plays a key role in epileptogenesis. Nevertheless, the immune-related mechanisms remain… read more here.
Keywords: infiltration; immune related; genes immune; epilepsy ... See more keywords
Investigating the possible mechanisms involved in aluminum tolerance through analysis of transcriptome data from different genotypes of soybean
Sign Up to like & getrecommendations! Published in 2020 at "Pakistan Journal of Botany"
DOI: 10.30848/pjb2020-6(19)
Abstract: Aluminum is one of the main factors limiting crop growth in acidic soils, thus, revealing the mechanism involved in soybean aluminum resistance is an important measure in order to improve soybean yield in acidic soils.… read more here.
Keywords: data different; aluminum tolerance; transcriptome data; different genotypes ... See more keywords
The Shared Mechanism and Candidate Drugs of Multiple Sclerosis and Sjögren’s Syndrome Analyzed by Bioinformatics Based on GWAS and Transcriptome Data
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Immunology"
DOI: 10.3389/fimmu.2022.857014
Abstract: Objective This study aimed to explore the shared mechanism and candidate drugs of multiple sclerosis (MS) and Sjögren’s syndrome (SS). Methods MS- and SS-related susceptibility genes and differentially expressed genes (DEGs) were identified by bioinformatics… read more here.
Keywords: shared mechanism; hla; susceptibility genes; gwas transcriptome ... See more keywords