scholarly journals Bioinformatics Analysis and High-Throughput Sequencing to Identify Differentially Expressed Genes in Nebulin Gene (NEB) Mutations Mice

2020 ◽  
Vol 26 ◽  
Author(s):  
Haoyong Wang ◽  
Xiaoyue Nie ◽  
Xin Li ◽  
Yi Fang ◽  
Dandan Wang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Bioinformatics Analysis ◽  
Differentially Expressed

scholarly journals UGM: a more stable procedure for large-scale multiple testing problems, new solutions to identify oncogene

2019 ◽  
Vol 16 (1) ◽  
Author(s):  
Chengyou Liu ◽  
Leilei Zhou ◽  
Yuhe Wang ◽  
Shuchang Tian ◽  
Junlin Zhu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Differentially Expressed Genes ◽  
High Throughput ◽  
Multiple Testing ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Type I Error ◽  
Differentially Expressed ◽  
Type I ◽  
Brca1 Brca2

AbstractVariations of gene expression levels play an important role in tumors. There are numerous methods to identify differentially expressed genes in high-throughput sequencing. Several algorithms endeavor to identify distinctive genetic patterns susceptable to particular diseases. Although these processes have been proved successful, the probability that the number of non-differentially expressed genes measured by false discovery rate (FDR) has a large standard deviation, and the misidentification rate (type I error) grows rapidly when the number of genes to be detected become larger. In this study we developed a new method, Unit Gamma Measurement (UGM), accounting for multiple hypotheses test statistics distribution, which could reduce the dependency problem. Simulated expression profile data and breast cancer RNA-Seq data were utilized to testify the accuracy of UGM. The results show that the number of non-differentially expressed genes identified by the UGM is very close to the real-evidence data, and the UGM also has a smaller standard error, range, quartile range and RMS error. In addition, the UGM can be used to screen many breast cancer-associated genes, such as BRCA1, BRCA2, PTEN, BRIP1, etc., provides better accuracy, robustness and efficiency, the method of identification differentially expressed genes in high-throughput sequencing.

scholarly journals Investigating the molecular basis for heterophylly in the aquatic plant Potamogeton octandrus (Potamogetonaceae) with comparative transcriptomics

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4448 ◽  
Author(s):  
Dingxuan He ◽  
Pin Guo ◽  
Paul F. Gugger ◽  
Youhao Guo ◽  
Xing Liu ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
High Throughput ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Pathway Enrichment ◽  
Floating Leaves

Many plant species exhibit different leaf morphologies within a single plant, or heterophylly. The molecular mechanisms regulating this phenomenon, however, have remained elusive. In this study, the transcriptomes of submerged and floating leaves of an aquatic heterophyllous plant, Potamogeton octandrus Poir, at different stages of development, were sequenced using high-throughput sequencing (RNA-Seq), in order to aid gene discovery and functional studies of genes involved in heterophylly. A total of 81,103 unigenes were identified in submerged and floating leaves and 6,822 differentially expressed genes (DEGs) were identified by comparing samples at differing time points of development. KEGG pathway enrichment analysis categorized these unigenes into 128 pathways. A total of 24,025 differentially expressed genes were involved in carbon metabolic pathways, biosynthesis of amino acids, ribosomal processes, and plant-pathogen interactions. In particular, KEGG pathway enrichment analysis categorized a total of 70 DEGs into plant hormone signal transduction pathways. The high-throughput transcriptomic results presented here highlight the potential for understanding the molecular mechanisms underlying heterophylly, which is still poorly understood. Further, these data provide a framework to better understand heterophyllous leaf development in P. octandrus via targeted studies utilizing gene cloning and functional analyses.

Bioinformatics Analysis and Validation of Differentially Expressed MicroRNAs with Their Target Genes Involved in GLP-1RA Facilitated Osteogenesis

2020 ◽  
Vol 15 ◽  
Author(s):  
Na Wang ◽  
Yukun Li ◽  
Sijing Liu ◽  
Liu Gao ◽  
Chang Liu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Bioinformatics Analysis ◽  
Differentially Expressed ◽  
Functional Study ◽  
Regulation Network ◽  
Glucagon Like Peptide 1 ◽  
G Protein Coupled ◽  
Lower Expression

Background: Recent studies revealed that the hypoglycemic hormone, glucagon-like peptide-1 (GLP-1), acted as an important modulator in osteogenesis of bone marrow derived mesenchymal stem cells (BMSCs). Objectives: The aim of this study was to identify the specific microRNA (miRNA) using bioinformatics analysis and validate the presence of differentially expressed microRNAs with their target genes after GLP-1 receptor agonist (GLP-1RA) administration involved in ostogenesis of BMSCs. Methods: MiRNAs were extracted from BMSCs after 5 days’ treatment and sent for high-throughput sequencing for differentially expressed (DE) miRNAs analyses. Then the expression of the DE miRNAs verified by the real-time RT-PCR analyses. Target genes were predicted, and highly enriched GOs and KEGG pathway analysis were conducted using bioinformatics analysis. For the functional study, two of the target genes, SRY (sex determining region Y)-box 5 (SOX5) and G protein-coupled receptor 84 (GPR84), were identified. Results: A total of 5 miRNAs (miRNA-509-5p, miRNA-547-3p, miRNA-201-3p, miRNA-201-5p, and miRNA-novel-272-mature) were identified differentially expressed among groups. The expression of miRNA-novel-272-mature were decreased during the osteogenic differentiation of BMSCs, and GLP-1RA further decreased its expression. MiRNA-novel-272-mature might interact with its target mRNAs to enhance osteogenesis. The lower expression of miRNA-novel-272-mature led to an increase in SOX5 and a decrease in GPR84 mRNA expression, respectively. Conclusions: Taken together, these results provide further insights to the pharmacological properties of GLP-1RA and expand our knowledge on the role of miRNAs-mRNAs regulation network in BMSCs’ differentiation.

Bioinformatics analysis on differentially expressed genes of alveolar macrophage in IPF

2019 ◽  
Vol 45 (9-10) ◽  
pp. 288-296 ◽  
Author(s):  
Huaibin Wang ◽  
Miaomiao Wang ◽  
Kun Xiao ◽  
Xu Zhang ◽  
Peng Wang ◽  
...  
Keyword(s):  
Alveolar Macrophage ◽  
Differentially Expressed Genes ◽  
Bioinformatics Analysis ◽  
Differentially Expressed
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