scholarly journals Network using Michaelis–Menten kinetics: constructing an algorithm to find target genes from expression data

2019 ◽  
Author(s):  
Mythreye Krishnan ◽  
Michael Small ◽  
Anthony Bosco ◽  
Thomas Stemler
Keyword(s):  
Gene Network ◽  
Target Genes ◽  
Underlying Mechanism ◽  
Relevant Information ◽  
Complex Data ◽  
Expression Data ◽  
Gene Expression Data Analysis ◽  
Biologically Relevant ◽  
Cell Responses ◽  
Network Patterns

Abstract The most challenging aspect of gene expression data analysis is to process the large and complex data using mathematical models and find biologically relevant information that gives insight to the underlying mechanism. We derived a simple ordinary differential equation-based model using Michaelis–Menten Kinetics to process the microarray data. Different biological systems of experimental rhinovirus infection in humans, atopic CD4 T cell responses in allergens and responses to cancer immunotherapy in mice have been studied. The resulting analysis extracts highly linked target genes, the changes in which might cause changes in the other genes, in other words, potential targets for modulating gene network patterns and emergent biological phenotypes. We illustrate the application of the algorithm to identify novel targets in addition to previously identified targets in different experimental contexts.

scholarly journals The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat

2020 ◽  
Vol 10 (10) ◽  
pp. 3675-3686 ◽  
Author(s):  
Sophie A. Harrington ◽  
Anna E. Backhaus ◽  
Ajit Singh ◽  
Keywan Hassani-Pak ◽  
Cristobal Uauy
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Candidate Gene ◽  
Web Application ◽  
Regulatory Networks ◽  
Target Genes ◽  
Gene Prediction ◽  
Relevant Information ◽  
Rna Seq ◽  
Biologically Relevant

Gene regulatory networks are powerful tools which facilitate hypothesis generation and candidate gene discovery. However, the extent to which the network predictions are biologically relevant is often unclear. Recently a GENIE3 network which predicted targets of wheat transcription factors was produced. Here we used an independent RNA-Seq dataset to test the predictions of the wheat GENIE3 network for the senescence-regulating transcription factor NAM-A1 (TraesCS6A02G108300). We re-analyzed the RNA-Seq data against the RefSeqv1.0 genome and identified a set of differentially expressed genes (DEGs) between the wild-type and nam-a1 mutant which recapitulated the known role of NAM-A1 in senescence and nutrient remobilisation. We found that the GENIE3-predicted target genes of NAM-A1 overlap significantly with the DEGs, more than would be expected by chance. Based on high levels of overlap between GENIE3-predicted target genes and the DEGs, we identified candidate senescence regulators. We then explored genome-wide trends in the network related to polyploidy and found that only homeologous transcription factors are likely to share predicted targets in common. However, homeologs which vary in expression levels across tissues are less likely to share predicted targets than those that do not, suggesting that they may be more likely to act in distinct pathways. This work demonstrates that the wheat GENIE3 network can provide biologically-relevant predictions of transcription factor targets, which can be used for candidate gene prediction and for global analyses of transcription factor function. The GENIE3 network has now been integrated into the KnetMiner web application, facilitating its use in future studies.

scholarly journals The Network Regulation of Yiqi Jiedu Formulae Against Cerebral Ischemia Based on Central-periphery Inflammation System

2021 ◽  
Author(s):  
Ruocong Yang ◽  
tingting Zhao ◽  
Liming Liu ◽  
Shaojing Li
Keyword(s):  
Gene Network ◽  
Target Genes ◽  
Underlying Mechanism ◽  
Peripheral Inflammation ◽  
Hub Genes ◽  
Promising Target ◽  
Disease Associations ◽  
The Common ◽  
Novel Strategy ◽  
Insight Into

Abstract Background:Connections between inflammation and gene-network regulation are suggested important in understanding the therapeutic target of stroke and in illuminating underlying mechanism. However, studies on the establishment of network relating with inflammation during stroke process are still in their early stages. Results:Herein, Message RNA chips were used to scan whole genome of stroke-model rats. We selected the inflammation genes from the whole mRNA expression results. And after a series of analysis, we tried to establish a central-peripheral inflammation network on MCAO rice which then be used as disease background network for our further study. As for the background network, we found and verified some key node genes (also named as hub-genes), which are joint in several inflammation and immune related pathways. While mapping genes from treatment group to the background network, we found the promising target genes of Yiqi Jiedu formulae, a traditional chinese prescription used in clinic for stroke, which might give an explanation to the common characteristic about TCM treatment called PK-PD inconsistent. Conclusions:The mRNA network-based analysis provides a foundation for elucidating inflammation-disease associations, a rather promising insight into the inflammation progress during stroke and a novel strategy to reveal the underlying mechanism of TCM.

scholarly journals NoRCE: non-coding RNA sets cis enrichment tool

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gulden Olgun ◽  
Afshan Nabi ◽  
Oznur Tastan
Keyword(s):  
Expression Patterns ◽  
Target Prediction ◽  
Enrichment Analysis ◽  
Fruit Fly ◽  
Relevant Information ◽  
R Package ◽  
Data Repository ◽  
Biologically Relevant ◽  
Gene Sets ◽  
Data Files

Abstract Background While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint at a functional association. Results We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast. Conclusions NoRCE is a platform-independent, user-friendly, comprehensive R package that can be used to gain insight into the functional importance of a list of ncRNAs of any type. The tool offers flexibility to conduct the users’ preferred set of analyses by designing their own pipeline of analysis. NoRCE is available in Bioconductor and https://github.com/guldenolgun/NoRCE.

scholarly journals Micro RNAs in Regulation of Cellular Redox Homeostasis

2021 ◽  
Vol 22 (11) ◽  
pp. 6022
Author(s):  
Sylwia Ciesielska ◽  
Izabella Slezak-Prochazka ◽  
Patryk Bil ◽  
Joanna Rzeszowska-Wolny
Keyword(s):  
Target Genes ◽  
Redox Homeostasis ◽  
Messenger Rnas ◽  
Cellular Redox ◽  
Cell Responses ◽  
Regulatory Circuits ◽  
Micro Rnas ◽  
Cellular Behaviors ◽  
Homeostasis Regulation ◽  
Thioredoxin Reductases

In living cells Reactive Oxygen Species (ROS) participate in intra- and inter-cellular signaling and all cells contain specific systems that guard redox homeostasis. These systems contain both enzymes which may produce ROS such as NADPH-dependent and other oxidases or nitric oxide synthases, and ROS-neutralizing enzymes such as catalase, peroxiredoxins, thioredoxins, thioredoxin reductases, glutathione reductases, and many others. Most of the genes coding for these enzymes contain sequences targeted by micro RNAs (miRNAs), which are components of RNA-induced silencing complexes and play important roles in inhibiting translation of their targeted messenger RNAs (mRNAs). In this review we describe miRNAs that directly target and can influence enzymes responsible for scavenging of ROS and their possible role in cellular redox homeostasis. Regulation of antioxidant enzymes aims to adjust cells to survive in unstable oxidative environments; however, sometimes seemingly paradoxical phenomena appear where oxidative stress induces an increase in the levels of miRNAs which target genes which are supposed to neutralize ROS and therefore would be expected to decrease antioxidant levels. Here we show examples of such cellular behaviors and discuss the possible roles of miRNAs in redox regulatory circuits and further cell responses to stress.

scholarly journals Discovery of MicroRNAs and Their Target Genes Related to Drought in Paulownia “Yuza 1” by High-Throughput Sequencing

2017 ◽  
Vol 2017 ◽  
pp. 1-11 ◽  
Author(s):  
Minjie Deng ◽  
Yabing Cao ◽  
Zhenli Zhao ◽  
Lu Yang ◽  
Yanfang Zhang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Plant Hormone ◽  
Target Genes ◽  
Reference Data ◽  
Relevant Information ◽  
Putative Target

Understanding the role of miRNAs in regulating the molecular mechanisms responsive to drought stress was studied in Paulownia “yuza 1.” Two small RNA libraries and two degradome libraries were, respectively, constructed and sequenced in order to detect miRNAs and their target genes associated with drought stress. A total of 107 miRNAs and 42 putative target genes were identified in this study. Among them, 77 miRNAs were differentially expressed between drought-treated Paulownia “yuza 1” and the control (60 downregulated and 17 upregulated). The predicted target genes were annotated using the GO, KEGG, and Nr databases. According to the functional classification of the target genes, Paulownia “yuza 1” may respond to drought stress via plant hormone signal transduction, photosynthesis, and osmotic adjustment. Furthermore, the expression levels of seven miRNAs (ptf-miR157b, ptf-miR159b, ptf-miR398a, ptf-miR9726a, ptf-M2153, ptf-M2218, and ptf-M24a) and their corresponding target genes were validated by quantitative real-time PCR. The results provide relevant information for understanding the molecular mechanism of Paulownia resistance to drought and reference data for researching drought resistance of other trees.

scholarly journals Maternal Folic Acid Impacts DNA Methylation Profile in Male Rat Offspring Associated With Neurodevelopment and Learning/Memory Abilities

2020 ◽  
Author(s):  
Xinyan Wang ◽  
Zhenshu Li ◽  
Yun Zhu ◽  
Jing Yan ◽  
Huan Liu ◽  
...  
Keyword(s):  
Folic Acid ◽  
Gene Network ◽  
Underlying Mechanism ◽  
Male Rat ◽  
Methylated Dna ◽  
Rat Offspring ◽  
Kegg Pathway Analysis ◽  
Differentially Methylated Genes ◽  
Dna Methylation Profile ◽  
Gene Network Analysis

Abstract Background: Periconceptional folic acid (FA) supplementation not only reduces the incidence of neural tube defects, but also improves cognitive performances in offspring. However, the genes or pathways that are epigenetically regulated by FA in neurodevelopment were rarely reported. Methods: To elucidate the underlying mechanism, the effect of FA on the methylation profiles in brain tissue of male rat offspring was assessed by methylated DNA immunoprecipitation chip. Differentially methylated genes (DMGs) and gene network analysis were identified using DAVID and KEGG pathway analysis. Results: Compared with the FA-N group, 1939 DMGs were identified in the FA-D group, and 1498 DMGs were identified in the FA-S group, among which 298 DMGs were overlapped. The pathways associated with neurodevelopment and learning/memory abilities were differentially methylated in response to maternal FA intake during pregnancy, and there were some identical and distinctive potential mechanisms under FA deficiency or supplemented conditions. Conclusions: In conclusion, genes and pathways associated with neurodevelopment and learning/memory abilities were differentially methylated in male rat offspring in response to maternal FA deficiency or supplementation during pregnancy.

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