Protein protein gene expression regulation bioinformatics gene regulatory networks. Medical search. Frequent questions

Yet another line of research pertains to Molecular Evolution, which includes evolution of the exonic structure of genes and splicing. (wikipedia.org)
In this group, research lines in Molecular Modeling, Protein Structure Prediction, and Complex Systems are in their nascent stages. (wikipedia.org)
The Gene Regulation, Stem Cells, and Cancer program focus on mechanisms of gene expression, mechanisms of epigenetic regulation, and the molecular underpinnings of cellular operations pertaining to tissue homeostasis and cancer. (wikipedia.org)
However, molecular regulation of flowering time variation in roses remains poorly characterized. (kib.ac.cn)
Therefore, the expansion and duplication of RwFAR1/FRS-like genes, followed by diversification in gene expression, might offer a novel leverage point for further understanding the molecular regulation of the variation in shoot-growth behavior and flowering time in roses. (kib.ac.cn)
Gene Myers is a director as well as a research group leader at the Max Planck Institute of Molecular Cell Biology and Genetics. (mpg.de)
We apply mathematical modeling and experimentation to study gene regulation, molecular transport and interplay between variability and robustness in biological systems. (ecmiindmath.org)
Our goal is to understand in which situations genetic variability leads to alteration of molecular phenotype and in which it is buffered due to mutual interactions of network genes. (ecmiindmath.org)
It is important to understand at this level how a specific molecular configuration of the regulatory sequence gets formed and, being formed, how it influences the basal transcriptional machinery initiating transcription. (ecmiindmath.org)
The ultimate goal of this approach is to formulate a quantitative map between the genotype (regulatory genetic sequence) and the corresponding molecular phenotype (gene expression level) with the single-nucleotide precision. (ecmiindmath.org)
Due to the discrete manner of molecular assembly in cell signalling and gene regulation, we define a framework of membrane systems equipped with discretised forms of reaction kinetics in concert with variable intramolecular structures. (springer.com)
Antoine W, de los Reyes BG, Miernyk JA, Stewart JM (2009) Molecular evolution of the plant SLT protein family. (ttu.edu)
Gene expression analysis is a crucial aspect of modern molecular biology research, enabling scientists to gain insights into the intricate mechanisms underlying gene regulation and cellular processes. (heartofamericanorthwest.org)
Circular RNAs (circRNAs) are molecular sponges that are involved in regulation of multiple types of cancer. (spandidos-publications.com)
A molecular regulatory network consisting of three circRNAs, seven miRNAs and seven mRNAs was constructed, resulting in identification of two signaling axes, hsa_circ_0035431/hsa‑miR‑940/fucosyltransferase 6 (FUT6) and hsa_circ_0035431/hsa‑miR‑940/cingulin‑like 1 (CGNL1). (spandidos-publications.com)
Thus, further investigations into the specific molecular mechanisms underlying circRNA/miRNA/mRNA regulation are required to aid discovery of effective therapeutic targets. (spandidos-publications.com)
Functional enrichment analysis was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and then Gene Set Enrichment Analysis (GSEA) was used to formulate the molecular functions and pathways based on the results of GO and KEGG analyses. (spandidos-publications.com)
Although NANOG plays a key role in germ cells, the molecular mechanism underlying its transcriptional regulation in PGCs has not been studied. (biomedcentral.com)
We first construct a p21 regulatory network based on data from the literature and further expand it using algorithms that predict molecular interactions. (hindawi.com)
a map is constructed that shows interactions among molecular entities (such as genes, proteins and RNAs), using information from literature and databases. (hindawi.com)
The network combining putative targets of TF and miRNA regulation with experimentally proven molecular interactions was constructed and visualized. (hindawi.com)
These strategies involve rearrangements at the molecular level starting from transcription, regulation of mRNA processing, translation, and protein modification or its turnover. (intechopen.com)
With the advent of molecular biology, bioinformatics and sequencing technology have become increasingly used in research. (xiahepublishing.com)

This is connected to research on Chromatin and Gene Expression, as well as research on RNA proteins interactions. (wikipedia.org)
Because the principles that underlie the behavior of proteins within and across cells are poorly understood, the CDB program aims to study the interactions between intercellular signaling systems and the cytoskeleton. (wikipedia.org)
Here, we develop a high-throughput indexed Chromatin ImmunoPrecipitation (iChIP) method coupled to massively parallel sequencing to systematically map protein-DNA interactions. (nih.gov)
Using over 180,000 TF-DNA interactions in these maps, we derive an initial dynamic physical model of a mammalian cell regulatory network. (nih.gov)
Further, many of the TF-DNA interactions at stimulus-activated genes are established during differentiation and maintained in a poised state. (nih.gov)
This study systematically analyzes multiple-omics data and builds a systems physical network including genome-wide interactions between miRNAs and their targets to reveal the systems mechanism of miRNA functions in mouse pluripotent stem cells. (biomedcentral.com)
These binary interactions between miRNAs and proteins would form a complex systematic network. (biomedcentral.com)
This present study employed systems physical network approaches [ 17 ] and constructed a comprehensive and unbiased map of genome-wide interactions between miRNAs and their targets to investigate the global basis of miRNA roles in pluripotent stem cells, from the pluripotent self-renewal state to the differentiation state. (biomedcentral.com)
To systematically reveal the roles of miRNAs in stem cells, this study first constructed a systems network [ 17 ] of interactions between miRNAs and proteins by combining multiple published datasets. (biomedcentral.com)
These interactions contain binary interactions from two directions, from miRNAs to mRNAs coding for proteins, and from proteins to miRNA promoters and enhancers. (biomedcentral.com)
On the methodological side, their research includes work on analysis of biological sequences, analysis and prediction of protein structure and function, analysis of intermolecular interactions and interaction networks, gene and protein expression patterns, and computational drug screening and drug design. (mpg.de)
The development of high-throughput technologies provides numerous experimental data such as DNA sequences, protein sequence, and RNA expression profiles makes it possible to study interactions and regulations among genes or other substance in an organism. (tsinghua.edu.cn)
We also present a novel way of combining prior biological knowledge and current observations to improve the quality of analysis and to model interactions between sets of genes rather than individual genes. (duke.edu)
We identify conserved TFs among these strains and suggest possible regulatory interactions. (biomedcentral.com)
By studying changes in gene expression levels, researchers can unravel the complex interactions between genes and their environment, leading to advancements in various fields such as medicine, agriculture, and biotechnology. (heartofamericanorthwest.org)
The present study aimed to screen and explore the key circRNA/microRNA (miRNA or miR)/mRNA interactions in head and neck squamous cell carcinoma (HNSCC) using bioinformatics. (spandidos-publications.com)
Gene regulatory networks are widely used by biologists to describe the interactions among genes, proteins and other components at the intra-cellular level. (biomedcentral.com)
We use Statecharts for modeling small and recurring patterns of interactions in gene regulatory networks, called motifs . (biomedcentral.com)
Their behavior is often represented by using gene regulatory networks (GRNs), which describe the interactions among genes, proteins and other components at the intra-cellular level. (biomedcentral.com)
We present a novel approach, the Local Edge Machine, for the inference of regulatory interactions directly from time-series gene expression data. (biomedcentral.com)

Preferentially retained introns and differentially used exons in the affected genes contain weak 5′ splice sites, but are otherwise indistinguishable from adjacent spliced introns. (biomedcentral.com)
Estimation of genewise variance arises from two important applications in microarray data analysis: selecting significantly differentially expressed genes and validation tests for normalization of microarray data. (tsinghua.edu.cn)
In this study, differentially expressed genes (DEGs) under drought and flooding conditions were investigated using Illumina RNA-Seq transcriptome profiling. (frontiersin.org)
Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed on differentially expressed genes (DEGs). (spandidos-publications.com)
The OA subchondral bone dataset GSE51588 was downloaded from the GEO database, and the differentially expressed genes (DEGs) were screened. (spandidos-publications.com)
Core genes were expressed differentially between OA subchondral bone and normal tissue samples. (spandidos-publications.com)
In this study, three independent microarray studies of CD were integrated and 9912 differentially expressed genes (DEGs) were analysed by NetworkAnalyst to screen candidate crucial genes. (hindawi.com)
Thus, stress response studies during these growth stages reveal novel differentially regulated genes or proteins with important functions in plant stress adaptation. (intechopen.com)

In Arabidopsis thaliana we use the spatial data to identify differences in expression levels of 141 genes and 189 pathways in eight inflorescence tissue domains. (nature.com)
The key targets and pathways were analyzed by network pharmacology. (bvsalud.org)
Through network pharmacology analysis, the effect pathways were related to signal transduction, carbohydrate, lipid, amino acid metabolism and mainly affected the endocrine and immune systems. (bvsalud.org)
This study will develop a new approach to reconstruct time delay Boolean networks as a tool for exploring biological pathways. (tsinghua.edu.cn)
Scholars@Duke publication: Modelling regulatory pathways in E. coli from time series expression profiles. (duke.edu)
The well-known arms-race between TEs and the host genome [5] has resulted in several regulatory pathways, including a combination of various epigenetic mechanisms i.e. (prolekarniky.cz)
Based on our findings, we infer SNHG4 may play a role in the formation of HCC via regulation of tumor-related pathways. (xiahepublishing.com)
To explore the common genes and pathogenic pathways among different fibrotic diseases, we collected all the reported genes of the eight fibrotic diseases: eye fibrosis, heart fibrosis, hepatic fibrosis, intestinal fibrosis, lung fibrosis, pancreas fibrosis, renal fibrosis, and skin fibrosis. (frontiersin.org)
Moreover, we interestingly found overlaps of pathways between renal fibrosis and skin fibrosis, such as GO:1901890-positive regulation of cell junction assembly, as well as common regulatory genes, such as CTGF, which is the key molecule regulating fibrogenesis. (frontiersin.org)
Resistance arises by mutation (influencing the target or efflux of the antimicrobial agent) or by the acquisition of resistance genes (encoding antimicrobial or target alteration, or alternate pathways) ( 2 , 3 ). (cdc.gov)

Some particular topics of investigation are: signal transduction, gene regulatory networks, multicellular patterning, chemotaxis, systems neuroscience, the evolution of networks, and the effect of stochastic noise at the organism level. (wikipedia.org)
His scientific interests lie mostly in Cell biology, Signal transduction, Genetics, Regulation of gene expression and Gene. (research.com)
His Signal transduction research is multidisciplinary, incorporating perspectives in Stimulus, Neuroscience, Ultrasensitivity and Bioinformatics. (research.com)

The Centre for Genomic Regulation (CRG, Centre de Regulació Genòmica in Catalan) is a biomedical and genomics research centre based on Barcelona. (wikipedia.org)
Another research line involves identification and characterization of genomic regions associated with gene regulation. (wikipedia.org)
Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. (weizmann.ac.il)
We find 116 887 and 137 557 nucleosome-depleted regions (NDRs) in human and mouse FGCs, covering a large set of germline-specific and highly dynamic regulatory genomic elements, such as enhancers. (nature.com)
In particular, they work on mathematical models for analyzing large genomic sequences, especially in the context of next generation sequencing, and data derived from mass spectrometry experiments, for example to detect differential expression of proteins between normal and diseased samples. (mpg.de)
One great challenge of genomic research is to efficiently and accurately identify complex gene regulatory networks. (tsinghua.edu.cn)
In the post-genomic research era, there has been a great shift in focus from simply collecting and archiving genomic data to dissecting and interpreting complex genomic/proteomic functions and networks. (uga.edu)
We are particularly interested in addressing critical problems and challenges in the rapidly evolving field of epigenetics that usually describes gene expression profile changes that are irrelevant to genomic sequence. (uga.edu)
Indeed, TEs may cause negative, neutral or positive effects upon insertion, increase genomic instability by chromosomal rearrangements [3] and act as central collaborators in genome-wide regulatory network creation and renewal [4] . (prolekarniky.cz)
The Cancer Genome Atlas (TCGA) database has accumulated abundant genomic and gene expression profiles for different diseases in the past decade. (xiahepublishing.com)

Gene regulation studies include the organization and evolution of the regulatory genome, chromatin composition and transcriptional regulation mediated by steroid hormones, epigenetic mechanisms in leukemia and stem cells, regulation of periodic splicing and mRNA translation, and gene function and epigenetic reprogramming in embryogenesis and the germline. (wikipedia.org)
Circular RNAs (circRNAs) are closed, long, non-coding RNAs that are formed via direct reverse splicing of precursor mRNA that function by regulating RNA transcription and protein production, as well as sponging miRNAs ( 4 ). (spandidos-publications.com)
In addition, a previous study demonstrated that circRNA/miRNA/mRNA networks are involved in the development and progression of multiple types of malignancy ( 7 ). (spandidos-publications.com)

Gene Ontology and pathway enrichment analyses and assessment of RNA binding proteins were performed by R software, circlncRNAnet and Encyclopedia of RNA Interactomes (ENCORI). (xiahepublishing.com)
We calculated the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment scores of all fibrotic disease genes. (frontiersin.org)

2023. Comparative genomics sheds light on transcription factor-mediated regulation in the extreme acidophilic Acidithiobacillia representatives. (openwetware.org)
2023. The gene regulatory network of Staphylococcus aureus ST239-SCCmecIII strain Bmb9393 and assessment of genes associated with the biofilm in diverse backgrounds. (openwetware.org)

Competition for PRPF8 availability alters the transcription-coupled splicing of RNAs in which weak 5′ splice sites predominate, enabling diversification of human gene expression during biological processes like mitosis. (biomedcentral.com)
Zhang Y, Xuan J, De los Reyes BG, Clarke R, Ressom HW (2008) Identification of network motifs for transcription factors by integrating multi-source biological data. (ttu.edu)
Gene expression analysis plays a crucial role in understanding the intricate mechanisms underlying biological processes. (heartofamericanorthwest.org)
By deciphering how genes are regulated under various conditions, scientists can gain insights into biological processes and develop novel approaches for diagnostics, therapeutics, and precision medicine applications. (heartofamericanorthwest.org)
We present a Statecharts-based approach for the modeling of gene regulatory network motifs in biological systems. (biomedcentral.com)
A largely studied class of biological systems is constituted by systems which regulate the expression of genes in an organism. (biomedcentral.com)
Such an approach is characterized by an iterative process, including biological data acquisition and integration, network construction, mathematical modeling and experimental validation. (hindawi.com)
Finally, the calibrated model is used to study the effect of different miRNA expression profiles and cooperative target regulation on p21 expression levels in different biological contexts. (hindawi.com)
However, experimental approaches have limitations when dealing with complex biological systems composed of multiple layers of regulation such as the transcriptional and post-transcriptional regulation by transcription factors (TFs) and miRNAs [ 2 ]. (hindawi.com)
In turn, these hypotheses, which provide reasonable explanations for the biological phenomenon, lead to an enhanced understanding of the gene regulatory network. (hindawi.com)
Achieving systematic, genome-scale perturbations within intact biological systems is important for elucidating gene function and epigenetic regulation. (cdc.gov)

Moreover, expression levels of DEGs were verified in HNSCC cells and tissues using reverse transcription‑quantitative (RT‑q)PCR. (spandidos-publications.com)
Further taking all DEGs together, Gene Set Enrichment Analysis (GSEA) brought out the NOD-like receptor (NLR) signaling pathway which could be regulated by ELAVL1. (hindawi.com)
For example, network analyses identified HNF4A and PTBP1 as effective biomarkers for Parkinson's disease [ 11 ] and 873 DEGs genetically related to insulin resistance [ 12 ]. (hindawi.com)
In this study, we launched a network-based bioinformatics analysis in an attempt to screen DEGs in the blood of CD patients, followed by the KEGG pathway enrichment analysis, GSEA, and interaction network of DEGs. (hindawi.com)

This complexity of miRNA interaction network presents a challenge for conventional approaches like gene-knockout to unbiasedly capture the real mechanisms of miRNA functions in stem cells. (biomedcentral.com)
and neurodegenerative and autoimmune diseases, studying underlying protein interaction networks. (mpg.de)
However, it is crucial to make inference of genetic regulatory networks from gene expression profiles and protein interaction data for systems biology. (tsinghua.edu.cn)
Weighted gene co‑expression network analysis was performed, and a protein‑protein interaction network was constructed and further analyzed using Cytoscape and STRING. (spandidos-publications.com)
In addition we will address important areas of modern epidemiology such as the influence of early life factors on adult health and disease, but also the importance of the gene-diet-microbiota interaction for body function and health. (lu.se)

Systems Biology research includes dynamic gene regulatory networks and systems neuroscience. (wikipedia.org)
Cell cycle gene expression networks discovered using systems biology: Significance in carcinogenesis. (genenetwork.org)
Nils Blüthgen combines subjects such as Systems biology, Gene expression and Cell fate determination with his study of Cell biology. (research.com)
It is straightforward to use the systems biology approach to answer on these questions, as systems biology studies both structure and dynamical behavior of genetic networks. (ecmiindmath.org)
Indeed, the network inference problem persists in systems biology, despite an abundance of regulatory evidence in the form of TF binding experiments, genetic screens for candidate nodes, and mutant expression profiling experiments. (biomedcentral.com)
For a better understanding of the regulatory role of miRNAs in coordinating gene expression, we here present a systems biology approach combining data-driven modeling and model-driven experiments. (hindawi.com)
The systems biology approach, combining data-driven modeling and model-driven experiments, provides a systematic and comprehensive perspective on the regulatory roles of miRNAs in gene regulatory networks [ 3 - 5 ]. (hindawi.com)
The application of the systems biology approach to the analysis of a gene regulatory network is demonstrated with a case study of the regulation of p21 by multiple miRNAs [ 4 ]. (hindawi.com)

Although the current generation of dCas9-based transcription activators is able to achieve up-regulation of some endogenous loci, the magnitude of transcriptional up-regulation achieved by individual single-guide RNAs (sgRNAs) 12 typically ranges from low to ineffective 8 - 11 . (cdc.gov)

In neutrophils, IL-8 binding to CXCR1 triggers G protein-coupled signalling and formation of second messengers that mediate cellular migration, exocytosis of effectors and a respiratory burst to facilitate oxygen-dependent killing of phagocytosed microorganisms [ 2 ]. (biomedcentral.com)
Hinck's lab has identified a family of cellular proteins that help regulate cell proliferation and migration and act as breast tumor suppressors. (ucsc.edu)
The second area of study is to understand the regulation of the immune response to cellular and solid organ grafts. (stanford.edu)
We develop methods that are based in statistics, machine learning, optimization and graph theory to understand how changes in the 3D genome affect cellular outcome such as development, differentiation and gene expression. (ucsd.edu)

Gene networks control organism phenotype in health and disease by dynamically processing information introduced by genotype and environment. (ecmiindmath.org)
Exploiting the functional genomics and bioinformatics studies paved the way in understanding the relationship between genotype and phenotype of an organism suffering from environmental stress. (intechopen.com)

Mohanty B, Yeo HC, Wijaya E, De los Reyes BG, Lee D-Y (2012) Patterns of cis-element enrichment revealed potential regulatory modules involved in the regulation of low-oxygen response transcriptome of rice. (ttu.edu)
Gene expression, Kaplan-Meier survival, microRNA and transcription factor target analyses were performed with the University of Alabama Cancer (UALCAN) Database, Kaplan-Meier Plotter, LinkedOmics, WebGestalt and gene set enrichment analysis, respectively. (xiahepublishing.com)
Functional enrichment analysis revealed SNHG4 involvement with regulation of ribosomal RNA synthesis and the RNA processing and surveillance pathway. (xiahepublishing.com)
Each gene was encoded using KEGG and GO enrichment scores, which reflected how much a gene can affect this function. (frontiersin.org)
For each fibrotic disease, by comparing the KEGG and GO enrichment scores between reported disease genes and other genes using the Monte Carlo feature selection (MCFS) method, the key KEGG and GO features were identified. (frontiersin.org)

Doug Kellogg's lab is working to elucidate these mechanisms, using biochemistry, genetics, and mathematical modeling to understand signaling networks that are required for control of cell size and cell growth. (ucsc.edu)
His MAPK/ERK pathway study integrates concerns from other disciplines, such as Cancer research, KRAS and Protein kinase A. In general Genetics study, his work on Transcription factor, Promoter and Codon usage bias often relates to the realm of Trichostatin A and Vorinostat, thereby connecting several areas of interest. (research.com)
It is generally hypothesized to be related to aging, trauma, inflammation, obesity, metabolism and genetics, and may also be related to genetic factors, chromosomal abnormalities and gene fusion ( 5 , 6 ). (spandidos-publications.com)

Moreover, we find that the distal NDRs are enriched specifically for binding motifs of the pluripotency and germ cell master regulators such as NANOG, SOX17, AP2γ and OCT4 in human FGCs, indicating the existence of a delicate regulatory balance between pluripotency-related genes and germ cell-specific genes in human FGCs, and the functional significance of these genes for germ cell development in vivo . (nature.com)
A germ cell-specific gene regulatory network is required to maintain the unique properties of primordial germ cells (PGCs) for transmission of genetic information to the next generation [ 6 ]. (biomedcentral.com)
Many studies have investigated germ cell-specific gene promoters to understand their regulatory mechanisms. (biomedcentral.com)

These include the expression of specific transcript isoforms and 3' untranslated regions. (nih.gov)
We also synthesize a library consisting of 70,290 guides targeting all human RefSeq coding isoforms to screen for genes which, upon activation, confer resistance to a BRAF inhibitor. (cdc.gov)

Since many of these mutations affect elements that control the expression of key determinants of cell fate and phenotype, understanding how these mutations affect the networks that control gene expression opens the way for the development of new classes of drugs. (umassmed.edu)
The Transcriptome study combines topics in areas such as Phenotype, Regulation of gene expression, Neuroepithelial cell and Gene expression profiling. (research.com)
By functional network, we mean a network such that an experimental perturbation will likely alter the dynamical phenotype of the network. (biomedcentral.com)

Many of the common genetic signals associated with disease are found far from the DNA sequence that encodes for protein sequence. (wikipedia.org)
The Myers lab is best known for the algorithm in BLAST and the paired-end whole-genome shotgun protocol and assembler-accomplishments in traditional sequence-based bioinformatics. (mpg.de)
This approach incorporates methods of statistical thermodynamics to calculate the activation probability of the target gene taking into account information about its regulatory genetic sequence (enhancers) and the transcription factors regulating the gene expression. (ecmiindmath.org)

Genome wide association studies (GWAS) have identified mutations in non-coding regulatory regions as the most common features associated with human disease. (umassmed.edu)
We apply iChIP to reconstruct the physical regulatory landscape of a mammalian cell, by building genome-wide binding maps for 29 transcription factors (TFs) and chromatin marks at four time points following stimulation of primary dendritic cells (DCs) with pathogen components. (nih.gov)
However, these recent studies have mostly focused on individual gene functions in stem cells although genome-wide data might be employed, and the conclusions drawn from these current studies are unavoidably biased on genes selected by these studies. (biomedcentral.com)

Homology-based reconstruction of regulatory networks for bacterial and archaeal genomes. (openwetware.org)

Gene Prediction and Modeling of Splicing is related to the research on Regulation of Alternative Splicing, Regulation of Protein Synthesis within the Gene Regulation program, and Genes and Diseases program. (wikipedia.org)
The expression of photosynthesis and chlorophyll synthesis related genes were significantly reduced under both types of stresses, which limit the metabolic processes and thus help prolong survival under extreme conditions. (frontiersin.org)
However, cell wall synthesis related genes were up-regulated under drought stress and down-regulated under flooding stress. (frontiersin.org)

His research links Computational biology with Gene. (research.com)
His Computational biology study incorporates themes from HEK 293 cells, Cell culture, Gene expression, Automated reasoning and Chromosome conformation capture. (research.com)
His Computational biology study combines topics from a wide range of disciplines, such as Transcriptome, Regulation of gene expression, Gene, Drug and Gene regulatory network. (research.com)
His main research concerns Transcriptome, Computational biology, Cell biology, MAPK/ERK pathway and Gene expression. (research.com)

Harenza JL, Muldoon PP, De Biasi M, Damaj MI, Miles MF (2014) Genetic variation within the Chrna7 gene modulates nicotine reward-like phenotypes in mice. (genenetwork.org)
These genes were selected based on their role in asthmatic inflammatory processes and History previously reported associations with asthma phenotypes. (cdc.gov)
Of these mediators, cytokines play a single nucleotide polymorphisms (SNP) in pro-inflammatory cytokine genes and asthma phenotypes (Che et al. (cdc.gov)

In Bioinformatics , 18 Suppl 1:S241-48, 2002. (duke.edu)

The fraction of conserved enhancers varies greatly across gene expression programs, with induced genes and early-response genes, in particular, being regulated by a higher fraction of conserved enhancers. (umassmed.edu)
Regulatory elements can include: CRMs and TF binding sites from REDfly and enhancers from FlyBase. (flymine.org)

Transcriptome analyses revealed that Caco-2 BBE cells respond to stimulation with IL-8 supporting the hypothesis that IL-8 induces G protein-coupled receptor signalling. (biomedcentral.com)
Our process includes high-throughput spatial transcriptome profiling followed by spatial gene and pathway analyses. (nature.com)
Mohanty B, Lakshmanan M, Kitazumi A, Cheung CYM, De los Reyes BG, Jang IC, Lee DY (2016) Validation of critical network hubs involved in drought stress response mechanisms by integrating transcriptome data and genome-scale metabolic model: Potential applications for drought tolerance breeding in rice. (ttu.edu)
Plants show stress-specific regulation of transcription that affects their transcriptome under stress conditions. (intechopen.com)

FAR1/FRS-like genes regulate light-signaling processes, shade avoidance, and flowering time in Arabidopsis thaliana . (kib.ac.cn)
However, it remains unclear what features of these genes dictate dynamic changes in their recognition and stepwise processing by spliceosome components to regulate splice site choice and splicing outcome. (biomedcentral.com)
Further, ELAVL1 expression correlating with multiple T cell proportions suggests that ELAVL1 may regulate T cell activation. (hindawi.com)

His studies in Regulation of gene expression integrate themes in fields like RNA, Protein biosynthesis, Three prime untranslated region, Messenger RNA and microRNA. (research.com)

This book presents an overview of recent developments in biostatistics and bioinformatics. (tsinghua.edu.cn)
Written by active researchers in these emerging areas, it is intended to give graduate students and new researchers an idea of where the frontiers of biostatistics and bioinformatics are as well as a forum to learn common techniques in use, so that they can advance the fields via developing new techniques and new results. (tsinghua.edu.cn)
In particulars, the book covers three important and rapidly advancing topics in biostatistics: analysis of survival and longitudinal data, statistical methods for epidemiology, and bioinformatics. (tsinghua.edu.cn)

This distribution is then linked to the probability of the target gene activation by assigning specific statistical weights to different configurations of the enhancer, and derivation of these weights is another essential direction of the research. (ecmiindmath.org)

However, existing strategies for generating and analysing high-throughput spatial expression profiles were developed for a limited range of organisms, primarily mammals. (nature.com)

To date, our understanding of mammalian gene regulation has been hampered by the difficulty of directly measuring in vivo binding of large numbers of transcription factors to DNA. (nih.gov)

Our modeling approach is able to simulate some interesting temporal properties of gene regulatory network motifs: the delay in the activation and the deactivation of the "output" gene in the coherent type-1 feedforward loop, the pulse in the incoherent type-1 feedforward loop, the bistability nature of double positive and double negative feedback loops, the oscillatory behavior of the negative feedback loop, and the "lock-in" effect of positive autoregulation. (biomedcentral.com)
Beginning with time-series gene expression data, the Local Edge Machine (LEM) seeks to find functional network models capable of generating the dynamic behavior of the data (Fig. 1 ). (biomedcentral.com)
One interesting feature of our approach is that it provides a coherent framework for modeling both the local motifs (e.g., edges) within the network and the global dynamical behavior of the system. (biomedcentral.com)

In the inference strategy, we will compare all pairs of input genes in those basic relationships by their corresponding -scores for every output gene. (tsinghua.edu.cn)
Gene regulatory network inference and gene module regulating virulence in Fusarium oxysporum. (openwetware.org)
We have ongoing interests in the systems level analysis and reconstruction of regulatory networks, inference of enhancer-promoter contacts, predictive models of gene expression and integration of three-dimensional chromatin structure with one-dimensional epigenetic measurements in the context of cancer, malaria, asthma and several autoimmune diseases. (ucsd.edu)
This project will focus on developing regulatory network inference methods for the joint analysis of gene expression and histone modification data from several different types of tumor infiltrating lymphocytes, which are gathered from a cohort of patients with solid tumors. (ucsd.edu)
Previous methods for network inference from dynamics data may be broadly classified according to the tools involved. (biomedcentral.com)
Most recently, several studies have developed inference methods based on nonlinear ordinary differential equations (ODEs) for the chemical kinetics and a Bayesian formalism on the network structure [ 24 - 27 ]. (biomedcentral.com)

We also have implemented this method on simulated and empirical yeast gene expression data sets. (tsinghua.edu.cn)
DI-fusion A web site for the computational analysis of yeast regulatory. (ac.be)
A web site for the computational analysis of yeast regulatory sequences. (ac.be)

She is currently a Senior Investigator leading the Chromosome Structure and Epigenetics Mechanism Unit within the Laboratory of Receptor Biology and Gene Expression at the Center for Cancer Research of the NCI/NIH in Bethesda. (elifesciences.org)
One in eight women in the United States will develop breast cancer in her lifetime, yet only about 15 percent of these cancers have been linked to inherited gene mutations. (ucsc.edu)
Recent work has shown that these proteins are also involved in hormonal regulation of breast cancer cells. (ucsc.edu)
Daniel Kim's lab studies the role of long noncoding RNA molecules (lncRNAs) in gene expression and cancer. (ucsc.edu)
His work in Colorectal cancer addresses issues such as Cell type, which are connected to fields such as Protein kinase A and Stromal cell. (research.com)
Zhang Y, Xuan J, De los Reyes BG, Clarke R, Ressom HW (2010) Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. (ttu.edu)
To illustrate the importance of gene expression analysis, consider a hypothetical case study involving cancer research. (heartofamericanorthwest.org)
Analyzing these data provides valuable information on which genes are upregulated or downregulated in lung cancer patients compared to healthy individuals. (heartofamericanorthwest.org)
MicroRNAs (miRNAs) are potent effectors in gene regulatory networks where aberrant miRNA expression can contribute to human diseases such as cancer. (hindawi.com)
These are responsible for abnormal gene expression, resulting in increased cancer cell proliferation and escape from immune surveillance, which can speed up the process of development into HCC. (xiahepublishing.com)
E7 from human papil omavirus type 16 cooperate to cancer: the European prospective investigation into doi:10.1093/carcin/bgp321 PMID:20047954 target the PDZ protein Na/H exchange regulatory cancer and nutrition study. (who.int)
Travel times along a street network from all residential ZIP Codes to all cancer surgery facilities were calculated using a geographic information system. (cdc.gov)

Construction and Analysis of Gene Co-Expression Network in the Pathogenic Fungus Ustilago maydis. (openwetware.org)
A Bibliometric Analysis of Mexican Bioinformatics: A Portrait of Actors, Structure, and Dynamics. (openwetware.org)
The analysis presented herein highlights the complexity of regulatory networks in S. aureus strains, identifies key conserved TFs among the Staphylococacceae , and offers unique insights into several as yet uncharacterized TFs. (biomedcentral.com)
De los Reyes BG, Mohanty B, Yun SJ, Park MR, Lee DY (2015) Upstream regulatory architecture of rice genes: Establishing the baseline for genus-wide comparative analysis of regulatory networks and allele mining. (ttu.edu)
Comparative analysis of putative pathogenesis-related gene expression in two Rhizoctonia solani pathosystems. (ttu.edu)
In recent years, the advancement of bioinformatics has revolutionized gene expression analysis by providing powerful tools for data management, integration, and interpretation. (heartofamericanorthwest.org)
This article aims to explore the significance of gene expression analysis in science and technology, with a particular focus on the role played by bioinformatics. (heartofamericanorthwest.org)
To investigate this hypothesis, they perform gene expression analysis using state-of-the-art techniques such as RNA-sequencing or microarray technologies. (heartofamericanorthwest.org)
Through gene expression analysis techniques, they compare the two groups' transcriptomes - that is, the complete set of RNA molecules produced by each individual's cells. (heartofamericanorthwest.org)
Moving forward to the next section on Applications of Gene Expression Analysis, we will explore how these methodologies have revolutionized diverse areas of research and their potential implications in improving human health. (heartofamericanorthwest.org)
We performed an integrated bioinformatics analysis to find key regulators by NetworkAnalyst [ 10 ], a web-based visual analytics platform. (hindawi.com)
Furthermore, GSEA data show that NOD-like receptor signaling-associated gene signatures are enriched and the xCell analysis indicated that most T cells are significantly decreased in the three microarray studies, which could help in understanding the role of ELAVL1 and APP in the blood of CD patients. (hindawi.com)

Functionally, the TFs are organized in a hierarchy of different types: Cell differentiation factors bind most of the genes and remain largely unchanged during the stimulation. (nih.gov)
Deep sequencing followed by abundancy ranking pinpointed six top hit genes potentially associated with either improved or impaired endodermal differentiation, which were selected for functional validation in CRISPR-Cas9 mediated knockout (KO) lines. (mdpi.com)

Experimental enhancement of splice-site strength in mini-gene constructs overcomes the effects of PRPF8 depletion on the kinetics and fidelity of splicing during transcription. (biomedcentral.com)
Most experimental approaches focus on the identification of miRNA targets and the investigation of physiological consequences when perturbing miRNA expressions but are unsuited to provide a system-level interpretation for observed phenomena. (hindawi.com)
Next, the network was translated into a detailed mechanistic model, which was characterized and validated with experimental data. (hindawi.com)
We always welcome applications from students looking for experimental and/or bioinformatics master or bachelor projects. (lu.se)

Gene transcription is mainly regulated by transcription factors (TFs) that bind to specific DNA sequences (called motifs) located in the promoter regions of genes [ 1 ]. (biomedcentral.com)
Furthermore, nucleotide sequences related to the cluster vanHAX are present in this DNA, suggesting that the prolonged use of avoparcin in agriculture led to the uptake of glycopeptide resistance genes by animal commensal bacteria, which were subsequently transferred to humans. (cdc.gov)
However, it is difficult to capture the complexity of transcript isoform variance using these libraries, and large cDNA sequences are often difficult to clone into size-limited viral expression vectors. (cdc.gov)

Long non-coding RNA small nucleolar RNA host genes (SNHGs) play a critical role in the occurrence and development of tumors. (xiahepublishing.com)

The actual origins of acquired resistance genes are unknown, but environmental microbes, including the strains producing antimicrobial agents, are believed to be important sources ( 4 , 5 ). (cdc.gov)
Substantial genetic and biochemical similarities exist between resistance determinants in antimicrobial agent-producing actinomycetes and resistance genes found in gram-positive and gram-negative pathogens ( 6 - 9 ). (cdc.gov)

Variants in blood pressure genes and the risk of Accardi R, Rubino R, Scalise M et col . (2011). (who.int)

The importance of epigenetic regulation in disease initiation and evolvement also signifies a new flow of challenges and opportunities to disease research and pharmaceutical discovery. (uga.edu)

Here, we used data from a large number of studies carried out in three mammalian species, mouse, chimpanzee and human, to uncover consistent changes in gene expression upon reprogramming of somatic cells. (nih.gov)
Although these techniques can provide spatially resolved or cell-type-specific gene expression data, they each have inherent limitations. (nature.com)
RESULTS: We describe an approach that naturally handles time series data with the capabilities of modelling causality, feedback loops, and environmental or hidden variables using a Dynamic Bayesian network. (duke.edu)
Our approach is evaluated on time series expression data measured in response to physiological changes that affect tryptophan metabolism in E. coli. (duke.edu)
We are rapidly entering an era of "personal genomics" wherein data on gene structure and expression will be available for large numbers of individuals. (ecmiindmath.org)
The generated data contain information about which genes are actively transcribed in both healthy individuals and those affected by the disorder. (heartofamericanorthwest.org)
Finally, we use an atlas of transcription data in a mammalian circadian system to illustrate how the method can be used for discovery in the context of large complex networks. (biomedcentral.com)
Based on the network structure, a detailed mechanistic model is established and its parameter values are determined using data. (hindawi.com)
The signature of our top screening hits is significantly correlated with gene expression data from clinical melanoma samples. (cdc.gov)

Her lab focuses on mutations that cause changes in gene expression by affecting a process called alternative splicing of RNA. (ucsc.edu)

Show all alleles for a specific Drosophila gene. (flymine.org)
We model transcriptional gene regulation by using a hybrid approach and applying it to the well characterized segmentation gene regulatory networks in Drosophila development. (ecmiindmath.org)
As a model genetic system, we use the Drosophila gap genes, which is a class of segmentation genes controlling the body plan formation during the early embryo development. (ecmiindmath.org)

FUT6 and CGNL1 were downregulated in HNSCC compared with adjacent healthy tissue and the expression levels of these genes were associated with tumor stage. (spandidos-publications.com)
Immunohistochemical staining was performed to confirm the expression of related proteins in OA and non‑OA tissue samples. (spandidos-publications.com)
Expression of SNHG4 in HCC is higher in HCC tissue than in normal healthy liver tissues and is mainly distributed in the nucleus. (xiahepublishing.com)
We compared the gene overlaps among eight fibrotic diseases and connective tissue growth factor (CTGF) was finally identified as the common key molecule. (frontiersin.org)

The FACS and INTACT methods require plant transgenic lines respectively expressing fluorescent proteins or the biotinylated nuclear envelope protein in the cell type of interest. (nature.com)
Park MR, Yun KY, Herath V, Mohanty B, Xu F, Bajic VB, Yun SJ, De los Reyes BG (2010) Supra-optimal expression of the cold-regulated OsMyb4 transcription factor in transgenic rice changes the complexity of transcriptional network with major effects on stress tolerance and panicle development. (ttu.edu)
Park MR, Baek SH, De los Reyes BG, Yun SJ (2007) Overexpression of a high-affinity transporter gene from tobacco (NtPT1) enhances phosphate uptake and accumulation in transgenic rice plants. (ttu.edu)

MicroRNAs (miRNAs or miRs) are involved in the post-transcriptional regulation of gene expression via complete or partial base pairing with the 3′untranslated region of target genes ( 3 ). (spandidos-publications.com)
Regulation of the NANOG gene by TFs, epigenetic factors, and autoregulatory factors is well characterized in ESCs, and transcriptional regulation of NANOG is well established in these cells. (biomedcentral.com)
Therefore, identification of regulatory elements within the promoter region is considered crucial to understand the mechanism underlying transcriptional regulation in specific cell types. (biomedcentral.com)

Thus, we integrated three independent microarray studies to screen crucial genes in the blood of CD patients. (hindawi.com)

As virulence determinant production is very tightly regulated in S. aureus , a thorough understanding of its regulatory network is necessary to fully comprehend the pathogenic processes of this bacterium. (biomedcentral.com)

Along with the reorganization of epigenetic and transcriptional networks, somatic cell reprogramming brings about numerous changes at the level of RNA processing. (nih.gov)
Most striking among these are ESRP1 and ESRP2, which accelerate and enhance the efficiency of somatic cell reprogramming by promoting isoform expression changes associated with mesenchymal-to-epithelial transition. (nih.gov)
Our results provide a general resource for gene expression and splicing changes that take place during somatic cell reprogramming. (nih.gov)
Furthermore, they support the concept that splicing factors with evolutionarily conserved, cell type-specific expression can modulate the efficiency of the process by reinforcing intermediate states resembling the cell types in which these factors are normally expressed. (nih.gov)
Dynamic binding of transcription factors to DNA elements specifies gene expression and cell fate, in both normal physiology and disease. (nih.gov)
Surprisingly, we discover using ODeGP that increasing cell density results in rapid generation of oscillations in the Bmal1 gene, thus highlighting our method's ability to discover unexpected and new patterns. (edu.in)
Forkhead box protein M1 (FOXM1) is a key transcription factor (TF) that regulates a common set of genes related to the cell cycle in various cell types. (mdpi.com)
The changes in expression of genes involved in regulating the flux of cell wall precursors and starch/sugar content can serve as an adaptive mechanism for soybean survival under stress conditions. (frontiersin.org)
MOTIVATION: Cells continuously reprogram their gene expression network as they move through the cell cycle or sense changes in their environment. (duke.edu)
We also study the influence of signaling proteins in different cell compartments onto the functioning of the EGFR signaling pathway as a whole. (ecmiindmath.org)
The goal of this project is to model the natural variation in gene expression across many immune cell types using an already established database at LJI ( https://dice-database.org ) and to identify cell type-specific epigenetic regulators of important immune genes. (ucsd.edu)
Mohanty B, Takahashi H, de los Reyes BG, Wijaya E, Nakazono M, Lee DY (2016) Transcriptional regulatory mechanism of alcohol dehydrogenase 1-deficient mutant of rice for cell survival under complete submergence. (ttu.edu)
Single-cell sequencing: With recent advances in technology, it has become possible to analyze gene expression at the single-cell level. (heartofamericanorthwest.org)
Furthermore, the CD4 + T cell, including Th1, Th17, and regulatory T (Treg) cells, were associated with the severity of CD, particularly with active inflammation [ 2 ]. (hindawi.com)
In addition, one T cell subtype from the blood of CD patients is enriched for the CD-risk gene [ 9 ]. (hindawi.com)
We show for the first time that different trans -regulatory elements control transcription of cNANOG in a cell type-specific manner. (biomedcentral.com)

To better understand conservation of enhancer activity, we recently used a comparative genomics approach that integrates temporal expression and epigenetic profiles in an innate immune system. (umassmed.edu)
Comparative Toxicogenomics Database and TargetScan were used to identify the hub‑gene‑related diseases and the microRNAs that regulated the central hub genes. (spandidos-publications.com)

The proximal region of the cNANOG promoter contains a positive transcriptional regulatory element (CCAAT/enhancer-binding protein ( CEBP )-binding site) in ESCs. (biomedcentral.com)
Direct binding of ZFP143 to the proximal region of the NANOG promoter regulates NANOG expression by modulating OCT4 binding [ 24 ]. (biomedcentral.com)
These dCas9-activator fusions targeted to the promoter region of endogenous genes can then modulate gene expression 7 - 11 . (cdc.gov)

This process is carried out by the human spliceosome machinery, in which over 300 proteins sequentially assemble with uridine-rich small nuclear RNA molecules (U snRNAs) to form distinct small nuclear ribonucleoprotein complexes (snRNPs). (biomedcentral.com)
By converting RNA molecules into complementary DNA (cDNA), followed by fragmentation and library preparation steps, NGS allows for comprehensive profiling of gene expression levels across an entire genome. (heartofamericanorthwest.org)

Temporally dynamic gene expression programs have been observed in a wide variety of organisms. (biomedcentral.com)

These results suggest that genetic variations in TNF, TGFB1, PTGS1 and PTGS2 genes contribute to DA susceptibility. (cdc.gov)

Zhang Y, Xuan J, De los Reyes BG, Clarke R, Ressom HW (2009) Reverse engineering module networks by PSO-RNN hybrid modeling. (ttu.edu)
We present an improved method for modeling gene regulatory network motifs using Statecharts and we describe the successful modeling of several motifs, including those which could not be modeled or whose models could not be distinguished using the method of a previous proposal. (biomedcentral.com)

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