Regulatory gene network. Medical search. Frequent questions

A gene (or genetic) regulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins which, in turn, determine the function of the cell. (wikipedia.org)
Some proteins though serve only to activate other genes, and these are the transcription factors that are the main players in regulatory networks or cascades. (wikipedia.org)
Each time a cell divides, two cells result which, although they contain the same genome in full, can differ in which genes are turned on and making proteins. (wikipedia.org)
In parallel with this process of building structure, the gene cascade turns on genes that make structural proteins that give each cell the physical properties it needs. (wikipedia.org)
At one level, biological cells can be thought of as "partially mixed bags" of biological chemicals - in the discussion of gene regulatory networks, these chemicals are mostly the messenger RNAs (mRNAs) and proteins that arise from gene expression. (wikipedia.org)
A typical gene regulatory network looks something like this: The nodes of this network can represent genes, proteins, mRNAs, protein/protein complexes or cellular processes. (wikipedia.org)
Edges between nodes represent interactions between the nodes, that can correspond to individual molecular reactions between DNA, mRNA, miRNA, proteins or molecular processes through which the products of one gene affect those of another, though the lack of experimentally obtained information often implies that some reactions are not modeled at such a fine level of detail. (wikipedia.org)
Genomic rearrangements in cancer cells can create gene fusions where the juxtaposition of two different genes leads to the production of chimeric proteins or altered gene expression through promoter-swapping. (lu.se)
These proteins regulate genes that help control cell division and the self-destruction (apoptosis) of cells that are no longer needed. (medlineplus.gov)
Binding of cAMP dissociates the complex, allowing monomeric catalytic subunits to phosphorylate cytosolic proteins or induce gene expression in the nucleus. (nih.gov)
Background: Connectivity networks, which reflect multiple interactions between genes and proteins, possess not only a descriptive but also a predictive value, as new connections can be extrapolated and tested by means of computational analysis. (hse.ru)
An understanding of the mechanistic interplay between individual genes and proteins that drive the development and progression of UC is therefore a high priority. (biomedcentral.com)

A key question in network inference, that has not been properly answered, is what accuracy can be expected for a given biological dataset and inference method. (diva-portal.org)
We present GeneSPIDER - a Matlab package for tuning, running, and evaluating inference algorithms that allows independent control of network and data properties to enable data-driven benchmarking. (diva-portal.org)
With GeneSPIDER we aim to move the goal of network inference benchmarks from simple performance measurement to a deeper understanding of how the accuracy of an algorithm is determined by different combinations of network and data properties. (diva-portal.org)
The results of the second approach in Chapter 4 can be applied to network inference and analysis of Boolean model sets. (fu-berlin.de)
Augmenting microarray data with literature-based knowledge to enhance gene regulatory network inference. (nih.gov)
In general, the existing models for network inference can be grouped into three categories: logical models, continuous models and single-molecule level models [ 1 ]. (biomedcentral.com)
There may be other models which could integrate prior knowledge to improve the performance, but we only considered the ab initio network inference approaches here as prior knowledge is able to be integrated into most de novo network reconstruction methods easily. (biomedcentral.com)
The inference of genome-wide gene regulatory networks (GRN) from large-scale gene expression data provides a promising approach for a detailed investigation of the underlying network structure associated to urothelial carcinogenesis. (biomedcentral.com)
In our study we inferred and compared three GRNs by the application of the BC3Net inference algorithm to large-scale transitional cell carcinoma gene expression data sets from Illumina RNAseq (179 samples), Illumina Bead arrays (165 samples) and Affymetrix Oligo microarrays (188 samples). (biomedcentral.com)
RNAseq based gene expression data is the data platform of choice for a GRN inference. (biomedcentral.com)
The inference of gene regulatory networks (GRN) from large-scale gene expression data of tumor samples from various grades and stages is a promising approach for the identification of novel putative targets in cancer [ 4 - 6 ]. (biomedcentral.com)

By using mRNA expression and DNA methylation and hydroxymethylation interaction analysis , 99 differentially expressed genes were identified. (bvsalud.org)
Using the limma package in R, the differentially expressed genes were screened. (medscape.com)
Followed by enrichment analysis was performed for the differentially expressed genes using database for annotation, visualization, and integrated discovery online tool. (medscape.com)
Results As a result, 1757, 354, and 396 differentially expressed genes separately were identified in aortic occlusive disease, large abdominal aortic aneurysm, and small abdominal aortic aneurysm samples. (medscape.com)
Additionally, the differentially expressed genes during reproductive development were identified using RNA-seq data. (frontiersin.org)

An interaction map of circulating metabolites, immune gene networks, and their genetic regulation. (broadinstitute.org)
To provide a coherent description of induced pluripotency from the gene regulation perspective, we use 35 microarray datasets to construct a reprogramming gene regulatory network. (nih.gov)
E ) Gene enrichment module 16 are highly enriched in genes involved in cell cycle regulation, and cells expressing these targets are found in greatest numbers at the center of the pseudotime pathway. (elifesciences.org)
We found that the set of 5' partners in miRNA host fusions is non-random, with overrepresentation of highly expressed genes in pathways active in cancer including epithelial-to-mesenchymal transition, translational regulation and estrogen signalling. (lu.se)
Understanding gene expression and regulation is essential for understanding biological mechanisms. (biomedcentral.com)
This complexity in DNA recognition may be important in gene regulation and in the evolution of transcriptional regulatory networks. (nih.gov)
Is the Subject Area "Gene regulation" applicable to this article? (plos.org)

We hypothesised that firstly, 5' partner genes should belong to pathways and transcriptional programmes that reflect the tumour phenotype and secondly, there should be a selection for fusion events that shape miRNA expression to benefit the tumour cell through the known hallmarks of cancer. (lu.se)
ONCO.IO is a database and tool for network analysis of cancer-associated signaling pathways. (onco.io)
Comparison to the component pathways of the KEGG Pathways in Cancer map reveals that the resulting networks contain both known and novel relationships. (nih.gov)
Th2 cells from asthmatic subjects expressed higher levels of several genes that promote their survival as well as alter their metabolic pathways to favor persistence at sites of allergic inflammation. (nih.gov)
We also identified new genes, pathways, and regulatory networks that modulated berry ripening in muscadine grape. (figshare.com)

Identification of Antinorovirus Genes in Human Cells Using Genome-Wide CRISPR Activation Screening. (broadinstitute.org)
The data deluge can leverage sophisticated ML techniques for functionally annotating the regulatory non-coding genome. (biomedcentral.com)
Critically, they implicate regions of the genome (loci) and do not necessarily pinpoint the causal variant(s), gene(s) or mechanism(s) underlying the association. (nih.gov)
Rare variant association studies identify genes across the genome that harbor more mutations than expected by chance in one group of subjects (e.g. (nih.gov)
Predictive models for gene and pathway function will be important for diagnosis and ultimately intervention, fulfilling the promise of the human genome project. (nih.gov)
National Genome Research Network (NGFN-Plus): medical genome research with focus on the Parkinson's disease (2009 - 2013, funding reference 01GS08134). (uni-tuebingen.de)
Explorative Project for the Reconstruction of Gene Regulatory Networks in the National Genome Research Network (2005 - 2009, funding reference 0313323). (uni-tuebingen.de)

Furthermore, 303 and 462 target genes unique to JLCMS9A and JLCMS9B, respectively, as well as 782 common targets were predicted based on the degradome analysis. (frontiersin.org)
Target genes differentially expressed between the CMS line and the maintainer line were revealed by an RNA-seq analysis. (frontiersin.org)
More importantly, this package can provide information about time delays between expression change in a regulator and that of its target genes. (biomedcentral.com)
The R package GeneReg is based on time delay linear regression, which can generate a model of the expression levels of regulators at a given time point against the expression levels of their target genes at a later time point. (biomedcentral.com)

All genes shown encode transcription factors that control the activity of genes encoding transcription factors. (biomedcentral.com)
Without this function, the protein cannot control the activity of genes during development. (medlineplus.gov)

The network model provides an explanatory framework that relates endoderm specification to the genomic regulatory code. (nature.com)
The identification of novel genomic target regions and gene targets that drive urothelial carcinogenesis is crucial in order to improve our current limited understanding of urothelial cancer (UC) on the molecular level. (biomedcentral.com)
Interestingly, the most prominent subnetworks of co-located genes were found on chromosome regions 5q31.3 (RNAseq), 8q24.3 (Oligo) and 1q23.3 (Bead), which all represent known genomic regions frequently deregulated or aberated in urothelial cancer and other cancer types. (biomedcentral.com)

Twenty nine additional experimental datasets are collectively used to test the model/network, and good agreement between experimental and predicted gene expression profiles is found. (nih.gov)

Moreover, integrated TF platform database and Cytoscape software were used for constructing transcriptional regulatory networks. (medscape.com)
SPARCL1 was another gene shared by these groups and regulated by NFIA, which had a high degree in transcriptional regulatory network. (medscape.com)
The small RNAs (sRNAs) are short [approximately 18-30 nucleotides (nt)] non-coding RNA molecules that can regulate gene expression in the cytoplasm and nucleus via post-transcriptional gene silencing, chromatin-dependent gene silencing, or RNA activation. (frontiersin.org)

Applied to the reconstruction of gene regulatory networks, we show th. (sciweavers.org)

To achieve a holistic understanding of highly complex biological systems, it is critical to understand the underlying Gene Regulatory Networks (GRNs). (genetics.org.uk)
Today, more than 50 years after Eric Davidson's original formulation of gene regulatory circuits that control developmental processes, the concept of GRNs has been universally adopted in biology. (genetics.org.uk)
To infer gene regulatory networks (GRNs), we applied an optimized version of the BC3Net algorithm, named BC3Net10, capable of deriving robust and coherent patterns. (fraunhofer.de)
Furthermore, the identified hub genes of the individual GRNs, e.g. (biomedcentral.com)
The GRNs were highly dataset specific on the interaction level between individual genes, but showed large similarities on the biological function level represented by subnetworks. (biomedcentral.com)
Based on our analysis of inferential and experimental networks the Bead UC GRN showed the lowest performance compared to the RNAseq and Oligo UC GRNs. (biomedcentral.com)
In this study we infer GRNs by the application of the BC3Net algorithm which is based on the aggregation of an ensemble of C3Net gene regulatory networks [ 4 ]. (biomedcentral.com)
Gene regulatory networks (GRNs), consisting of transcription factors and their target sites, control neurogenesis and cell-fate specification in the developing central nervous system. (wustl.edu)
In this study, we use integrated single-cell RNA and single-cell ATAC sequencing (scATAC-seq) analysis in developing mouse and human retina to identify multiple interconnected, evolutionarily conserved GRNs composed of cell-type-specific transcription factors that both activate genes within their own network and inhibit genes in other networks. (wustl.edu)

A panoply of candidate genes have been discovered through synergy of animal models and human genetics. (nih.gov)

A genetic algorithm is then used to optimize the strength of interactions using microarray data and an artificial neural network fitness function. (nih.gov)
Integration of different types of connectivity data (such as co-expression and genetic interactions) in one network has proven to benefit 'guilt by association' analysis. (hse.ru)
A new SPF-based algorithm has been applied to genetic interactions sub-networks adjacent to the clusters of co-expressed genes for ranking the most likely gene expression regulators causal to eQTLs. (hse.ru)
Results: We have demonstrated that known co-expression and genetic interactions between C. elegans genes can be complementary in predicting gene expression regulators. (hse.ru)
We found that genes associated with eQTLs are highly clustered in a C. elegans co-expression sub-network, and their adjacent genetic interactions provide the optimal functional connectivity environment for application of the new SPF-based algorithm. (hse.ru)
Cells follow a genetic blueprint composed of complex webs of interacting genes. (nih.gov)

In principle, this approach initially leverages the power of literature knowledge to extract AD specific genes for generating viable networks. (fraunhofer.de)
Moreover, iNetModels includes tissue- and cancer-specific Gene Co-expression Networks (GCNs) for exploring the connections between the specific genes. (nih.gov)

We have a reasonable understanding of the functions of some individual genes, but we know very little about how they work together. (nih.gov)

These approaches are vulnerable to noise and other changes which mask driver-gene activity. (nih.gov)
At the macro-level, the group uses data science and data-driven approaches―merging computational biology, functional genomics, and molecular biology―to reconstruct and characterize environmentally- and developmentally-responsive gene networks that underlie cell identity and response. (nih.gov)
We investigate the impact of augmenting microarray data with semantic relations automatically extracted from the literature, with the view that relations encoding gene/protein interactions eliminate the need for random selection of components in non-exhaustive approaches, producing a more accurate model of cellular behavior. (nih.gov)
Computational pathway modeling of these motifs and their combinations occurring in molecular signaling networks will be a key element in new risk assessment approaches based on in vitro cellular assays. (nih.gov)
Thus, information-theoretic approaches can deal with steady-state gene expression data or with time-series data given that the sampling interval is long enough to assume that each point is independent of the previous points. (biomedcentral.com)
In Banjo, heuristic approaches are used to search the network space to find the network graph G, which requires large datasets in which the number of genes is much smaller than the number of experiments. (biomedcentral.com)
Approaches that take into account the cumulative effects of these many, subtle changes in gene activity may thus be more informative with regard to disease risk than those focusing on individual variants or genes associated with disease. (nih.gov)
System-based approaches allow us to investigate the underlying network structure associated with carcinogenesis and thus facilitate a novel perspective for the identification of molecular targets that drive urothelial carcinogenesis. (biomedcentral.com)

Reiterative AP2a activity controls sequential steps in the neural crest gene regulatory network. (medlineplus.gov)
Transcriptome analysis reveals novel players in the cranial neural crest gene regulatory network. (ox.ac.uk)
To elaborate on the CNC gene regulatory network, we evaluated the effects of knocking down known neural plate border genes and early neural crest specifier genes on selected neural crest-enriched transcripts. (ox.ac.uk)

Further research that uses this information to create predictive computational models of the complex gene regulatory networks that coordinate vertebrate embryogenesis. (nih.gov)
Hilger-Eversheim K, Moser M, Schorle H, Buettner R. Regulatory roles of AP-2 transcription factors in vertebrate development, apoptosis and cell-cycle control. (medlineplus.gov)

Several methods to infer such networks exist, but most of them do not elaborate on context specificity and completeness of the generated networks, missing out on lesser-known candidates. (fraunhofer.de)
Various computational models rely on random gene selection to infer such networks from microarray data. (nih.gov)

Molecular Profiling of Cancer: Identification and Characterization of Candidate Biomarkers and Regulatory Genes. (nih.gov)
K ) Known distal and proximal genes markers are expressed in their corresponding cell clusters at E16.5 but not E11.5, validating cluster identification. (elifesciences.org)
Protein complex identification from protein-protein interaction (PPI) networks is crucial for understanding cellular organization principles and functional mechanisms. (biomedcentral.com)
One major focus of our research has been the identification and characterization of small, regulatory RNAs in E. coli. (nih.gov)
CIT): Women Scientists Advisory WSA Anita Roberts Lecture The hidden secrets of small genes One major focus of our research has been the identification and characterization of small, regulatory RNAs in E. coli. (nih.gov)
Identification and analysis of metabolic networks given experimental data , 2006 - 2008, contract number 7532.22-26-18). (uni-tuebingen.de)

The central hypothesis is that grouping cells based on the photoreceptor gene regulatory network and applying bioinformatics analysis to the data can show that TOP2B plays an essential role in proper photoreceptor differentiation. (rutgers.edu)
In this study, we preform bioinformatics analysis on publically available single-cell RNA-seq (scRNA-seq) dataset of postnatal day 14 mouse retina (GSE63473) to determine to role of TOP2B in the photoreceptor gene regulatory network and identify novel genes which contribute to this pathway. (rutgers.edu)

Several algorithms were compared in respect to their predictive potential in different network connectivity contexts. (hse.ru)

Reconstructing and testing interactions within Gene Regulatory Networks enables the discovery of emerging properties of complex biological processes in a manner not previously possible using individual gene perturbations. (genetics.org.uk)
In addition to studies aimed at identifying and understanding the roles of gene variants, environmental perturbations, and other factors causing structural birth defects, DBCAB supports studies intended to advance our understanding of the fundamental processes underlying the formation and differentiation of the embryo. (nih.gov)
Subtle perturbations in gene networks are likely to cause much of inherited disease susceptibility, but understanding how complex genotypes and environmental interactions result in disease will require experimental systems biology using model organisms. (nih.gov)

Among these, variants in interferon regulatory factor 6 (IRF6) cause syndromic orofacial clefting and contribute risk toward isolated cleft lip and palate (1/700 live births). (nih.gov)
Several transcript variants encoding the same protein have been found for this gene. (nih.gov)

These molecules and their interactions comprise a gene regulatory network. (wikipedia.org)
Finally, a network was built based on the interactions. (frontiersin.org)
Our results demonstrate the advantage of combining gene interactions extracted from the literature in the form of semantic relations with microarray analysis in generating contribution-weighted gene regulatory networks. (nih.gov)
WormNet has been used to obtain pair-wise gene interactions. (hse.ru)

We confirm that NFI transcription factors selectively activate expression of genes promoting late-stage temporal identity in primary retinal progenitors and identify other transcription factors that regulate rod photoreceptor specification in postnatal retina. (wustl.edu)

E-F ) Gene expression levels correlate with the presence of a nearby region of open chromatin, particularly when it is located within the promoter region. (elifesciences.org)
During development and in response to environmental insults, various signaling cascades culminate in the activation of appropriate master transcription factors (TFs) and chromatin remodeling enzymes to establish gene expression programs controlling cell fate decisions. (nih.gov)
To identify gene regulatory networks that reprogram Müller glia into progenitor cells, we profiled changes in gene expression and chromatin accessibility in Müller glia from zebrafish, chick, and mice in response to different stimuli. (johnshopkins.edu)
Please confirm that you want to SAVE all your changes for 'Determination of Fungal Chromatin Regulatory Network and Its Impact on Gene Expression' . (doe.gov)

For testing, we used invasive ductile carcinoma of the breast to query the literature and a microarray set containing gene expression changes in these cells over several time points. (nih.gov)

One module of gene expression is consistent with the predicted distal differentiation trajectory and consists of genes related to processes important to lung development, including epithelial/respiratory system branching and development. (elifesciences.org)
Thus, this study provides further insight into the photoreceptor differentiation processes that could be affected by the gene regulatory pathway. (rutgers.edu)
Logical models such as Boolean networks and Petri nets could represent the network structure but are unable to describe dynamic processes. (biomedcentral.com)

The Drosophila schnurri gene acts in the Dpp/TGFβ signaling pathway and encodes a transcription factor homologous to the human MBP family. (nature.com)
The TFAP2A gene provides instructions for making a protein called transcription factor AP-2 alpha (AP-2α). (medlineplus.gov)
As its name suggests, this protein is a transcription factor, which means it attaches (binds) to specific regions of DNA and helps control the activity of particular genes. (medlineplus.gov)
Most TFAP2A gene mutations involved in this condition change single protein building blocks (amino acids) in the transcription factor AP-2α protein. (medlineplus.gov)

Background: Recently, supervised learning methods have been exploited to reconstruct gene regulatory networks from gene expression data. (sciweavers.org)
GeneReg is an easy-to-use, simple, fast R package for gene regulatory network construction from short time course gene expression data. (biomedcentral.com)
Because Banjo implements both Bayesian and dynamic Bayesian networks, it can infer gene networks from steady-state gene expression data or from time-series gene expression data. (biomedcentral.com)

Analysis of photoreceptor scRNA-seq data reveals that TOP2B expression is correlated with the expression of photoreceptor marker genes, confirming its role in photoreceptor differentiation. (rutgers.edu)
The Jothi group is interested in understanding how transcription regulators and epigenetic modifications regulate gene expression programs during cellular development and differentiation, and apply this knowledge to aid in the development of diagnostic and therapeutic strategies for cancer and other diseases. (nih.gov)
These network motifs are basic building blocks of molecular circuits underpinning a variety of cellular functions, including adaptation, homeostasis, proliferation, differentiation, and apoptosis. (nih.gov)
Our long-term goal is to develop predictive models of gene function with a specific focus on sex differentiation in the germline. (nih.gov)

The TFAP2A gene is found on chromosome 6 . (medlineplus.gov)

Time delay is the time lag during which expression change of the regulator is transmitted to change in target gene expression. (biomedcentral.com)

Unlike Mendelian diseases, for psychiatric disorders there is no clear one-to-one relationship between a gene and disease. (nih.gov)
Many diseases run in families due to the inheritance of particular sets of genes. (nih.gov)

Elucidation of gene networks (Figure 1) associated with specific biological phenotypes thus becomes key to understanding the molecular basis of development and pathogenesis. (nih.gov)

Therefore, methods are urgently needed which can separate the impact of true regulatory elements from stochastic changes and downstream effects. (nih.gov)

Epigenetic Analyses of Human Left Atrial Tissue Identifies Gene Networks Underlying Atrial Fibrillation. (broadinstitute.org)
Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. (broadinstitute.org)
L ) Monocle 3 analysis of isolated epithelial populations identifies multiple gene modules with specific expression patterns. (elifesciences.org)
Taken together, our analysis provides unprecedented characterization of the migratory CNC transcriptome and identifies new links in the gene regulatory network responsible for development of this critical cell population. (ox.ac.uk)

To address these problems, we developed HiLoop, a toolkit that enables discovery, visualization, and analysis of several types of high-feedback loops in large biological networks. (biomedcentral.com)
Previously, bulk RNA-seq analysis of the retina revealed TOP2B controls expression of genes in the photoreceptor gene-regulatory network. (rutgers.edu)
Differential network analysis has become an important approach in identifying driver genes in development and disease. (nih.gov)
While incorporation of prior knowledge into data analysis has been deemed important, in practice, it has generally been limited to referencing genes in probe sets and using curated knowledge bases. (nih.gov)

Research aimed at providing comprehensive analyses of gene regulatory networks at the single- and multi-cellular level for all developmental stages using model organisms and human cell-based models. (nih.gov)
Based on string online tool and Cytoscape software, protein-protein interaction network and module analyses were carried out. (medscape.com)

Similar to eukaryotic miRNAs, many of these bacterial RNAs act by base pairing with mRNA targets to modulate mRNA stability and translation and are integral to most regulatory networks. (nih.gov)
Interestingly, while it was initially assumed these small RNAs are encoded as independent genes, recent studies have shown that many small RNAs are derived from the 3' end of protein coding genes and the distinction between coding and noncoding is becoming increasingly blurred. (nih.gov)

Some direct cis -regulatory targets of these signals have been found 10 , 11 and various phenomenological patterns of gene expression have been observed in the pre-gastrular endomesoderm. (nature.com)

Comprising 276 nodes and 4471 links, the resulting network is, to the best of our knowledge, the largest gene regulatory network constructed for human fibroblast reprogramming and it is the only one built using a large number of experimental datasets. (nih.gov)

C-D ) Gene enrichment modules 4 and 12 are highly enriched for components of the ciliated and secretory cell epithelium respectively. (elifesciences.org)
F-G ) Gene set enrichment categories for modules 4 and 12 ( F ) and module 16 ( G ) are shown. (elifesciences.org)

Feedback loops in gene regulatory networks play pivotal roles in governing functional dynamics of cells. (biomedcentral.com)
It is therefore unclear whether such high-feedback loops with functional dynamical properties exist widely in gene regulatory networks. (biomedcentral.com)
He is now developing new functional bionanomaterials for drug and gene delivery for cancer therapy and for cancer targeting. (nih.gov)

GeneSPIDER is uniquely suited to address this question by first extracting salient properties from the experimental data and then generating simulated networks and data that closely match these properties. (diva-portal.org)
To build the network, a model that relates the expression profiles of the initial (fibroblast) and final (induced pluripotent stem cell) states is proposed and the model parameters (link strengths) are fitted using the experimental data. (nih.gov)
We expect HiLoop's usefulness to increase as experimental data of regulatory networks accumulate. (biomedcentral.com)
Despite the availability of modeling and experimental studies on high-feedback structures in several specific biological systems, there is a lack of computational tools for systematically identifying and characterizing these network structures in large-scale biological networks. (biomedcentral.com)

Gene regulatory networks are a crucial aspect of systems biology in describing molecular mechanisms of the cell. (nih.gov)
The Division of Genetics and Molecular, Cellular, and Developmental Biology (GMCDB) supports research to understand the structure and function of cells and cellular components, and the cellular and molecular mechanisms that underlie inheritance, gene expression, and development. (nih.gov)

We identified evolutionarily conserved and speciesspecific gene networks controlling glial quiescence, reactivity, and neurogenesis. (johnshopkins.edu)

The conference will bring together experts with both biological and quantitative backgrounds to cross-fertilise and formulate interdisciplinary ways to model and study complex Gene Regulatory Networks across different organisms and cell types. (genetics.org.uk)
However, it remains challenging to identify and visualize high-feedback loops in complex gene regulatory networks due to the myriad of ways in which the loops can be combined. (biomedcentral.com)
Through random parameterization of mathematical models derived from target networks, HiLoop presents characteristic features of the underlying systems, including complex multistability and oscillations, in a unifying framework. (biomedcentral.com)
HiLoop makes the study of complex networks accessible without significant computational demands. (biomedcentral.com)
In recent years, computational models based on differential equations, and more recently on Boolean logic, have become useful tools for dissecting and quantifying the complex regulatory relationships underlying the clock's oscillatory dynamics. (easychair.org)
The encoded protein is a regulatory subunit of the cAMP-dependent protein kinase (PKA) complex, which is responsible for transducing most of the cAMP signals in eukaryotic cells. (nih.gov)
The inactive PKA complex contains two regulatory and two catalytic subunits. (nih.gov)
Urothelial pathogenesis is a complex process driven by an underlying network of interconnected genes. (biomedcentral.com)

Mutations in the TFAP2A gene cause a condition called branchio-oculo-facial syndrome, which is characterized by skin anomalies on the neck, malformations of the eyes and ears, and distinctive facial features. (medlineplus.gov)
TFAP2A gene mutations disrupt the development of structures derived from the branchial arches, which results in the characteristic features of branchio-oculo-facial syndrome. (medlineplus.gov)

M ) The expression patterns of example genes in this module are visualized and include genes known to be essential for proper distal lung development including Sox9 , Wnt7b , Hmga2, and Bmp4 . (elifesciences.org)
We propose the differential network flow (DNF) method to identify key regulators of progression in development or disease. (nih.gov)
The TFAP2A gene appears to be especially important for the development of tissues derived from the first and second branchial arches. (medlineplus.gov)
This logic, presented here, as the bio-logic of artificial creature, needs not only newsimulators such as chemical or hydrodynamic environments but also new mechanisms such as an artificial regulatory network to control the development process. (springer.com)
Our ultimate goal is to determine how the collective action of genes results in an individual with specific characteristics, development, and disease susceptibilities. (nih.gov)
Project under the umbrella of the National Resource for Network Biology Summer of Code for the development of CySBML as a new Cytoscape App for SBML support. (uni-tuebingen.de)

The Shortest Path Function (SPF) has been adopted for statistical validation of the co-expressed gene clusters and for computational prediction of their potential gene expression regulators from a network context. (hse.ru)

Four types of models will be considered: interaction graphs, Boolean networks, models based on differential equations and discrete abstractions of differential equations. (fu-berlin.de)
It will be proven that certain invariant sets are preserved during the conversion from a Boolean network to a model based on ODEs. (fu-berlin.de)
We demonstrate that this constitutes an approach to link the interaction graph to the dynamics of certain sets of Boolean networks and models based on differential equations. (fu-berlin.de)
The abstracted dynamics - or more precisely the restrictions on the abstracted behavior - of such sets of Boolean networks or models based on differential equations will be represented as Boolean state transitions graphs themselves. (fu-berlin.de)
We will show that these state transition graphs can be considered as asynchronous Boolean networks. (fu-berlin.de)
This leads to the question how different asynchronous Boolean networks or different behaviours of a single asynchronous Boolean network can be distinguished. (fu-berlin.de)

Reconstruction of gene networks controlling cellular response or fate. (nih.gov)
We conclude that network motifs provide a basis for understanding thresholds for cellular responses. (nih.gov)

A statistical classifier is trained to recognize the relationships between the activation profiles of gene pairs. (sciweavers.org)

Here, we present iNetModels, an interactive database and visualization platform of Multi-Omics Biological Networks (MOBNs). (nih.gov)

Anatomy18

Organisms31

Diseases2

Chemicals and Drugs52

Analytical, Diagnostic and Therapeutic Techniques and Equipment35

Phenomena and Processes100

Disciplines and Occupations5

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture3

Information Science24

Health Care9

Proteins12

Inference11

Differentially expressed genes5

Regulation7

Pathways5

Genome7

Target genes4

Control the activity of genes2

Genomic3

Predicted gene expression1

Transcriptional3

Reconstruction of gene regulato1

GRNs9

Candidate genes1

Genetic6

Specific genes2

Individual genes1

Approaches8

Neural3

Vertebrate2

Infer such networks2

Identification6

Bioinformatics2

Algorithms1

Perturbations3

Variants2

Interactions4

Progenitors1

Chromatin4

Microarray1

Processes3

Transcription factor4

Expression Data3

Differentiation4

Chromosome1

Regulator1

Diseases2

Phenotypes1

Stochastic1

Identifies4

Analysis4

Analyses2

RNAs2

Targets1

Datasets1

Enrichment2

Functional3

Experimental4

Molecular2

Neurogenesis1

Complex8

Mutations2

Development6

Regulators1

Boolean6

Cellular2

Statistical1

Biological networks1