Among genes framework gene regulatory networks. Medical search. Frequent questions

However, the inherent complexity of transcriptional signatures, with thousands of differentially expressed genes, makes them hard to interpret, thus giving poor mechanistic insights and hampering translation to clinics. (biomedcentral.com)
Multiple miRNA-mRNA prediction databases were searched by differentially expressed genes (DEGs) to obtain pairs of a miRNA-DEG regulatory network. (frontiersin.org)

Changes in chromatin state can affect how and when genes are expressed. (nih.gov)
Three chromatin states were associated with regulatory regions known as promoters, which sit close to genes and allow them to be read. (nih.gov)
Four chromatin states were associated with regions known as enhancers, which act at a distance and are not always easy to tie to particular genes. (nih.gov)
To connect enhancer regions to likely target genes, the researchers compared patterns of chromatin activity with gene expression across the 9 cell types. (nih.gov)
Light responsive elements, especially G-, E- and GT-boxes were over-represented in accessible chromatin around C 4 genes. (sciety.org)
Whenever you are signaling training typically do not work with TFs, chromatin-centered inference out-of TF craft only methods the result off TF binding into the chromatin, which may or may not end up in transcriptional changes of their address genes, while TF hobby inferred away from target gene term can be confounded by indirect outcomes. (micsem.org)
A variety of one another causal need and you can head usage of entry to info is found in strategies like CellOracle [ 129 ] and you can Inferelator3.0 [ 130 ] that use chromatin accessibility data so you can describe the fresh new cellphone-type certain earlier in the day regulating circle that is following simple by knowledge an excellent regularized linear regression model towards the gene phrase data. (micsem.org)
Utilizing these paired multi-omics data, we define domains of regulatory chromatin (DORCs) of immune stimulation and find that cells alter chromatin accessibility and gene expression at timescales of minutes. (nih.gov)
This paradigm considers only interactions of genes through expressed transcription factors and does not incorporate chromatin modification processes. (sontaglab.org)

These data have spawned a variety of methods to infer the structure of gene-regulatory networks or to study their high-level properties, as recently reviewed [ 5 ]. (biomedcentral.com)
Advancing tools to integrate multi-omics data, we develop functional inference of gene regulation (FigR), a framework to computationally pair scA-TAC-seq with scRNA-seq cells, connect distal cis-regulatory elements to genes, and infer gene-regulatory networks (GRNs) to identify candidate transcription factor (TF) regulators. (nih.gov)
with such abundant high-throughput screening data available, researchers have tried to infer, or reverse-engineer, gene networks. (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)

Gene regulatory network inference remains a challenging problem in systems biology despite numerous approaches. (videolectures.net)
When substantial knowledge on a gene regulatory network is already available, supervised network inference also is appropriate. (videolectures.net)
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)
Gupta R, Stincone A, Antczak P, Durant S, Bicknell R, Bikfalvi A, Falciani F. (2011) A Computational framework for gene regulatory network inference that combines multiple methods and datasets. (u-bordeaux.fr)

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)
finally a 3rd test measures the ability of the method to predict new interactions with new genes. (videolectures.net)
We recently reported a procedure for inferring gene-regulatory network models by integrating gene-expression profiles with high-throughput measurements of protein interactions [ 18 ]. (biomedcentral.com)
Many of these models contain transcriptional interactions for which the regulatory effects (inducer versus repressor) are ambiguous and cannot be determined from publicly available expression profiles. (biomedcentral.com)
Our loss- and gain-of-function studies, as well as the observed genetic interactions among Dorsocross, tinman and pannier , suggest that co-expression of these three genes in the cardiac mesoderm, which also involves cross-regulation, plays a major role in the specification of cardiac progenitors. (biologists.com)
It works out a great ligand-target gene interaction rating, and you may predicated on this, predicts phone-mobile interactions. (micsem.org)
Overall, FigR enables elucidation of regulatory interactions across single-cell data, providing new opportunities to understand the function of cells within tissues. (nih.gov)
The miRNA-mRNA interactions were verified by dual-luciferase reporter gene assays and experiments using mimics miRNA or their inhibitors. (frontiersin.org)
Arena-Idb provides a framework for network reconstruction of ncRNA heterogeneous interactions (i.e., with other type of molecules) and relationships with human diseases which guide the integration of data, extracted from different sources, via mapping of entities and minimization of ambiguity. (biomedcentral.com)
Arena-Idb provides a schema and a visualization system to integrate ncRNA interactions that assists in discovering ncRNA functions through the extraction of heterogeneous interaction networks. (biomedcentral.com)
For example, an individual miRNA may regulate multiple mRNAs, and in contrast, an individual gene may also be regulated by multiple miRNAs, thus representing a complex network of miRNA-mRNA interactions. (biomedcentral.com)
Post-genomic analysis techniques such as next-generation sequencing have produced vast amounts of data about micro organisms including genetic sequences, their functional annotations and gene regulatory interactions. (uni-bielefeld.de)
In this article we introduce the updated version 6.0 of CoryneRegNet and describe the updated database content which includes, 6352 corynebacterial regulatory interactions compared with 4928 interactions in release 5.0 and 3235 regulations in release 4.0, respectively. (uni-bielefeld.de)
We also demonstrate how we support the community by integrating analysis and visualization features for transiently imported custom data, such as gene regulatory interactions. (uni-bielefeld.de)
Evolutionary constraints on the complexity of genetic regulatory networks allow predictions of the total number of genetic interactions. (uni-bielefeld.de)

Although microRNAs (miRNAs) are physically small, they have been shown to play an important role in gene regulation [ 1 ]. (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)
Such a method builds a binary classifier able to assign a class (Regulation/No regulation) to an ordered pair of genes. (videolectures.net)
As genome-scale measurements lead to increasingly complex models of gene regulation, systematic approaches are needed to validate and refine these models. (biomedcentral.com)
Understanding gene expression and regulation is essential for understanding biological mechanisms. (biomedcentral.com)
This paper introduces a mathematical model that seamlessly combines gene regulatory networks and DNA methylation, with the goal of quantitatively characterizing the contribution of epigenetic regulation to gene silencing. (sontaglab.org)
More recently, other layers of regulation have added further complexity in regulatory networks. (biomedcentral.com)
The proposed method provides an open framework to incorporate transcriptome expression data and biological regulation network to predict cancer subtypes. (biomedcentral.com)
PRODORIC2: the bacterial gene regulation database in 2018. (uni-bielefeld.de)
A rapid overview of this morphologic scheme provides the framework for further studying the processes and regulation involved in development. (medscape.com)

The scientists were then able to piece together enhancer regulatory networks and their target genes. (nih.gov)
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)

Using a novel iterative framework developed in a companion manuscript, we have analyzed single-cell RNA-seq data obtained from mouse embryonic stem cells taken at various time points during early germ layer differentiation to identify cell types as well as the lineage relationships between these individual cell types. (harvard.edu)
This allowed us to essentially map out a lineage tree in gene expression space that describes the continuous gene expression dynamics of early germ layer differentiation. (harvard.edu)
The integration of this new information with previous findings has allowed us to draw a more complete pathway of regulatory events during cardiac induction and differentiation in Drosophila . (biologists.com)
Recently, miRNA-messenger RNA (mRNA) regulatory relationships have been confirmed during biological processes, including osteogenic differentiation. (frontiersin.org)
An MC3T3-E1-based microarray dataset (accessioned as GSE46400) downloaded from the Gene Expression Omnibus included MC3T3-E1 cells with or without 14-day osteoblast differentiation osteoblast induction. (frontiersin.org)
The Arhgap11a, H2afx, Chek2, Dlgap5, and Chek1 were hub genes downregulated in MC3T3-E1 cells after osteogenic differentiation, verified by RT-qPCR results. (frontiersin.org)
The student will evaluate gene expression in relation to measures of genetic diversity, differentiation, and neutrality across the genome to evaluate whether the sequences or the flanking regions of genes with stage-specific expression demonstrate signs of selection. (lu.se)

The new data support two out of three novel regulatory pathways predicted to mediate expression changes downstream of the yeast transcriptional regulator SWI4 . (biomedcentral.com)
To systematically study these pathways by modulating individual components-or in the case of synthetic biology, building new network architectures by creating DNA circuit-it is critical to control multiple genes simultaneously under tightly regulated or inducible expression. (atcc.org)
Together, these signaling and transcriptional pathways set up complex and only partially defined regulatory networks that result in the progressive delineation and specification of heart progenitors. (biologists.com)
Most network biology capitalizes on the observation that genes whose function is altered in a particular phenotype tend to be co-expressed in common pathways and, therefore, co-localized in specific network regions [ 19 ]. (biomedcentral.com)
Such as [ 131 ], modified this new TieDIE signaling network diffusion algorithm [ 132 ] so you're able to phosphoproteomics and transcriptomics data discover druggable kinase pathways. (micsem.org)

Currently, an increasing number of studies are being carried out to deepen our understanding of miRNA regulatory mechanisms and functions. (hindawi.com)
The refined networks support previously unknown regulatory mechanisms downstream of SOK2 and SWI4 . (biomedcentral.com)
Studies in several vertebrate models and Drosophila have uncovered a surprising degree of evolutionary conservation of regulatory mechanisms and genes that control early cardiogenesis. (biologists.com)
We apply our approach to 189 drugs tested in 671 cancer cell lines and observe a connection between gene expression levels of the modules and mechanisms of action of the drugs. (biomedcentral.com)

MicroRNAs (miRNAs) are potent effectors in gene regulatory networks where aberrant miRNA expression can contribute to human diseases such as cancer. (hindawi.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)
For 14 cell types, we identified 26,597 independent cis-expression quantitative trait loci (eQTLs), and 62,305 trans-eQTL, with the majority showing cell type specific effects on gene expression. (iscb.org)
This assembly system combined with DNA parts will be useful for constructing large-scale gene circuit libraries with reliable gene expression and for designing logic operations for a complex network in S. cerevisiae . (atcc.org)
Patterns of activity for enhancer elements, they found, correlated strongly with patterns of expression for the nearest gene. (nih.gov)
Importantly, our results show that cell types occupy discrete locations in gene expression space and correspondingly, cells exhibit abrupt changes in gene expression profile as they transition from one cell type to another. (harvard.edu)
Taking advantage of the finding that certain locations in gene expression space are more "stable" (i.e., far more cells are found in these locations than expected by chance) than others, we used a novel framework to build a probabilistic model of the underlying gene regulatory network. (harvard.edu)
These models allowed us to make and experimentally test predictions as to how cells respond to various signals and gene expression changes. (harvard.edu)
In an early step, the Dorsocross genes act in parallel with tinman to activate the expression of pannier , a cardiogenic gene encoding a Gata factor. (biologists.com)
Her lab has recently worked with gene expression patterns during sexual reproduction and regeneration of syllids. (uni-goettingen.de)
In this respect, he is using a broad range of methods including immunohistochemical analyses, histological staining procedures and ultrastructural investigations as well as gene expression analyses and phylogenomic approaches. (uni-goettingen.de)
Gene expression profiling has become a mainstay approach to characterize cell properties and status, unveiling links between gene activities and disease phenotypes. (biomedcentral.com)
Although providing a rich account of disease biology, these studies have failed to yield better drug therapies, as causality and response to drug perturbations cannot be inferred directly from two-state (diseased vs. healthy) differential gene expression analysis [ 2 , 3 ]. (biomedcentral.com)
Provided that the panel of cell lines is large enough, this approach allows for a new type of gene expression analysis where basal expression levels are correlated to drug response phenotypes. (biomedcentral.com)
In all cases, gene expression is modified such that C 4 proteins accumulate to levels matching those of the photosynthetic apparatus. (sciety.org)
To better understand this rewiring of gene expression we undertook RNA- and DNaseI-SEQ on de-etiolating seedlings of C 4 Gynandropsis gynandra , which is sister to C 3 Arabidopsis. (sciety.org)
Changes in chloroplast ultrastructure and C 4 gene expression were coordinated and rapid. (sciety.org)
Overall, the data support a model in which rapid and robust C 4 gene expression following light exposure is generated through modifications in cis to allow integration into high-level transcriptional networks including those underpinned by conserved light responsive elements. (sciety.org)
This paper analyses the de-etiolation process in Gynandropsis gynandra as a proxy to catch photosynthesis genes whose expression is affected using time course RNA-seq and DNaseI-seq. (sciety.org)
Festival [ 126 ], specifically, clearly rates TF- and path-products [ 128, thirteen ] on the gene expression investigation playing with earlier in the day studies, and therefore enhances the abilities of the approach as compared to almost every other causal reason steps. (micsem.org)
Cells require coordinated control over gene expression when responding to environmental stimuli. (nih.gov)
Time delay is the time lag during which expression change of the regulator is transmitted to change in target gene expression. (biomedcentral.com)
more than thirty percent of the modeled regulations, based entirely on gene expression files, were found to be consistent with previous discoveries from known databases. (biomedcentral.com)
GeneReg is an easy-to-use, simple, fast R package for gene regulatory network construction from short time course gene expression data. (biomedcentral.com)
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)
MicroRNAs (miRNAs) are well-recognized for their abilities to regulate gene expression post-transcriptionally in plants and animals. (frontiersin.org)
It regulates Sp7 protein expression and induces expression of major bone matrix protein genes, such as Col1a1, Spp1, Ibsp, Bglap2, and Fn1 ( 7 , 8 ). (frontiersin.org)
In this paper, we propose a method, CSPRV, to improve the cancer subtype prediction by incorporating multi-sources transcriptome expression data and heterogeneous biological networks. (biomedcentral.com)
We extract multiple expression features of each genome element based on the regulatory associations in the heterogeneous biological networks and use a generalized matrix correlation method ( RV 2 ) to predict the similarities between samples in each view of expression data. (biomedcentral.com)
15 ]). In some cases, two-dimensional relationships (e.g., gene expression mean-variance) are explored (e.g. (biomedcentral.com)
How Reliable Are Gene Expression-Based and Immunohistochemical Biomarkers Assessed on a Core-Needle Biopsy? (lu.se)
miRNAs are small noncoding RNAs that have broad regulatory functions on gene expression. (lu.se)
Changes in gene expression mediate growth and development in all living organisms. (lu.se)
Strong selection pressures experienced during one stage of development may differ from those experienced in other stages, and with consequences for the underlying patterns of gene expression. (lu.se)
We want to understand differences in life stage-specific gene expression in the peacock fly and relate these patterns to signatures of selection across the genome. (lu.se)
The student will analyze gene expression in a reference-based pipeline using existing RNA sequencing data from larvae, pupae, and adult flies from each of the two host forms. (lu.se)
This will include co-expression network analyses to identify groups of genes that are expressed similarly and might belong to the same or linked gene regulatory networks. (lu.se)
Imposed upon this gross morphological description is the modern understanding of gene expression and protein elucidation, which bring about these developmental processes. (medscape.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)

Gene regulatory networks (GRNs) provide system level explanations of developmental and physiological functions in the terms of the genomic regulatory code. (nature.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)
To investigate a gene regulatory network, an iterative process of four steps is needed. (hindawi.com)
SNF integrates multiple types of genomic data to identify cancer subtypes, while it uses iterative method to fuse similarity networks between samples, and the model is complex and hard to be interpreted in practice [ 16 ]. (biomedcentral.com)

Developmental gene regulatory networks in the zebrafish embryo. (nature.com)
Researchers have identified numerous TFs essential to lens development in vertebrates, and each has its own set of TFBS, which integrate into a complex developmental regulatory gene network . (evolutionnews.org)

The student will be responsible for improving the annotations, especially for the untranslated regions that lie up and downstream of protein coding genes. (lu.se)
The disease is caused by a mutated gene that leads to a lack of the building blocks needed to form the cell's protein factories (known as ribosomes). (lu.se)

Structural characteristics of downstream effector gene cassettes and their control functions. (nature.com)
His efforts are focused on the identification of the complete set of biomineralizing effector genes in the pulmonate gastropod Lymnaea stagnalis , and on identifying the gene regulatory and cellular communication events that coordinate the initiation of shell formation in the early snail embryo. (uni-goettingen.de)

Recent advances in genomics and computational biology are enabling construction of large-scale models of gene-regulatory networks. (biomedcentral.com)
We have developed a powerful computational framework for revealing the genetic basis of bacterial traits by correlating the inheritance patterns of genes and phenotypes across all the sequenced bacterial genomes (Jim et al. (columbia.edu)

There are other hypothesis on how transcriptional networks could be rewired to generate novel traits that are not explored during this work. (sciety.org)

Stathopoulos, A. & Levine, M. Genomic regulatory networks and animal development. (nature.com)
This work provides a transcriptional framework to study de-etiolation in G. gynandra and genomic and epigenomic insights on the gene regulatory networks underlying this process. (sciety.org)

Alon, U. Network motifs: theory and experimental approaches. (nature.com)

My research focuses on the study of macroevolutionary patterns of taxononomic diversity, morphological disparity and biogeographic distribution in a phylogenetic framework. (uni-goettingen.de)
C 3 photosynthesis and C 4 genes showed similar induction patterns, but C 4 genes from G. gynandra were more strongly induced than orthologs from Arabidopsis. (sciety.org)

To gain insights into these non-coding regions, a team of scientists partly supported by NIH's National Human Genome Research Institute (NHGRI) carried out a genome-wide survey of epigenetic marks - factors that change the way genes are read, or expressed, without changing the DNA sequence itself. (nih.gov)
Furthermore, we have developed a genome-wide epistasis analysis framework that efficiently reveals the organization of these genes within signaling and regulatory networks such as the Rcs phosphorelay pathway and the cyclic-di-GMP second-messenger system. (columbia.edu)

Non-coding RNAs (ncRNAs), for a long time believed to be non-functional, are emerging as one of the most important and large family of gene regulators and key elements for genome maintenance. (biomedcentral.com)

The vast majority of these, however, lie outside of known genes, as 98.5% of our genome doesn't code for proteins. (nih.gov)

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)

Finally, we prove the predictive capability of the modules and demonstrate how they can be used as gene sets in conventional enrichment analyses. (biomedcentral.com)

To simplify drug signatures, we have developed a network-based methodology to identify functionally coherent gene modules. (biomedcentral.com)

Since then, research into how genes affect our traits, health and disease has grown to include entirely new forms of medicines. (lu.se)

The analysis is focused also in transcription factor genes and their potential regulatory networks associated with genes participating in C3 and C4 photosynthesis. (sciety.org)

The project will rely on published whole genome assemblies and gene annotations of various qualities. (lu.se)

A gene regulatory network predicted transcription factors operating at the top of the de-etiolation network, including those responding to light, act upstream of C 4 genes. (sciety.org)

It is widely accepted that the regulatory associations between features play important roles in cancer subtype studies. (biomedcentral.com)
The consideration of regulatory associations between biological features and data-views contribution is important to improve the understanding of cancer subtypes. (biomedcentral.com)
WSNF incorporates the mRNA-TF-miRNA regulatory network information to predict the importance of each feature, and thus to identify cancer subtypes using SNF framework based on the weighted similarity information between samples. (biomedcentral.com)
Gene and cell therapies that improve cancer treatments. (lu.se)

Dual-luciferase reporter gene assays demonstrated Arhgap11a as the target of miR-211-5p. (frontiersin.org)

Basically, if miRNA repression is evolutionarily important for a gene, we expect the miRNA binding sites to be shared across closely related species. (lu.se)
The student will create a pipeline for identifying conserved miRNA binding sites across several sparrow species using TargetScan as a framework. (lu.se)

In the case of network construction in Saccharomyces cerevisiae , there has been a lack of both suitable, well-characterized parts (promoters and regulators) as well as a standardized platform for DNA assembly and delivery of gene circuits. (atcc.org)
These results give researchers a framework for uncovering genetic regulators that could be potential targets for drug development. (nih.gov)

However, if we are to accurately model large gene networks in complex organisms, including fly, worm, mouse, and human, automated procedures will be essential for analyzing the network, choosing the best new experiments to test the model, conducting the experiments, and integrating the resulting data. (biomedcentral.com)
In all these organisms, cardiac induction in the lateral mesoderm involves the concerted action of signals mediated by Bmp, Wnt and Fgf family members, which act upon cardiogenic genes encoding NK homeodomain, Gata and T-box transcription factors (reviewed by Zaffran and Frasch, 2002 ). (biologists.com)

We trained a Bayesian machine learning neural network model to generate a neuroimaging phenotype and AD score representing the probability of AD using structural MRI data in the Alzheimer's Disease Neuroimaging Initiative (ADNI) Cohort (cut-off 0.5, AUC 0.92, PPV 0.90, NPV 0.93). (cdc.gov)

To these ends his team is also developing methods to characterize gene function in this nontraditional model organism. (uni-goettingen.de)

It requires specific regulatory regions to bind to well over four new transcription factors . (evolutionnews.org)

Based on the network structure, a detailed mechanistic model is established and its parameter values are determined using data. (hindawi.com)
Next, the network was translated into a detailed mechanistic model, which was characterized and validated with experimental data. (hindawi.com)
Network biology offers means to integrate a large amount of omics data [ 18 ]. (biomedcentral.com)
Modellen är anpassad till experimentell data och förutsäger en tillståndsbytande kinematik som valideras med klondata. (lu.se)
However, few of them consider the regulatory associations between genome features and the contribution weights of different data-views in data integration. (biomedcentral.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)
Modern breakthroughs, such as the mapping of the human genome, the Nobel Prize-winning CRISPR gene editing scissors, the ability to rapidly map large amounts of DNA, and the Nobel Prize-winning discovery of how mature cells can be reprogrammed, have led to an increasing number of innovative biological therapies reaching patients. (lu.se)
These medicines differ from 'ordinary' medicines because the active substance is produced in or purified from materials of biological origin such as living cells, genes or tissue," says Johan Flygare, researcher at the Lund Stem Cell Center and the Division of Molecular Medicine and Gene Therapy at Lund University. (lu.se)

Peter, I. S. & Davidson, E. H. Modularity and design principles in the sea urchin embryo gene regulatory network. (nature.com)
Davidson, E. H. Network design principles from the sea urchin embryo. (nature.com)
Soulet F, Kilarski WW, Antczak P, Herbert J, Bicknell R, Falciani F, Bikfalvi A. (2010) Gene signatures in wound tissue as evidenced by molecular profiling in the chick embryo model. (u-bordeaux.fr)

Starting in the early 2000s, sophisticated technologies have been developed for the rational construction of synthetic genetic networks that implement specified logical functionalities. (sontaglab.org)

Complex behavior within eukaryotic cells manifest from layered regulatory networks changing the transcription of many genes. (atcc.org)
For example, active promoter states in skeletal muscle were associated with extracellular structure genes, while active promoter states in lymphoblastoid cells were associated with immune response genes. (nih.gov)
Promoters active in both cells types were associated with general metabolism genes. (nih.gov)
These are therapies based on cells, genes or tissues and fall under the umbrella term ATMP (Advanced Therapy Medicinal Products). (lu.se)
We collect them and make sure to insert a healthy copy of the mutated gene into the cells which are then returned to the patient. (lu.se)

Single-molecule level models are not suitable for large scale regulatory network reconstruction. (biomedcentral.com)

Using this procedure, we evaluate 38 candidate regulatory networks in yeast and perform four high-priority gene knockout experiments. (biomedcentral.com)

Logical models such as Boolean networks and Petri nets could represent the network structure but are unable to describe dynamic processes. (biomedcentral.com)

The manuscript "Induction of C4 genes evolved through changes in cis allowing integration into ancestral C3 gene regulatory networks" by Singh and colleagues represent an important contribution to the field of comparative studies of C3 and C4 photosynthesis. (sciety.org)

A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation. (nature.com)

Koide, T., Hayata, T. & Cho, K. W. Y. Xenopus as a model system to study transcriptional regulatory networks. (nature.com)
This study demonstrates the feasibility for the quick and easy construction of gene circuits for delivery into S. cerevisiae and the utility of a fully characterized set of diverse promoters, activators, and repressors. (atcc.org)
Our present study identifies the Dorsocross T-box genes as key mediators of combined Dpp and Wg signals during this process. (biologists.com)

Our strategy starts with the calculation of drug-gene correlations and is followed by a pathway-oriented filtering and a network-diffusion analysis across the interactome. (biomedcentral.com)
CoryneRegNet is the reference database and analysis platform for corynebacterial gene regulatory networks. (uni-bielefeld.de)

Anatomy11

Organisms15

Chemicals and Drugs16

Analytical, Diagnostic and Therapeutic Techniques and Equipment22

Psychiatry and Psychology2

Phenomena and Processes55

Disciplines and Occupations4

Information Science16

Health Care9

Differentially expressed genes2

Chromatin9

Infer4

Inference5

Interactions17

Regulation10

Target genes3

Differentiation7

Pathways5

Mechanisms4

Expression38

Datasets1

GRNs1

Iterative3

Developmental2

Protein2

Effector2

Computational2

Transcriptional networks1

Genomic2

Approaches1

Patterns2

Genome-wide2

RNAs1

Proteins1

Systems biology1

Analyses1

Functionally1

Traits1

Transcription factor1

Annotations1

Upstream1

Cancer4

Assays1

MiRNA2

Regulators2

Organisms2

Bayesian1

Characterize1

Specific regulatory1

Data5

Biological3

Embryo3

Genetic networks1

Cells5

Reconstruction1

Experiments1

Boolean1

Induction1

Roles1

Study3

Analysis2