Functionally related framework gene regulatory networks. Medical search. Frequent questions

Using a treatment and sex interaction model, 13 and 4 differentially expressed genes were identified in liver and muscle respectively. (biomedcentral.com)
Sex-specific differentially expressed (DE) genes were identified in both sexes. (biomedcentral.com)
Six of the nine differentially expressed microRNAs target genes in the extended network, including CLSPN , an important checkpoint regulator in the cell cycle that was down-regulated, and FZD5 , a receptor for Wnt proteins that was up-regulated. (biomedcentral.com)

Although some key flowering responsive genes have been identified in spinach, non-coding RNA molecules like long non-coding RNAs (lncRNAs) were not investigated yet. (biomedcentral.com)
Promising regulatory molecules in this respect are small non-coding RNAs, like microRNAs, which regulate gene expression post-transcriptionally. (biomedcentral.com)
Network representation is frequently used to capture the presence of these molecules as well as their relationship. (biomedcentral.com)
Such technological improvements enable a large number of molecules, including genes, transcripts, and proteins to be simultaneously measured in different conditions over time. (biomedcentral.com)
A qualitative mathematical model of the notion of immunocompetence is developed, based on the formalism of Memory Evolutive Systems (MES), from which, immunocompetence is defined as an emergent structure of a higher order arising from the signal networks that are established between effector cells and molecules of the immune response in the presence of a given antigen. (biorxiv.org)

Here, we discuss approaches to avoid this curse of dimensionality ( n ≪ p ), which will involve analyzing intermediate phenotypes such as molecular traits and component traits related to plant morphology or physiology. (springer.com)
Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. (stanford.edu)
The rapid improvement of descriptive genomic technologies has fueled a dramatic increase in hypothesized connections between cardiovascular gene expression and phenotypes. (mdpi.com)
We describe a computational methodology allowing to systematically and quantitatively characterize a Boolean mathematical model of a biological network in terms of genetic interactions between all loss of function and gain of function mutations with respect to all model phenotypes or outputs. (researchgate.net)
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)

In all cases, gene expression is modified such that C 4 proteins accumulate to levels matching those of the photosynthetic apparatus. (sciety.org)
posttranslational modifications, amino acid variations, computational mutation analysis, protein PTM predictor, network biology Introduction Protein PTMs are biochemical alterations of amino acids that change the physicochemical properties of target proteins, leading to structural changes and therefore regulating protein-protein interactions and cellular signal transduction in developmental and cancer pathways [1]. (deepdyve.com)
With the wealth of data accumulated from completely sequenced genomes and other high-throughput experiments, global studies of biological systems, by simultaneously investigating multiple biological entities (e.g. genes, transcripts, proteins), has become a routine. (biomedcentral.com)
Our studies have demonstrated that several of the proteins encoded by cellular oncogenes function in fundamental aspects of gene regulation. (stanford.edu)
However, most current approaches used for functional annotation simply focus on the use of protein-level information but ignore inter-relationships among annotations.Here, we established PFresGO, an attention-based deep-learning approach that incorporates hierarchical structures in Gene Ontology (GO) graphs and advances in natural language processing algorithms for the functional annotation of proteins. (giwebb.com)

Pathway analysis revealed 15 significantly altered pathways: eight more general mostly cell cycle-related pathways and seven cancer-specific pathways. (biomedcentral.com)
The more general pathways were merged into one network and then extended with known protein-protein and transcription factor-gene interactions. (biomedcentral.com)
These networks range from those involving gene regulatory and protein-protein interactions underlying intracellular signalling pathways, and single-cell responses, to increasingly complex networks of in vivo cellular interaction, positioning, and migration that determine the overall immune response of an organism ( Subramanian 2015 ). (biorxiv.org)
This review will focus on the four-floral inductive pathways which operate in Arabidopsis: Photoperiodic, autonomous, gibberellin promotion, and vernalization pathways and how in this network of pathways, different nodes signify a site of signal integration and how the pathways are integrated, leading to a co-ordinated initiation of flowering. (jabonline.in)
Enriched pathways analysis of these positively correlated genes featured Toll-like receptor and SUMOylation pathways. (preprints.org)

Gene co-expression networks are of biological interest since co-expressed genes are controlled by the same transcriptional regulatory program, functionally related, or members of the same pathway or protein complex. (wikipedia.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 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)
There are other hypothesis on how transcriptional networks could be rewired to generate novel traits that are not explored during this work. (sciety.org)
MicroRNAs (MiRNAs) are important regulators that can strongly affect cellular functions including proliferation, differentiation, and apoptosis through post-transcriptional negative regulation of target gene expression [ 1 ]. (biomedcentral.com)
Finally, a practical method to measure the immunocompetence status is established, using elements of the theory of small random graphs and taking into account the characteristics of the immune networks, established through transcriptional studies, of patients with severe COVID-19 and healthy patients, assuming that both types of patients were vaccinated with an effective biological against SARS-CoV-2. (biorxiv.org)

Large tumor genome sequencing projects have now uncovered a few hundred genes involved in the onset of tumorigenesis, or drivers, in some two dozen malignancies. (biomedcentral.com)

Exploiting the aforementioned catalogs of driver genes, for example, we recently revealed the mutational landscape of chromatin regulatory factors (CRFs) in cancer [ 5 ]. (biomedcentral.com)
Light responsive elements, especially G-, E- and GT-boxes were over-represented in accessible chromatin around C 4 genes. (sciety.org)
Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. (stanford.edu)
2) We have discovered a group of oncoproteins that are implicated in long-term maintenance of gene expression through their effects on the state of chromatin. (stanford.edu)
We are studying the role that normal chromatin structure plays in gene regulation in hematopoietic cells and how its disruption leads to altered development and cancer. (stanford.edu)
Peak evaluation is complex, as gene expression regulation involves interactions between combinatorial transcription factor binding sites and chromatin states. (biomedcentral.com)

There are two main reasons why the catalogs of cancer drivers produced by the aforementioned projects and others need to be broken down into related sets of genes for deeper analysis. (biomedcentral.com)
The ability of the proposed methodology to efficiently identify sets of genes with similar expression patterns is shown to be instrumental in the discovery of relevant biological phenomena, leading to more convincing evidence of specific regulatory mechanisms. (biomedcentral.com)

In this study, we present a computational framework to identify miRNA-disease associations, and further construct a bipartite miRNA-disease network for systematically analyzing the global properties of miRNA regulation of disease genes. (biomedcentral.com)
The GO and KEGG analyses carried out on the cis target gene of lncRNAs showed that the lncRNAs play an important role in the regulation of flowering spinach. (biomedcentral.com)
This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach. (biomedcentral.com)
Network algorithms were used to (1) identify active network modules and (2) integrate microRNA regulation in the network. (biomedcentral.com)
Adding microRNA regulation to the network enabled the identification of gene targets of significantly expressed microRNAs after 1,25(OH) 2 D 3 treatment. (biomedcentral.com)
Focus of my research for the last 10 years has been on gene regulation, initially based on transcription factors, promoters and enhancers, but increasingly also including epigenetics, in particular histone modifications. (ntnu.edu)

Compared to a GRN, a GCN does not attempt to infer the causality relationships between genes and in a GCN the edges represent only a correlation or dependency relationship among genes. (wikipedia.org)

We developed a computational framework to identify miRNA-disease associations by performing random walk analysis, and focused on the functional link between miRNA targets and disease genes in protein-protein interaction (PPI) networks. (biomedcentral.com)
The development of better methods for mutation analysis-related protein PTMs will help to facilitate the development of personalized precision medicine. (deepdyve.com)
In this regard, comprehensive studies of the impact of amino acid variation on protein PTMs will be helpful for further understanding of how genetic polymorphisms are involved in regulating biological and pathological processes and providing instructive information for drug development of various related diseases. (deepdyve.com)
ncRNAs with more than 200 nucleotides are considered as lncRNAs, which originate from intronic and exonic regions of protein-coding genes in both sense and antisense strands, as well as from the intergenic regions [ 21 ]. (biomedcentral.com)
These structures provide the backbone upon which proteome-wide connectivity, and in turn, protein networks become disturbed and ultimately dysfunctional. (nature.com)
Current technical limitations curb our ability to explore global changes in protein level connectivity, restricting how to translate key network changes into AD therapies. (nature.com)
When a cell needs to make a particular protein, it first copies the instructions from the matching gene into a molecule known as a messenger RNA (or an mRNA for short). (elifesciences.org)
Combining these new datasets with existing published gene expression and protein expression data have identified selected panels of novel biomarkers which have been evaluated on over 100 cervical cancer and pre-cancer cases using standard immunohistochemistry approaches. (europa.eu)
However, writing such summaries is a daunting task, given the number of genes in each organism (e.g. 13,929 protein coding genes in Drosophila melanogaster). (stanford.edu)

Using this database, researchers can quickly retrieve the expression level data for target genes in different tissues and in response to different treatments to elucidate gene functions and explore the biology of rapeseed at the transcriptome level. (preprints.org)

The hypergeometric distribution method considers the number of overlapping genes while neglecting the functional link between them, and the scoring system used in their study only considered the direct neighbour information of each miRNA in the miRNA functional network. (biomedcentral.com)
6 ] assessed potential miRNA-disease interactions through a miRNA-miRNA functional similarity network that was constructed based on the similarity of miRNA-associated diseases. (biomedcentral.com)
Functional connections between miRNA targets and disease genes could be obtained via PPI network. (biomedcentral.com)
We show at cellular and target organ levels that network connectivity and functional imbalances revert to normal levels upon epichaperome inhibition. (nature.com)
Although a number of approaches have been used to predict gene functions and interactions, tools that analyze the essential coordination of functional components in cellular processes still need to be developed. (biomedcentral.com)
In this work, we present a new approach to study the cooperation of functional modules (sets of functionally related genes) in a specific cellular process. (biomedcentral.com)
A cooperative module pair is defined as two modules that significantly cooperate with certain functional genes in a cellular process. (biomedcentral.com)

Our study reveals a sex-dependent effect of EO diet in both tissues, and an influence on the expression of genes mainly involved in immune, inflammatory and stress pathway. (biomedcentral.com)
The changes in the G1-to-S cell cycle pathway showed that 1,25(OH) 2 D 3 down-regulates the genes influencing the G1-to-S phase transition. (biomedcentral.com)
Pathway- and network-based approaches are meaningful for the integrated analysis of these two types of omics data. (biomedcentral.com)
The present study demonstrates how pathway analysis can be combined with network analysis to perform an integrated analysis of transcriptomics and microRNA-omics data. (biomedcentral.com)
The integrative analysis uses two widely adopted open source tools for pathway and network analysis: PathVisio (Kutmon et al. (biomedcentral.com)
In the present study, we will combine pathway- and network-based methods to decipher the regulatory action of 1,25(OH) 2 D 3 in prostate cancer cells on mRNA and microRNA level. (biomedcentral.com)

Gene co-expression networks are usually constructed using datasets generated by high-throughput gene expression profiling technologies such as Microarray or RNA-Seq. (wikipedia.org)
Few nutrigenomics studies have used a high-throughput RNA-Sequencing (RNA-Seq) approach, despite great potential of RNA-Seq data in gene expression quantification and in co-expression network analyses. (biomedcentral.com)

Nutrigenomics investigations represent innovative approaches in understanding the relation between diet effect and gene expression related to the animal performance. (biomedcentral.com)
An especially uncharted territory is the integration of statistical and network-based approaches for studying global lipidome changes. (mdpi.com)
Herein, we used bioinformatic approaches to analyze the transcriptome datasets from two different accessions Viroflay and Kashan at two vegetative and reproductive stages to reveal novel lncRNAs and the construction of the lncRNA-mRNA co-expression network. (biomedcentral.com)
Using cancer as an example, we review how network biology can facilitate system-wide approaches to identify targeted small molecule inhibitors. (biomedcentral.com)
SYSTEMCERV, Systems biology approaches to cervical pre-cancer and cancer, is a SME targeted collaborative research project funded through the European Union Seventh Framework Programme Health programme [Grant number 306037]. (europa.eu)

Importantly, multiple genomic innovations including gene losses, independent contraction and expansion of specific gene families and their associated regulatory networks likely moulded the evolution of the nautilus pinhole eye. (nature.com)
In the study of genomic cis -regulatory elements, generation of mice featuring transgenic reporters or cis -regulatory element knockout remains the standard approach. (mdpi.com)

Modules or the highly connected subgraphs in gene co-expression networks correspond to clusters of genes that have a similar function or involve in a common biological process which causes many interactions among themselves. (wikipedia.org)
This phase is characterized by the development of methods for biological design of plant varieties, including transformation and gene editing techniques directed toward causal loci. (springer.com)
To determine the scope and impact of agency across diverse levels of biological organization, from gene networks to cells, organs, individuals and social groups. (agencyinlivingsystems.com)
Experimentally characterized genetic interaction networks in model organisms provide important insights into relationships between different biological functions. (researchgate.net)
In the first case study, we observed that the real biological networks were most sensitive to overexpression/state-flip and edge-addition/-reverse mutations among node-based and edgetic mutations, respectively. (researchgate.net)
The type of biological networks that studies gene coexpression, known as Gene Coexpression Networks, consist of an undirected graph depicting genes and their coexpression relationships. (mdpi.com)
The ability to monitor the change in expression patterns over time, and to observe the emergence of coherent temporal responses using gene expression time series, obtained from microarray experiments, is critical to advance our understanding of complex biological processes. (biomedcentral.com)
The identification of co-regulated genes, involved in specific biological processes, remains one of the main avenues open to researchers studying gene regulatory networks. (biomedcentral.com)
Time series gene expression data, obtained from microarray experiments performed in successive instants of time, can be used to study a wide range of biological problems [ 1 ], and to unravel the mechanistic drivers characterizing cellular responses [ 2 ]. (biomedcentral.com)
9 ] have also described the use of biclustering as critical to identify the dynamics of biological systems as well as the different groups of genes involved in each biological process. (biomedcentral.com)

The catalog of driver genes involved in the development of several malignancies has grown in recent years, as a result of whole-exome and whole-genome analyses of cohorts of tumors, mainly within the framework of large international consortia [ 3 , 4 ]. (biomedcentral.com)
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)
Survival and gene signature analyses were performed on hepatocellular carcinoma (HCC) data. (preprints.org)

Recently, co-expression networks are used to analyze single cell RNA-Seq data, in order to better characterize the gene to gene relations in a cohort of cells from a specific cell type. (wikipedia.org)

Gene coexpression analysis refers to the en masse discovery of coexpressed genes from a large variety of transcriptomic experiments. (mdpi.com)
We present results in real data showing the effectiveness of e -CCC-Biclustering and its relevance in the discovery of regulatory modules describing the transcriptomic expression patterns occurring in Saccharomyces cerevisiae in response to heat stress. (biomedcentral.com)

Park H, Imoto S , Miyano S. Comprehensive information-based differential gene regulatory networks analysis (CIdrgn): Application to gastric cancer and chemotherapy-responsive gene network identification. (google.com)

We also observed that most diseases in the same co-regulated module tended to belong to the same disease category, indicating that these diseases might share similar miRNA regulatory mechanisms. (biomedcentral.com)
For the occurrence of floral transition at an opportune time, these regulatory mechanisms integrate varied environmental cues with the endogenous physiological ones. (jabonline.in)
In this context, biclustering algorithms have been recognized as an important tool for the discovery of local expression patterns, which are crucial to unravel potential regulatory mechanisms. (biomedcentral.com)

These domestication traits likely consisted of a few major genes controlling dramatic changes in crop physiology, as is suggested by genetic studies comparing maize to its ancestor teosinte (Doebley et al. (springer.com)
then, we tested if variants surrounding those genes were enriched in disease variants with ancestry-specific effect sizes by leveraging ancestry-matched GWAS of 31 diseases and complex traits (average N = 90K and 267K in EAS and EUR, respectively). (bvsalud.org)
However, the development of cultivars to increase spinach production is positively related to other morphological traits such as plant height and bolting, induced by long-day exposure. (biomedcentral.com)

In addition, it can be used to predict genetic interactions [3] by comparing the sensitivity value of a double gene mutation from the value predicted from single mutations, and reveal the network intervention [4] by applying the state-flip mutation subject to a single gene. (researchgate.net)
This could reveal genes that work together, helping to unravel their roles inside cells. (elifesciences.org)
Brief summaries describing the function of each gene's product are of great value to the research community, especially when interpreting genome-wide studies that reveal changes to hundreds of genes. (stanford.edu)

Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties. (stanford.edu)
Network biology has been widely used in molecular biology and genetics, where several network properties have been shown to be functionally important. (biomedcentral.com)
The mammalian immune system is a dynamic multiscale system composed of a hierarchically organized set of molecular, cellular, and organismal networks that act in concert to promote effective host protection against pathogens. (biorxiv.org)
This mechanism also applies to hematopoietic cells transformed by other HOX genes, including CDX2, which is highly expressed in a majority of acute myeloid leukemias, thus providing a molecular approach based on GSK-3 inhibitory strategies to target HOX-associated transcription in a broad spectrum of leukemias. (stanford.edu)
Recently, numerous gene expression and molecular interaction experiments have been reported in Saccharomyces cerevisiae , and these have enabled systematic studies. (biomedcentral.com)

We used this information to develop the BrassicaEDB, including eFP, Treatment, Coexpression, and SRA Project modules based on gene expression profiles and Gene Feature, qPCR Primer, and BLAST modules based on gene sequences. (preprints.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)

Liu Y, Zhang YZ, Imoto S . Microbial Gene Ontology informed deep neural network for microbe functionality discovery in human diseases. (google.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 date, only a few predictors are available for identifying general bacterial promoters with limited predictive performance.In this study, we developed TIMER, a Siamese neural network-based approach for identifying both general and species-specific bacterial promoters. (giwebb.com)
Specifically, TIMER uses DNA sequences as the input and employs three Siamese neural networks with the attention layers to train and optimize the models for a total of 13 species-specific and general bacterial promoters. (giwebb.com)

However, the comparative transcriptome analysis of two spinach accessions with different bolting times identified genome-wide gene expression profiling and large-scale discovery of flowering-related genes from vegetative and reproductive leaves [ 13 ]. (biomedcentral.com)

Using the reference-free alignment across 241 mammalian genomes produced by the Zoonomia Consortium, we charted evolutionary trajectories for 0.92 million human candidate cis-regulatory elements (cCREs) and 15.6 million human transcription factor binding sites (TFBSs). (bvsalud.org)
Nautilus shows a compact, minimalist genome with few encoding genes and slow evolutionary rates in both non-coding and coding regions among known cephalopods. (nature.com)

One step in this direction is thus to understand exactly which downstream genes and cellular processes become affected in the outcome of driver alterations. (biomedcentral.com)
Genes near constrained elements perform fundamental cellular processes, whereas genes near primate-specific elements are involved in environmental interaction, including odor perception and immune response. (bvsalud.org)

In this work, we propose e -CCC-Biclustering, a biclustering algorithm that finds and reports all maximal contiguous column coherent biclusters with approximate expression patterns in time polynomial in the size of the time series gene expression matrix. (biomedcentral.com)
The advantages of biclustering in the discovery of local expression patterns, described by a coherent behavior of a subset of genes in a subset of the conditions under study, have been extensively studied and documented [ 4 - 8 ]. (biomedcentral.com)
We determined the expression patterns of 101,040 genes via FPKM analysis and displayed the results using the eFP browser. (preprints.org)

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)

Using network based analysis, different clusters of co-expressed genes that were highly correlated to the diet were detected in males vs. females, in agreement with DE analysis. (biomedcentral.com)

By systematically analyzing the global properties of the miRNA-disease network, we found that only a small number of miRNAs regulated genes involved in various diseases, genes associated with neurological diseases were preferentially regulated by miRNAs and some immunological diseases were associated with several specific miRNAs. (biomedcentral.com)
Identification of disease-related miRNAs will aid in the pathological classification of diseases and help to formulate individualized treatment regimes [ 3 ]. (biomedcentral.com)
However, this method is not applicable to diseases that have no known related miRNAs. (biomedcentral.com)
Here, we discuss how such methodology can be useful to translational biomedical research, where scientists traditionally focus on one or a small set of genes, diseases, and drug candidates at any one time. (biomedcentral.com)
From the clinicians' point of view, it is necessary to bridge the gap between theoretical network biology and practical biomedical research, in order to improve the diagnosis, prevention, and treatment of the world's major diseases. (biomedcentral.com)

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)
In particular, the results show the advantage of considering approximate patterns when compared to state of the art methods that require exact matching of gene expression time series. (biomedcentral.com)

Type III secretion system effectors form robust and flexible intracellular virulence networks. (tau.ac.il)

whereas in a gene regulatory network (GRN) a directed edge connects two genes, representing a biochemical process such as a reaction, transformation, interaction, activation or inhibition. (wikipedia.org)

We observed that ancDE genes tend to be cell-type-specific, to be enriched in genes interacting with the environment, and in variants with ancestry-specific disease effect sizes, suggesting the impact of shared cell-type-specific gene-by-environment (GxE) interactions between regulatory and disease architectures. (bvsalud.org)

Moreover, after 1,25(OH) 2 D 3 treatment the gene expression in several cancer-related processes was down-regulated. (biomedcentral.com)
2011 ) clearly showed that 1,25(OH) 2 D 3 can modulate gene and microRNA profiles in LCNaP cells and affects processes involved in cell cycle arrest, calcium ion homoeostasis and phosphoinositide-mediated signalling. (biomedcentral.com)
Optimal functioning of neuronal networks is critical to the complex cognitive processes of memory and executive function that deteriorate in Alzheimer's disease (AD). (nature.com)
Guidelines are constantly being refined to outline the most practical and appropriate screening processes to minimize donor-related infections. (medscape.com)

High expression of genes that positively correlated with overexpression of DPP4, DPP8, and DPP9 were associated with very poor survival in HCC. (preprints.org)

Network representations have been widely used in physics and social science for decades, and are now among the most frequently used tools in systems biology. (biomedcentral.com)
Cell cycle gene expression networks discovered using systems biology: Significance in carcinogenesis. (genenetwork.org)

Through the service and infrastructure activities the group has also been involved in several other projects, like research on prokaryotes, including oil well metagenomics, biodegradation, pathogenic bacteria, and characterization of novel bacterial genes. (ntnu.edu)

Butte and Kohane used this approach later with mutual information as the co-expression measure and using gene expression data for constructing the first gene co-expression network. (wikipedia.org)
Next, we find that factors from FactorGo are more enriched with relevant tissue-specific annotations than those identified by tSVD (p = 2.58E-10) and validate our approach by recapitulating brain-specific enrichment for BMI and the height-related connection between reproductive system and muscular-skeletal growth. (bvsalud.org)
In this work, we propose a new approach to identifying condition-related cooperative interactions, and importantly, we establish a cell cycle-specific cooperation module network. (biomedcentral.com)
Recently, biclustering [ 4 - 6 ], a non-supervised approach that performs simultaneous clustering on the gene and condition dimensions of the gene expression matrix, has been shown to be remarkably effective in a variety of applications. (biomedcentral.com)
This approach yielded 1,800 gene snapshots within a three month period. (stanford.edu)

In this study, we performed an integrative network-based analysis using a publicly available data set studying the role of 1,25-dihydroxyvitamin D 3 (1,25(OH) 2 D 3 ) in prostate cancer cells on mRNA and microRNA level. (biomedcentral.com)
For some years we have also built up a cancer-related research activity, in particular on colorectal cancer (CRC) and prostate cancer (PCa). (ntnu.edu)

RMut can be used to analyze large-scale networks because it is implemented in a parallel algorithm using the OpenCL library. (researchgate.net)
An in-house algorithm predicts and ranks expert authors for each gene based on the data within FlyBase and extracts their email addresses from papers that we have curated. (stanford.edu)

Here we use cellular and animal models as well as human biospecimens to show that AD-related stressors mediate global disturbances in dynamic intra- and inter-neuronal networks through pathologic rewiring of the chaperome system into epichaperomes. (nature.com)

Shortening or removal of mRNA poly(A) tails (deadenylation) represses gene expression in eukaryotes. (elifesciences.org)

A gene co-expression network (GCN) is an undirected graph, where each node corresponds to a gene, and a pair of nodes is connected with an edge if there is a significant co-expression relationship between them. (wikipedia.org)
In addition, random walk analysis is a global network distance measurement that is usually used to measure similarities between the nodes of a network, and previous reports have demonstrated its effectiveness in candidate disease gene prioritization [ 9 , 10 ]. (biomedcentral.com)
We first give an overview of network representation frequently used in biology: what nodes and edges represent, and review its application in preclinical research to date. (biomedcentral.com)

Genetic interaction can be defined as a deviation of the phenotypic quantitative effect of a double gene mutation from the effect predicted from single mutations using a simple (e.g., multiplicative or linear additive) statistical model. (researchgate.net)
We demonstrate this methodology on three published models for each of which we derive the genetic interaction networks and analyze their properties. (researchgate.net)
There have been many in silico studies based on a Boolean network model to investigate network sensitivity against gene or interaction mutations. (researchgate.net)

a snoRNA orthological gene database providing comprehensive information about snoRNAs, snoRNA gene loci and target RNAs. (flybase.org)
Quantitative Trait Loci and Candidate Genes for Neutrophil Recruitment in Sterile Inflammation Mapped in AXB-BXA Recombinant Inbred Mice. (genenetwork.org)

In this context, several machine learning methods have been used in the analysis of gene expression data [ 3 ]. (biomedcentral.com)

ABSTRACT {Promoters are DNA regions that initiate the transcription of specific genes near the transcription start sites. (giwebb.com)

For instance, in a microarray experiment the expression values of thousands of genes are measured for several samples. (wikipedia.org)

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)

SAM's phase conversion to the reproductive stage is demonstrated by morphological changes accompanied by an alteration in gene expression [ 3 ]. (jabonline.in)

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 expressed3

Molecules5

Phenotypes5

Proteins5

Pathways5

Transcriptional6

Hundred genes involved1

Chromatin6

Sets of genes2

Regulation6

Among genes1

Protein9

Target genes1

Functional7

Pathway6

High-throughput2

Approaches5

Genomic2

Biological10

Analyses3

Single cell RNA-Seq data1

Transcriptomic2

Differential gene1

Mechanisms3

Traits3

Reveal3

Molecular5

Coexpression1

Rewiring of gene expression1

Deep neural network1

Neural3

Genome-wide1

Evolutionary2

Cellular processes2

Expression patterns3

Potential regulatory1

Clusters1

Diseases5

Patterns2

Intracellular1

Biochemical1

Tend1

Processes4

Overexpression1

Systems Biology2

Bacterial1

Approach5

Prostate cancer2

Algorithm2

Neuronal1

Eukaryotes1

Nodes3

Interaction3

Loci2

Analysis of gene1

Abstract1

Microarray1

Transcription factors1

Reproductive1