Reconstruct gene expression regulation bioinformatics gene regulatory networks. Medical search. Frequent questions

We validate our approach in two ways: by demonstrating that it accurately models expression data and by demonstrating that our reconstructed model is similar to previously-published models of transcriptional regulation of the cell cycle. (biomedcentral.com)
Our regression-based approach allows us to build a general model of transcriptional regulation of the yeast cell cycle that includes additional factors and couplings not reported in previously-published models. (biomedcentral.com)
A variety of methods have been developed that utilize both expression data and transcription factor binding data to model transcriptional regulation. (biomedcentral.com)
Previous studies have demonstrated that lncRNAs act as one of the molecular mechanisms for the post-transcriptional regulation and modulation of protein function. (biomedcentral.com)
The precision of transcriptional regulation is made possible by the specificity of physical interactions between transcription factors and their cognate binding sites on DNA. (biomedcentral.com)
Transcriptional regulation is modulated by a complex network of interactions between regulatory proteins and their binding targets on DNA. (biomedcentral.com)
We have demonstrated the use of these methods to identify potential new and known targets for engineering improved growth and IgG production, as well as the general observation that CHO cells seem to have less strict transcriptional regulation of protein secretion than healthy mouse cells. (biomedcentral.com)

A fundamental problem in network biology is the reconstruction of a subnetwork that underlies a process of interest by efficiently connecting a set of implicated proteins (e.g. derived by some genome-wide screen) in a network of physical interactions. (biomedcentral.com)
Here we tackle this multiple-condition scenario, where the reconstructed subnetwork should explain in a coherent manner multiple experiments driven by the same set of proteins (referred to here as anchor proteins) while producing different sets of affected proteins, or terminals . (biomedcentral.com)
Although, several Fe/S cluster proteins and their roles have been identified in Leishmania, some of the components of how T[SH] 2 is involved in the regulation of Fe/S proteins remains to be explored. (frontiersin.org)
In pursuit of this aim, a systems biology approach was undertaken to get an insight into the overall picture to unravel how T[SH] 2 synthesis and reduction is linked with the regulation of Fe/S cluster proteins and controls the redox homeostasis at a larger scale. (frontiersin.org)
The gene network of ADHD included 599 genes/proteins and 148,978 interactions, while that of dyslexia included 167 genes/proteins and 27,083 interactions. (biomedcentral.com)
When the ANDSystem and GeneCards data were combined, a total of 213 genes/proteins for ADHD and dyslexia were found. (biomedcentral.com)
It unravels the secrets of genes, which are segments of genetic material, such as DNA, containing instructions for building proteins and controlling various cellular processes. (freescience.info)
By investigating nucleic acids like DNA and RNA, as well as proteins and other biomolecules, scientists gain insights into gene expression, protein synthesis, gene transfer, and more. (freescience.info)
By studying genes, proteins, and other molecules within cells, biologists can identify genetic mutations responsible for inherited disorders. (freescience.info)
The actual protein traffic is regulated by the organised action of numerous structural and regulatory proteins. (biomedcentral.com)
Additionally, a number of regulatory proteins are dedicated to secure the proper response of the protein secretion pathway to environmental changes, nutrient availability, stress conditions, as well as differentiation signals [ 24 ]. (biomedcentral.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)
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)

One great challenge of genomic research is to efficiently and accurately identify complex gene regulatory networks. (tsinghua.edu.cn)
REDUCE requires only a single expression dataset and makes use of the entire genomic dataset (both signal and background) to assess the significance of individual motifs. (biomedcentral.com)
Furthermore, we show that integration of two separate phylogenomic pipelines yields increased accuracy, suggesting that their sources of error are independent, and finally, we leverage the resulting annotation of homologous genes to study the functional impact of gene duplication and loss in the context of rich gene expression and functional genomic datasets of the modENCODE, mouse ENCODE, and human ENCODE projects. (biorxiv.org)
The very premise of using model organisms to inform human biology relies on the fact that many biological processes, and the underlying genomic elements that encode them, are frequently conserved across large evolutionary distances, especially for protein-coding genes. (biorxiv.org)
The most rigorous and general method for creating a comparative genomic mapping of functionally-equivalent genes across species is through the use of phylogenetics to infer evolutionary relationships. (biorxiv.org)
By employing our mouse RECON to the CHO-K1 genome in a comparative genomic approach, we could reconstruct the protein secretory pathway of CHO cells counting 764 CHO components. (biomedcentral.com)

Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). (uthscsa.edu)

These typically involve metabolic networks or cell signaling networks. (wikipedia.org)
Integrated multi-omics analyses and genome-wide association studies reveal prime candidate genes of metabolic and vegetative growth variation in canola. (ipk-gatersleben.de)
Functional annotation resulted in the identification of almost all genes involved in diverse lipid-metabolic pathways, including the novel fatty acid desaturase/epoxygenase, diacylglycerol acyltransferase 1 and 2, and phospholipid:diacylglycerol acyltransferases. (researchsquare.com)
Synopsis： Participants will learn how to set up computer models of biological systems (e.g. metabolic or signalling networks) using experimental kinetic data and how to simulate them in different systems biology platforms. (aeplan.co.jp)
However, there are few well-defined biochemical reactions in protein secretion, and metabolic models fail to capture all of the regulatory processes and protein interactions. (biomedcentral.com)
Moreover, genetic and simple obesity share similar structural and functional features of dysbiosis, such as higher production of toxins with known potential to induce metabolic deteriorations (e.g. trimethylamine-N-oxide and indoxyl sulphate), higher abundance of genomes containing genes coding enzymes involved in the production of these toxic co-metabolites and higher abundance of pathways for biosynthesis of bacterial antigens (such as endotoxin) [13-15]. (deepdyve.com)

By functional network, we mean a network such that an experimental perturbation will likely alter the dynamical phenotype of the network. (biomedcentral.com)
In GWAS experiments, we integrate multi-omic data to identify the most likely gene-mechanism-phenotype paths. (ipk-gatersleben.de)
Gene regulatory network is the architecture of transcription factors (TFs) and their gene targets, which help in controlling their expression as required by a phenotype during various environmental perturbations. (bvsalud.org)
Pooled CRISPR screen is a promising tool in drug targets or essential genes identification combined with different phenotype readouts. (hep.com.cn)
On the other hand, environmental factors have been reported to modulate epigenetic modifications and thereby affect gene expression and phenotype [ 11 , 12 ]. (researchsquare.com)

However, it is crucial to make inference of genetic regulatory networks from gene expression profiles and protein interaction data for systems biology. (tsinghua.edu.cn)
Reverse-engineering regulatory networks is one of the central challenges for computational biology. (biomedcentral.com)
Articles from this conference have also been published in BMC Bioinformatics , BMC Medical Genomics , BMC Medical Informatics and Decision Making and BMC Systems Biology . (biomedcentral.com)
Indeed, the focus on the dynamics of the studied systems is the main conceptual difference between systems biology and bioinformatics. (wikipedia.org)
Indeed, the network inference problem persists in systems biology, despite an abundance of regulatory evidence in the form of TF binding experiments, genetic screens for candidate nodes, and mutant expression profiling experiments. (biomedcentral.com)
Bioinformatics is a distinct science from biological computation , the latter being a computer science and computer engineering subfield using bioengineering and biology to build biological computers , whereas bioinformatics simply uses computers to better understand biology. (ind.in)
Bioinformatics is similar to computational biology and has similar aims to it but differs on scale: whereas bioinformatics works with basic biological data (e.g. (ind.in)
Recent advances in genomics and computational biology are enabling construction of large-scale models of gene-regulatory networks. (biomedcentral.com)
Deep learning has emerged as a powerful tool for solving complex problems, including reconstruction of gene regulatory networks within the realm of biology. (bvsalud.org)
With the increasing availability of high-throughput data, network biology has become the method of choice for filtering, interpreting and representing these data. (biomedcentral.com)
Thanks to molecular biology techniques like DNA sequencing and gene expression analysis, biologists have made significant strides in understanding genetics and genomics. (freescience.info)
Molecular biology techniques are instrumental in designing safe and effective gene delivery systems for the manipulation of DNA and genome. (freescience.info)
The elucidation of the cell biology of the secretory machinery is of great importance, as it drives protein expression for biopharmaceutical industry, a 140 billion USD global market. (biomedcentral.com)
A particularly useful tool is a network reconstruction - a compilation of a list of the known components in a specific area of cell biology and the interaction of said components. (biomedcentral.com)
Students have an opportunity to integrate training in bioinformatics with chemistry and biology. (ucsd.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)
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)
Using cancer as an example, we review how network biology can facilitate system-wide approaches to identify targeted small molecule inhibitors. (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)
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)
In this review, we aim to improve the understanding of challenges in biomedical research and establish a common ground between clinicians and systems biologists to further promote the application of network biology in translational medicine. (biomedcentral.com)

Most recently, several studies have developed inference methods based on nonlinear ordinary differential equations (ODEs) for the chemical kinetics and a Bayesian formalism on the network structure [ 24 - 27 ]. (biomedcentral.com)
A Bayesian approach to reconstructing genetic regulatory networks with hidden factors. (ucsd.edu)

Estimation of genewise variance arises from two important applications in microarray data analysis: selecting significantly differentially expressed genes and validation tests for normalization of microarray data. (tsinghua.edu.cn)
The simplest models identify transcription factor binding sites (or cis regulatory motifs) that are over-represented in the promoters of differentially-expressed genes [ 9 ]. (biomedcentral.com)
Over the past decade, gene expression data has been widely used for reconstructing dGRN by computing correlations between the differentially expressed genes (DEGs). (bvsalud.org)
GSEA measures the enrichment of annotated gene sets that represent biological processes for differentially expressed genes (DEGs) in clinical samples. (molcells.org)

This study will develop a new approach to reconstruct time delay Boolean networks as a tool for exploring biological pathways. (tsinghua.edu.cn)
In practice, the network dynamically changes over time or conditions, calling for reconstructions that can integrate such data to a coherent picture of the activity dynamics of the underlying pathways. (biomedcentral.com)
Model organisms can serve the biological and medical community by enabling the study of conserved gene families and pathways in experimentally-tractable systems. (biorxiv.org)
Correspondingly, most cancer signaling pathways seem to converge on one or more TFs, termed "master regulators" (MRs) [ 4 ], which direct tumor development, progression, and metastasis through hierarchical control of gene expression patterns. (aging-us.com)
In this study, we have developed and evaluated a computational approach, known as Mechanism and Drug Miner (MD-Miner), using a network-based computational approach to predict effective drugs and reveal potential drug mechanisms of action at the level of signaling pathways. (biomedcentral.com)

In contrast, here we focus on reverse-engineering the network of relationships among transcription factors that regulate the cell cycle in S. cerevisiae . (biomedcentral.com)
We have developed a technique to reverse-engineer networks of the time-dependent activities of transcription factors that regulate the cell cycle in S. cerevisiae . (biomedcentral.com)
Does the binding of a specific transcription factor to the promoter of a gene regulate its expression? (biomedcentral.com)
These networks consist of transcription factors and their associations with genes they regulate. (bvsalud.org)
We discuss the possibility that C. virgata phytohormone signaling and biosynthesis genes regulate early germination and growth advantages. (frontiersin.org)
Knockdown experiments of FOXM1 and MYBL2 suggest that these factors regulate genes involved in controlling cell cycle progression and cell division. (prolekarniky.cz)

The primary goal of bioinformatics is to increase the understanding of biological processes. (ind.in)
Growth is regulated by gene expression variation at different developmental stages of biological processes such as cell differentiation, disease progression, or drug response. (bvsalud.org)
Additionally, it was revealed that the most relevant genes are involved in biological processes related to signal transduction, positive regulation of transcription from RNA polymerase II promoters, chemical synaptic transmission, response to drugs, ion transmembrane transport, nervous system development, cell adhesion, and neuron migration. (biomedcentral.com)
Mathematical modeling, particularly when combined with dynamical systems theories, is a valuable tool for understanding how gene regulatory networks (GRNs) influence biological processes. (cbirt.net)
Gene set enrichment analysis (GSEA) is a popular tool to identify underlying biological processes in clinical samples using their gene expression phenotypes. (molcells.org)

It uses a local approximation to the system of differential equations that relies on sparse priors, which localizes uncertainty and renders the algorithm scalable to complex networks. (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)
Then, I collect a list of downstream targets of the all driver transcription factors (TFs), and identify which of them exhibit a differential expression upon alterations of driver transcription factors. (biomedcentral.com)
The researchers from MIT Cambridge, USA, and collaborators at the University of Pittsburgh School of Medicine, present DYNAMO - an analytical framework that infers absolute RNA velocity, reconstruct continuous vector fields that predict cell fates, uses differential geometry to obtain underlying regulations, and anticipates optimal reprogramming routes and perturbation results. (cbirt.net)

The protocol focuses on the genome-wide prediction of regulatory interactions between transcription factors and genes, leveraging publicly available gene expression data in conjunction with well-established benchmarks. (bvsalud.org)
We used the RNAseq data to update the existing grape gene prediction with 2,258 new coding genes and 3,336 putative long non-coding RNAs. (biomedcentral.com)
The reverse gene set enrichment analysis (i.e., connectivity mapping) approach and its variants have been widely and successfully used for drug prediction. (biomedcentral.com)

To date, our understanding of mammalian gene regulation has been hampered by the difficulty of directly measuring in vivo binding of large numbers of transcription factors to DNA. (nih.gov)
We apply iChIP to reconstruct the physical regulatory landscape of a mammalian cell, by building genome-wide binding maps for 29 transcription factors (TFs) and chromatin marks at four time points following stimulation of primary dendritic cells (DCs) with pathogen components. (nih.gov)
Using over 180,000 TF-DNA interactions in these maps, we derive an initial dynamic physical model of a mammalian cell regulatory network. (nih.gov)
Our method, which allowed us to map routinely temporal binding profiles of dozens of TFs, provides a foundation for future understanding of the mammalian regulatory code. (nih.gov)
Finally, we use an atlas of transcription data in a mammalian circadian system to illustrate how the method can be used for discovery in the context of large complex networks. (biomedcentral.com)
One of the best examples of a large functional network is the mammalian circadian oscillator, for which the current core network contains about 30 nodes. (biomedcentral.com)
We study a median of 16,101 genes across 2 mammalian genomes (human, mouse), 12 Drosophila genomes, 5 Caenorhabditis genomes, and an outgroup yeast genome, and demonstrate that accurate inference of evolutionary relationships and events across these species must account for frequent gene-tree topology errors due to both incomplete lineage sorting and insufficient phylogenetic signal. (biorxiv.org)
Despite the efforts to perform whole-cell simulations of bacteria, recreating the vector field that indicates the temporal variations of a genome-wide expression state in mammalian cells from experimental data remains a significant challenge. (cbirt.net)

The development of high-throughput technologies provides numerous experimental data such as DNA sequences, protein sequence, and RNA expression profiles makes it possible to study interactions and regulations among genes or other substance in an organism. (tsinghua.edu.cn)
The reconstruction of gene regulatory network (GRN) from gene expression data can discover regulatory relationships among genes and gain deep insights into the complicated regulation mechanism of life. (biomedcentral.com)

To overcome this shortcoming, we developed network-based GSEA (NGSEA), which measures the enrichment score of functional gene sets using the expression difference of not only individual genes but also their neighbors in the functional network. (molcells.org)

Of these approaches, several have focused on the reconstruction of the cell cycle regulatory network of Saccharomyces cerevisiae . (biomedcentral.com)
These approaches usually work with the logarithm of the expression and binding data, and typically assume a linear or affine relationship between the two. (biomedcentral.com)
As genome-scale measurements lead to increasingly complex models of gene regulation, systematic approaches are needed to validate and refine these models. (biomedcentral.com)
Despite intense work in this area, current algorithmic approaches are largely limited to analyzing a single screen and are, thus, unable to account for information on condition-specific genes, or reveal the dynamics (over time or condition) of the process in question. (biomedcentral.com)
provide an overview on the application of CRISPR screens and bioinformatics approaches to analyzing different types of CRISPR screen data. (hep.com.cn)
Compared with the reverse gene signature based drug repositioning approaches, the proposed method can provide clues of mechanism of action in terms of signaling transduction networks. (biomedcentral.com)
The analytical limitations of over-representation approaches can be overcome by aggregate score approaches, which assign scores to each annotated gene set based on all the gene-specific scores of the member genes. (molcells.org)

Further, many of the TF-DNA interactions at stimulus-activated genes are established during differentiation and maintained in a poised state. (nih.gov)
Functionally, the TFs are organized in a hierarchy of different types: Cell differentiation factors bind most of the genes and remain largely unchanged during the stimulation. (nih.gov)
Motivation: The analysis of RNA-Seq data from individual differentiating cells enables us to reconstruct the differentiation process and the degree of differentiation (in pseudo-time) of each cell. (keio.ac.jp)
Such analyses can reveal detailed expression dynamics and functional relationships for differentiation. (keio.ac.jp)
To further elucidate differentiation processes, more insight into gene regulatory networks is required. (keio.ac.jp)
Composed of multiple constituent enhancers, super enhancers (SEs) are powerful cis-regulatory elements that identify genes that ensure sequential differentiation. (nature.com)
We develop methods that are based in statistics, machine learning, optimization and graph theory to understand how changes in the 3D genome affect cellular outcome such as development, differentiation and gene expression. (ucsd.edu)

We applied SCODE to three single-cell RNASeq datasets and confirmed that SCODE can reconstruct observed expression dynamics. (keio.ac.jp)
We implement the ILP algorithm, MKL , and apply it to two datasets in humans concerning the response to influenza infection and ER export regulation. (biomedcentral.com)
Since strong consensus regarding commonly altered MRs in hepatocellular carcinoma (HCC) is lacking, we generated a compendium of HCC datasets from 21 studies and identified a comprehensive signature consisting of 483 genes commonly deregulated in HCC. (aging-us.com)
Since the expression of genes defining discrete phenotypes is highly coordinated, application of reverse engineering algorithms to transcriptome datasets allows interpreting transcriptional networks by defining MRs and their associated regulons and gene circuits. (aging-us.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)

One interesting feature of our approach is that it provides a coherent framework for modeling both the local motifs (e.g., edges) within the network and the global dynamical behavior of the system. (biomedcentral.com)
Inferring the regulatory network from the high-throughput data needs an algorithmic approach involving statistical analysis. (bvsalud.org)
This paper describes an approach to supply chain network optimization for a petrochemical enterprise. (hse.ru)
Here, we present a phylogenomics-based approach for the identification of orthologous and paralogous genes in human, mouse, fly, and worm, which forms the foundation of the comparative analyses of the modENCODE and mouse ENCODE projects. (biorxiv.org)
An approach for ranking genes implicated in the comorbid condition of the two diseases was proposed. (biomedcentral.com)
The approach is based on ten criteria for ranking genes by their importance, including relevance scores of association between disease and genes, standard methods of gene prioritization, as well as original criteria that take into account the characteristics of an associative gene network and the presence of known polymorphisms in the analyzed genes. (biomedcentral.com)
According to the proposed approach, the genes OPRM1, CHRNA4 and SNCA had the highest priority in the development of comorbidity of these two diseases. (biomedcentral.com)
This work provides a signaling network-based drug repositioning approach. (biomedcentral.com)

Paulien Hogeweg coined the term 'Bioinformatics' in 1970 to refer to the study of information processes in biotic systems. (ind.in)
This definition placed bioinformatics as a field parallel to biophysics (the study of physical processes in biological systems) or biochemistry (the study of chemical processes in biological systems). (ind.in)
To inform each other and human, model organism studies require a complete map of functionally-equivalent genes and processes across species, in order to facilitate mapping of biological and experimental findings across species, but such maps are extremely difficult to obtain experimentally. (biorxiv.org)
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)
Nevertheless, to date, the actual misregulation of genes or processes downstream these cliques has not been systematically proven or exploited with the purpose of identifying them. (biomedcentral.com)
Many of the molecular processes that play a role in the activity and dynamics of the microbiota go beyond species and genic composition and thus, their understanding requires advanced bioinformatics support. (deepdyve.com)
For clinical samples, the general purpose of gene set analysis of genome-wide expression profiles is to identify underlying disease-associated molecular processes, which can facilitate disease diagnosis and therapeutic intervention. (molcells.org)

For example, gene therapy offers promising solutions by delivering functional genes or gene-editing tools directly into affected cells. (freescience.info)
however, because DEGs from the expression dataset may not be functional genes per se but dysregulated genes perturbed by bona fide functional genes. (molcells.org)

The emphasis of these studies has been to model the relationships between transcription factors and their target genes. (biomedcentral.com)
We are working on a toolbox of deep learning algorithms that can elucidate predictive relationships between sequence of non-coding gene regulatory elements, protein-DNA binding events, and expression patterns of their target genes. (ipk-gatersleben.de)

As such, the search for candidate genes related to the comorbid conditions of ADHD and DD can help in elucidating the molecular mechanisms underlying the comorbid condition, and can also be useful for genotyping and identifying new drug targets. (biomedcentral.com)

In particulars, the book covers three important and rapidly advancing topics in biostatistics: analysis of survival and longitudinal data, statistical methods for epidemiology, and bioinformatics. (tsinghua.edu.cn)
Network analysis pinpointed several well-known flowering-related genes such as ELF , COL1 , FLT , and FPF1 and also some putative TFs like MYB, WRKY, GATA, and MADS-box that are important regulators of flowering in spinach and could be potential targets for lncRNAs. (biomedcentral.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)
Another early contributor to bioinformatics was Elvin A. Kabat , who pioneered biological sequence analysis in 1970 with his comprehensive volumes of antibody sequences released with Tai Te Wu between 1980 and 1991. (ind.in)
With the public availability of data tools for their analysis were quickly developed and described in journals such as Nucleic Acids Research which published specialized issues on bioinformatics tools as early as 1982. (ind.in)
Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data. (ind.in)
In this protocol, we have outlined a step-by-step guide for the analysis of DEGs using RNA-Seq data, beginning from data acquisition, pre-processing, mapping to reference genome, and construction of a correlation-based co-expression network to further downstream analysis. (bvsalud.org)
Gene coexpression analysis refers to the en masse discovery of coexpressed genes from a large variety of transcriptomic experiments. (mdpi.com)
The sheer amounts of biological data that are generated in recent years have driven the development of network analysis tools to facilitate the interpretation and representation of these data. (biomedcentral.com)
Focusing on computational and statistical aspects of MR discovery, the ARACNe-MRA (Algorithm for the Reconstruction of Accurate Cellular Networks-Master Regulator Analysis) method has shown competent performance in this regard [ 4 ]. (aging-us.com)
Through integrated analysis, we identified the most common SE-targeted and osteoporosis-related osteogenic gene, ZBTB16 . (nature.com)
To analyze the regulatory mechanism involved in the high growth potential of C. virgata , we performed RNA-seq-based transcriptome analysis and illustrated a comprehensive gene expression map of the species. (frontiersin.org)
Using the ANDSystem tool, the reconstruction and analysis of gene networks associated with ADHD and dyslexia was carried out. (biomedcentral.com)
The application of methods of reconstruction and analysis of gene networks is a powerful tool for studying the molecular mechanisms of comorbid conditions. (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)
As RECONs allow the analysis of gene- or protein-level data in their biological context, they become tools for hypothesis-driven biological discovery [ 34 ]. (biomedcentral.com)
A quantitative analysis of the isoforms indicated that most of the spliced genes have one major isoform and tend to simultaneously co-express a low number of isoforms, typically two, with intron retention being the most frequent alternative splicing event. (biomedcentral.com)
We have ongoing interests in the systems level analysis and reconstruction of regulatory networks, inference of enhancer-promoter contacts, predictive models of gene expression and integration of three-dimensional chromatin structure with one-dimensional epigenetic measurements in the context of cancer, malaria, asthma and several autoimmune diseases. (ucsd.edu)
This project will focus on developing regulatory network inference methods for the joint analysis of gene expression and histone modification data from several different types of tumor infiltrating lymphocytes, which are gathered from a cohort of patients with solid tumors. (ucsd.edu)
Then a co-expressed network analysis was conducted to explore potential asthma-related lncRNAs using WGCNA R package. (researchsquare.com)
Module analysis disclosed 17 genes associated to asthma at distinct level. (researchsquare.com)
Subsequent network analysis based on PCC figured out several key lncRNAs related to asthma, i.e. (researchsquare.com)

Then, we will combine those consistent relationships to reveal the most probable relationship and reconstruct the genetic network. (tsinghua.edu.cn)

Identification of master regulator (MR) genes offers a relatively rapid and efficient way to characterize disease-specific molecular programs. (aging-us.com)

Dynamic binding of transcription factors to DNA elements specifies gene expression and cell fate, in both normal physiology and disease. (nih.gov)
The model utilizes linear regression to first estimate the activities of transcription factors from expression time series and genome-wide transcription factor binding data. (biomedcentral.com)
Using chromatin immunoprecipitation in conjunction with microarrays, it is now possible to measure the binding of many transcription factors to the promoters of most genes, thus elucidating the underlying structure of the transcriptional regulatory network. (biomedcentral.com)
Transcription factors (TFs) drive gene expression programs that shape specific phenotypes [ 3 ], and are frequently dysregulated in cancer [ 4 ]. (aging-us.com)
Here, I focus on driver transcription factors and their connection to tumorigensis in several tumor types through the alteration of the expression of their targets. (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)
We construct intricate molecular networks that serve as the game engines, driving the complex interactions that govern plant life and responses to environmental challenges. (ipk-gatersleben.de)
Thus, MRs comprise typically a small number of TF-encoding genes (and their products) that control a disproportionate level of gene expression, giving rise to distinct molecular phenotypes associated with a particular disease. (aging-us.com)
Comprehensive molecular profiling of lung adenocarcinoma: The cancer genome atlas research network. (prolekarniky.cz)
Gene expression profiling is probably the most accessible strategy for molecular phenotyping of clinical samples. (molcells.org)

Transcriptome data were further confirmed by quantitative real-time PCR for twelve key genes in EFA biosynthesis. (researchsquare.com)
Moreover, our transcriptome map demonstrated the expression profiles of orthologs involved in the biosynthesis of these phytohormones and their signaling networks. (frontiersin.org)

Furthermore, I am able to identify other driver genes that cause tumorigenesis through the alteration of very similar sets of targets. (biomedcentral.com)
In parallel, a drug mechanism of action network is constructed by integrating drug targets and z-score profiles of drug-induced gene expression (pre vs. post-drug treatment). (biomedcentral.com)

Specifically, the patient-specific signaling network is constructed by integrating known disease associated genes with patient-derived gene expression profiles. (biomedcentral.com)
We also observed that NGSEA substantially improved the ability to retrieve known anti-cancer drugs from patient-derived gene expression data using drug-target gene sets compared with another method, Connectivity Map. (molcells.org)

Second, from discontinuous, sparse, and stochastic single-cell observations, they create a universal technique for robustly reconstructing the continuous transcriptomic vector field. (cbirt.net)

Hello darkness, my old friend: 3-KETOACYL-COENZYME A SYNTHASE4 is a branch point in the regulation of triacylglycerol synthesis in Arabidopsis thaliana. (ipk-gatersleben.de)
Recently, deep sequencing of the transcriptome using high-throughput RNA sequencing (RNAseq) increased this estimate showing that more that 60% of intron-containing genes in Arabidopsis are alternatively spliced [ 12 ]. (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)

The refined networks support previously unknown regulatory mechanisms downstream of SOK2 and SWI4 . (biomedcentral.com)

We also have implemented this method on simulated and empirical yeast gene expression data sets. (tsinghua.edu.cn)
Many techniques have been developed to accomplish this by utilizing transcription factor binding data in conjunction with expression data. (biomedcentral.com)
In the future, we plan to apply our technique to reverse-engineer other systems where both genome-wide time series expression data and transcription factor binding data are available. (biomedcentral.com)
To answer these questions, one must analyze the transcription factor binding data in conjunction with expression data collected from multiple conditions. (biomedcentral.com)
Expression data is typically obtained using microarrays that allow monitoring of changes in the transcription of all mRNAs between samples. (biomedcentral.com)
the pluralism of causes and effects in biological networks is better addressed by observing, through quantitative measures, multiple components simultaneously and by rigorous data integration with mathematical models. (wikipedia.org)
Previous methods for network inference from dynamics data may be broadly classified according to the tools involved. (biomedcentral.com)
Beginning with time-series gene expression data, the Local Edge Machine (LEM) seeks to find functional network models capable of generating the dynamic behavior of the data (Fig. 1 ). (biomedcentral.com)
Although time-course data are useful for inferring networks, conventional inference algorithms for such data suffer from high time complexity when the number of samples and genes is large. (keio.ac.jp)
Bioinformatics is an interdisciplinary scientific field that develops methods for storing, retrieving, organizing and analyzing biological data. (ind.in)
Bioinformatics uses many areas of computer science , statistics , mathematics and engineering to process biological data. (ind.in)
We train our algorithms on large resources of genetic variation, DNA binding and gene expression data across multiple species, tissues and treatments. (ipk-gatersleben.de)
Our other focus is are methods for integration of multi-omic data and identification of causal/predictive interactions between genetic variation, gene expression, metabolite levels and emergence of crop quality traits. (ipk-gatersleben.de)
We present fREDUCE, a computational method specialized for the detection of weak or degenerate binding motifs from gene expression or ChIP-chip data. (biomedcentral.com)
fREDUCE is built upon the widely applied program REDUCE, which elicits motifs by global statistical correlation of motif counts with expression data. (biomedcentral.com)
For example, the algorithm REDUCE (Regulatory Element Detection Using Correlation with Expression) avoids subgroup selection in a natural way by genome-wide fitting of motif counts to expression data [ 15 ]. (biomedcentral.com)
REDUCE is a deterministic method that first enumerates oligonucleotides and then identifies words whose occurrence in promoter sequences correlate most strongly with expression data. (biomedcentral.com)
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)
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)
These repositories are majorly used for predicting the complex structure of GRNs either with or without gene expression data. (bvsalud.org)
Here we described and discussed the step-wise procedures to extract the interaction data for a desired set of target-TFs from the JASPAR database, and used that information to infer the network by using the igraph library. (bvsalud.org)
Aside from continuous improvements in technology, more and more bioinformatics methods have been developed to analyze the data obtained by CRISPR screens which facilitate better understanding of physiological effects. (hep.com.cn)

We found that NGSEA outperformed GSEA in identifying pathway gene sets for matched gene expression phenotypes. (molcells.org)
We, therefore, expect that NGSEA will facilitate both pathway interpretation of gene expression phenotypes and anti-cancer drug repositioning. (molcells.org)

Thus we have established the most elaborate reconstruction (RECON) of the functional secretion pathway network to date, counting 801 different components in mouse. (biomedcentral.com)

We use our toolbox to estimate the regulatory impact of structural genetic variation, highlight gene candidates in GWAS studies and design gene editing strategies for gene expression modulation. (ipk-gatersleben.de)

A pair of genes from the same gene family is said to be homologous to each other, and the assumption is that homologous genes are likely to have similar biological functions. (biorxiv.org)

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)
Network representation is frequently used to capture the presence of these molecules as well as their relationship. (biomedcentral.com)

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

Like the Butterfly effect, these somatic mutations lead to a series of regulatory function changes, including gene expression dysregulation. (hep.com.cn)
hypothesized that associations between gene expression and somatic mutations can be translated into the associations between gene expression and mutational signatures for showing the regulation effects between somatic mutation and gene expression dysregulation. (hep.com.cn)
This work reveals the key message that some somatic mutations can lead to gene expression alteration consequences. (hep.com.cn)

Despite the utility of deep learning methods in studying gene expression and regulation, their accessibility remains limited for biologists, mainly due to the prerequisites of programming skills and a nuanced grasp of the underlying algorithms. (bvsalud.org)

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)

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)

Anatomy22

Organisms23

Diseases1

Chemicals and Drugs43

Analytical, Diagnostic and Therapeutic Techniques and Equipment41

Psychiatry and Psychology2

Phenomena and Processes97

Disciplines and Occupations9

Anthropology, Education, Sociology and Social Phenomena1

Information Science36

Health Care12

Transcriptional regulation7

Proteins13

Genomic6

International Conference on1

Metabolic6

Phenotype5

Biology21

Bayesian2

Differentially4

Pathways5

Regulate6

Biological processes5

Differential4

Prediction3

Mammalian8

Among genes2

Individual genes1

Approaches7

Differentiation7

Datasets4

Protein-codin1

Approach8

Processes7

Functional genes2

Target genes2

Candidate genes1

Analysis22

Reveal1

Regulator1

Transcription factors5

Molecular5

Biosynthesis2

Targets2

Patient-derived gene expression2

Transcriptomic1

Arabidopsis2

Chromatin1

Downstream1

Data22

Phenotypes2

Pathway1

Modulation1

Homologous1

Molecules2

Experiments1

Somatic3

Algorithms1

Tumors1

Consist1