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

In particular, they work on mathematical models for analyzing large genomic sequences, especially in the context of next generation sequencing, and data derived from mass spectrometry experiments, for example to detect differential expression of proteins between normal and diseased samples. (mpg.de)
In the past few decades, studies have focused on investigating the genes and proteins responsible for the development and progression of HCC ( 3 ). (spandidos-publications.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)
It may increase expression of viral proteins by acting as the DNA binding partner of a viral transactivator. (cancerindex.org)
It has been found that upon accumulation of unfolded proteins in the endoplasmic reticulum (ER), the mRNA of this gene is processed to an active form by an unconventional splicing mechanism that is mediated by the endonuclease inositol-requiring enzyme 1 (IRE1). (cancerindex.org)
As a largest plant-specific transcription factor family, NAC domain proteins play an important role in plant development and regulation of abiotic stress tolerance. (frontiersin.org)
Genetic and Molecular Regulation of Seed Storage Proteins (SSPs) to Improve Protein Nutritional Value of Oilseed Rape (Brassica napus L.) Seeds. (uni-bielefeld.de)
In this process, mRNA molecules are guided by RNA-binding proteins that control their expression [ 6 ]. (biomedcentral.com)
Programmable DNA binding proteins have emerged as an exciting platform for engineering synthetic transcription factors for modulating endogenous gene expression 5 - 11 . (cdc.gov)

Gene regulatory network inference and gene module regulating virulence in Fusarium oxysporum. (openwetware.org)
We have ongoing interests in the systems level analysis and reconstruction of regulatory networks, inference of enhancer-promoter contacts, predictive models of gene expression and integration of three-dimensional chromatin structure with one-dimensional epigenetic measurements in the context of cancer, malaria, asthma and several autoimmune diseases. (ucsd.edu)
This project will focus on developing regulatory network inference methods for the joint analysis of gene expression and histone modification data from several different types of tumor infiltrating lymphocytes, which are gathered from a cohort of patients with solid tumors. (ucsd.edu)
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)
Previous methods for network inference from dynamics data may be broadly classified according to the tools involved. (biomedcentral.com)
Most recently, several studies have developed inference methods based on nonlinear ordinary differential equations (ODEs) for the chemical kinetics and a Bayesian formalism on the network structure [ 24 - 27 ]. (biomedcentral.com)
We demonstrate the applicability of the learned features for targeted omics inference tasks: transcription factor (TF)-target prediction, integrated omics network (ION) inference, and module identification. (biomedcentral.com)

Hannenhalli's current research focuses on comparative genomics, transcriptional regulation, and evolution. (umd.edu)
No resource currently exists that offers all available high and low-throughput data on transcriptional regulation in Escherichia coli K-12 to easily use both as whole datasets, or as individual interactions and regulatory elements. (microbiologyresearch.org)

The well-known arms-race between TEs and the host genome [5] has resulted in several regulatory pathways, including a combination of various epigenetic mechanisms i.e. (prolekarniky.cz)
Statistical analysis of microarray data might aid gene discovery by revealing pathways related to the target gene and facilitating identification of candidate genes. (bvsalud.org)
What pathways are this gene/protein implicaed in? (cancerindex.org)
Resistance arises by mutation (influencing the target or efflux of the antimicrobial agent) or by the acquisition of resistance genes (encoding antimicrobial or target alteration, or alternate pathways) ( 2 , 3 ). (cdc.gov)

2023. Comparative genomics sheds light on transcription factor-mediated regulation in the extreme acidophilic Acidithiobacillia representatives. (openwetware.org)
Four keynote speakers who are world-renowned leaders in bioinformatics, genomics, systems biology and computational medicine delivered lectures on their cutting-edge research and shared their views and perspectives of their research fields. (biomedcentral.com)
Recent advances in genomics and computational biology are enabling construction of large-scale models of gene-regulatory networks. (biomedcentral.com)
Exploiting the functional genomics and bioinformatics studies paved the way in understanding the relationship between genotype and phenotype of an organism suffering from environmental stress. (intechopen.com)
Studies focused on cancer, in particular using genomics and bioinformatics approaches. (senescence.info)
Genomics has set the basis for a variety of methodologies that produce high-throughput datasets identifying the different players that define gene regulation, particularly regulation of transcription initiation and operon organization. (microbiologyresearch.org)

However, how these factors and microRNAs interact to globally modulate gene expression and mediate oncogenesis is not fully understood. (houstonmethodist.org)
These dCas9-activator fusions targeted to the promoter region of endogenous genes can then modulate gene expression 7 - 11 . (cdc.gov)

CRMs are stretches of DNA, usually 100-1000 DNA base pairs in length, where a number of transcription factors can bind and regulate expression of nearby genes and regulate their transcription rates. (wikipedia.org)
Bari-Jheh is a natural transposon that mediates resistance to oxidative stress by adding cis-regulatory sequences that affect expression of nearby genes. (nature.com)
TEs can contain cis-regulatory sequences that affect the expression of nearby genes. (nature.com)
In this work, we hypothesized that Bari-Jheh could also be affecting the expression of nearby genes by remodeling the local chromatin state. (nature.com)
Hence, although rare, IAP-induced local heterochromatin spreading into nearby genes may influence expression and, in turn, host fitness. (prolekarniky.cz)

Gene regulation is a complex process that involves mechanisms at the DNA sequence level and at the epigenetic level. (nature.com)
Although all these studies strongly suggest that TEs may play a role in gene regulation through different molecular mechanisms, detailed analyses that link changes in expression with fitness effects are needed to conclude that TEs have a functional impact on gene expression. (nature.com)
miRNAs are highly conserved, small, non-coding RNAs that negatively regulate gene expression in vertebrates through multiple mechanisms, such as complimentary base pairing with the 3′-UTR of their target mRNAs, resulting in translational repression, mRNA cleavage and mRNA decay initiated by miRNA-guided rapid deadenylation ( 10 ). (spandidos-publications.com)
Our results elucidating the cross-regulations among NF-κB, p53, and microRNAs provide insights into the complex regulatory mechanisms underlying HNSCC, and shows an efficient approach to inferring gene regulatory programs in biological complex systems. (houstonmethodist.org)
The refined networks support previously unknown regulatory mechanisms downstream of SOK2 and SWI4 . (biomedcentral.com)
These regulatory mechanisms have strong connections with cellular metabolism. (biomedcentral.com)
Omics technologies give access to these regulatory mechanisms and are thus able to provide large amounts of data at each molecular level. (biomedcentral.com)

Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)
These datasets are available in public repositories, such as the Gene Expression Omnibus, or ArrayExpress. (microbiologyresearch.org)
In this paper we present a radical upgrade to more than 2000 high-throughput datasets, processed to facilitate their comparison, introducing up-to-date collections of transcription termination sites, transcription units, as well as transcription factor binding interactions derived from ChIP-seq, ChIP-exo, gSELEX and DAP-seq experiments, besides expression profiles derived from RNA-seq experiments. (microbiologyresearch.org)

"Identifying All of Cancer's Manifestations through Integrated Pan Cancer Analysis" Dr. Josh Stuart presented the recent work of The Pan-Cancer Initiative of The Cancer Genome Atlas (TCGA) Research Network, including the analysis of thousands of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels in order to uncover data-driven tumor subtypes. (biomedcentral.com)
Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapeutics effective in one cancer type to others with a matching genomic profile, and to construct personalized networks for use in developing combinatorial therapy. (biomedcentral.com)
A recent demonstration of the differential expression of miRNAs and their target mRNAs in cancer and the discovery that some miRNAs can function as oncogenes or tumor suppressors have sparked considerable interest in elucidating their role in tumorigenesis ( 5 , 6 ). (spandidos-publications.com)
Recent studies have established that, similar to mutations, methylation-mediated silencing of tumor suppressor genes plays a major role in tumorigenesis. (spandidos-publications.com)
We found that the majority of the predicted p53 targets overlapped with those for NF-κB, suggesting that the two transcription factors exert a concerted modulation on regulatory programs in tumor cells. (houstonmethodist.org)
We experimentally validated our findings by determining expression of the predicted NF-κB and p53 target genes by siRNA knock down, and by examining p53 binding activity on promoters of predicted target genes in the tumor cell lines. (houstonmethodist.org)
And the expression levels of KCNK1/2/4/5/6/7/15 were correlated with the tumor stage. (jcancer.org)
Identification of suppressor genes in deleted regions, determination of promoter hypermethylation and their protein expression in tumor biopsies. (dry-lab.org)

citation needed] Cis-regulatory modules are one of several types of functional regulatory elements. (wikipedia.org)
There are two types of transcription factor inputs: those that determine when the target gene is to be expressed and those that serve as functional drivers, which come into play only during specific situations during development. (wikipedia.org)
Moreover, we find that the distal NDRs are enriched specifically for binding motifs of the pluripotency and germ cell master regulators such as NANOG, SOX17, AP2γ and OCT4 in human FGCs, indicating the existence of a delicate regulatory balance between pluripotency-related genes and germ cell-specific genes in human FGCs, and the functional significance of these genes for germ cell development in vivo . (nature.com)
This project focuses on developing computational tools for better analysis of the wealth of data from chromosome conformation capture assays with the ultimate goal of inferring functional chromatin contacts such as those between enhancers and promoters. (ucsd.edu)
We are particularly interested in the functional components of networks (rather than the most expansive or inclusive network), where the function of the network is manifested by the dynamics of the network. (biomedcentral.com)
By functional network, we mean a network such that an experimental perturbation will likely alter the dynamical phenotype of the network. (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)
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)

Modern high-throughput methods have not solved the problem of identifying disease genes. (bvsalud.org)
Oral squamous cell carcinoma (OSCC) is used as a model disease to show how systems biology can be used successfully to identify and prioritize disease genes. (bvsalud.org)

Liu Y, Zhang YZ, Imoto S . Microbial Gene Ontology informed deep neural network for microbe functionality discovery in human diseases. (google.com)

CREs are vital components of genetic regulatory networks, which in turn control morphogenesis, the development of anatomy, and other aspects of embryonic development, studied in evolutionary developmental biology. (wikipedia.org)
In this study, we extended the analysis of the FANTOM5 Cap Analysis of Gene Expression (CAGE) transcriptome data to focus on understanding the genetic regulators involved in mouse cerebellar development. (ubc.ca)
Conceptually, TWAS is a test for the genetic correlation between cis-regulated gene expression and disease. (ucsd.edu)
However, only half of the genetic regulation of gene expression is expected to be in cis, e.g. by genetic variation within 1 Mb of the gene. (ucsd.edu)
As a result, our ability to identify disease-associated genes via TWAS should substantially improve due to (1) the enhanced identification of genes regulated by genetic variation and (2) the increased accuracy with which we can predict an individual's gene expression. (ucsd.edu)
Towards this goal, we describe an automated procedure for prioritizing genetic perturbations in order to discriminate optimally between alternative models of a gene-regulatory network. (biomedcentral.com)
A curated database of genes associated with dietary restriction in model organisms either from genetic manipulation experiments or gene expression profiling. (senescence.info)
Substantial genetic and biochemical similarities exist between resistance determinants in antimicrobial agent-producing actinomycetes and resistance genes found in gram-positive and gram-negative pathogens ( 6 - 9 ). (cdc.gov)
These results suggest that genetic variations in TNF, TGFB1, PTGS1 and PTGS2 genes contribute to DA susceptibility. (cdc.gov)

The event promoted all attendees to exchange ideas, showcase recent innovative work, and foster interdisciplinary and multidisciplinary research collaborations, and provided education and training opportunities to students and junior investigators in bioinformatics, systems biology, intelligent computing, and computational medicine. (biomedcentral.com)
This chapter demonstrates systems biology approaches to identify candidate genes using public database. (bvsalud.org)
Nils Blüthgen combines subjects such as Systems biology, Gene expression and Cell fate determination with his study of Cell biology. (research.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)

2023. The gene regulatory network of Staphylococcus aureus ST239-SCCmecIII strain Bmb9393 and assessment of genes associated with the biofilm in diverse backgrounds. (openwetware.org)

This gene encodes a transcription factor that regulates MHC class II genes by binding to a promoter element referred to as an X box. (cancerindex.org)

Cis-regulatory elements (CREs) or Cis-regulatory modules (CRMs) are regions of non-coding DNA which regulate the transcription of neighboring genes. (wikipedia.org)
CREs are found in the vicinity of the genes that they regulate. (wikipedia.org)
CREs typically regulate gene transcription by binding to transcription factors. (wikipedia.org)
One cis-regulatory element can regulate several genes, and conversely, one gene can have several cis-regulatory modules. (wikipedia.org)
The most efficient way for an organism to regulate gene expression is at the transcriptional level. (wikipedia.org)
The first class of small RNAs identified were the micro RNAs (miRNAs), which are small (~22 nt) non-coding RNAs that regulate gene expression by base pairing to mRNAs where they direct either mRNA cleavage or repress translation [ 8 ]. (biomedcentral.com)
The regulatory genes primarily the transcription factors that exert their activity by binding to certain cis DNA elements and consequently either up regulated or down regulate to target expression. (scielo.br)
These transcription factors are known as masters regulators because its single transcript regulate more than one gene, in this context the regulon word is fascinating more in compass of transcription factors. (scielo.br)
In general, microRNAs, a class of small (~21 nucleotide) non-coding RNAs, negatively regulate the expression of their target genes. (spandidos-publications.com)
The resulting gene networks indicate that interactions among NF-κB, p53, and the two miRNAs likely regulate progression of HNSCC. (houstonmethodist.org)

Gene Myers is a director as well as a research group leader at the Max Planck Institute of Molecular Cell Biology and Genetics. (mpg.de)
One of the most recent advances in experimental molecular biology is microarrays, which allow researchers to simultaneously monitor the expression levels of thousands of genes. (bvsalud.org)
The system biology approach allows us to rapidly identify disease-causing genes and assess their viability as therapeutic targets. (bvsalud.org)
His scientific interests lie mostly in Cell biology, Signal transduction, Genetics, Regulation of gene expression and Gene. (research.com)
His research links Computational biology with Gene. (research.com)
His Computational biology study incorporates themes from HEK 293 cells, Cell culture, Gene expression, Automated reasoning and Chromosome conformation capture. (research.com)
His Computational biology study combines topics from a wide range of disciplines, such as Transcriptome, Regulation of gene expression, Gene, Drug and Gene regulatory network. (research.com)
His main research concerns Transcriptome, Computational biology, Cell biology, MAPK/ERK pathway and Gene expression. (research.com)
Students have an opportunity to integrate training in bioinformatics with chemistry and biology. (ucsd.edu)
Sridhar Hannenhalli is a professor in the Department of Cell Biology and Molecular Genetics and holds joint appointments in the Center for Bioinformatics and Computational Biology (CBCB) and UMIACS. (umd.edu)
He has served on program committee for numerous bioinformatics conferences and chaired Workshop on Algorithms in Bioinformatics (WABI) and Research in Computational Molecular Biology (RECOMB) conferences. (umd.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)
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)
The BioVis aims to educate, inspire, and engage bioinformatics and biology researchers in state-of-the-art visualization research and visualization researchers in problems in biological data visualization. (iscb.org)

Monitoring gene expression values in different samples using microarray technology is one of the best and most accurate ways to identify disease-causing genes. (bvsalud.org)

To this end, computational approaches such as mathematical modeling and virtual screening are important tools to unveil the dynamics of these signaling networks and identify critical components that could be further explored as therapeutic targets. (bvsalud.org)
As genome-scale measurements lead to increasingly complex models of gene regulation, systematic approaches are needed to validate and refine these models. (biomedcentral.com)

One approach to infer causal genes in disease is a transcriptome-wide association study (TWAS). (ucsd.edu)
We employed this method to infer the gene regulatory networks in HNSCC. (houstonmethodist.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)

These strategies involve rearrangements at the molecular level starting from transcription, regulation of mRNA processing, translation, and protein modification or its turnover. (intechopen.com)
Furthermore, the lncRNA-miRNA-mRNA interactions such as KCNQ1OT1-has-miR-1202-ETS1 were revealed in the present ceRNA network. (biomedcentral.com)
The isoform encoded by the unspliced mRNA, XBP1(U), is constitutively expressed, and thought to function as a negative feedback regulator of XBP1(S), which shuts off transcription of target genes during the recovery phase of ER stress. (cancerindex.org)
We found that TRIM13 mRNA and protein expression was reduced in NSCLC tissues and cell lines in comparison to paired non-cancerous tissues and a human normal bronchial epithelial cell line, respectively. (cancerindex.org)
We found that the mRNA expression of KCNK1, KCNK5, KCNK6, KCNK7, and KCNK15 were significantly higher in thyroid cancer tissues than that in normal tissues, while KCNK2, KCNK4, KCNK9, KCNK16 and KCNK17 mRNA levels were decreased compared to normal tissues. (jcancer.org)
B) In situ hybridization for lefty expression at stage 10 in control, E2a -depleted, and e2a mRNA-injected embryos (red, lacZ lineage tracer). (xenbase.org)

On the methodological side, their research includes work on analysis of biological sequences, analysis and prediction of protein structure and function, analysis of intermolecular interactions and interaction networks, gene and protein expression patterns, and computational drug screening and drug design. (mpg.de)
3DSIG focuses on structural bioinformatics and computational biophysics. (iscb.org)

However, this definition has changed to define cis-regulatory modules as a DNA sequence with transcription factor binding sites which are clustered into modular structures, including -but not limited to- locus control regions, promoters, enhancers, silencers, boundary control elements and other modulators. (wikipedia.org)
The Myers lab is best known for the algorithm in BLAST and the paired-end whole-genome shotgun protocol and assembler-accomplishments in traditional sequence-based bioinformatics. (mpg.de)

In the genus Corynebacterium , AmtR is a key component of the nitrogen regulatory system, and it belongs to the TetR family of transcription regulators. (frontiersin.org)
The goal of this project is to model the natural variation in gene expression across many immune cell types using an already established database at LJI ( https://dice-database.org ) and to identify cell type-specific epigenetic regulators of important immune genes. (ucsd.edu)
This approach is based on matrix decomposition modeling under the joint constraints of sparseness and regulator-target connectivity, and able to integrate gene expression profiling and binding data of regulators. (houstonmethodist.org)
Separately, E2a is necessary to drive transcription of Smad2 /3 target genes, including critical regulators of dorsal cell fate and morphogenesis. (xenbase.org)

Database of human genes associated with cellular senescence. (senescence.info)
100.000 cCREs in total), dispersed within the genome and present in cis-regulatory regions of ~81% of human genes, as calculated following gene enrichment analysis. (mdpi.com)

The interactions between AmtR and the promoter regions of the three operons were confirmed by electrophoretic mobility shift assays (EMSAs). (frontiersin.org)
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)
These relationships may reflect gene co-expression/regulation, protein-protein interactions (PPIs) or information about production or consumption of metabolites [ 14 ]. (biomedcentral.com)

Forkhead box protein M1 (FOXM1) is a key transcription factor (TF) that regulates a common set of genes related to the cell cycle in various cell types. (mdpi.com)
Real-time quantitative PCR (RT-qPCR) analysis and sfGFP (superfolder green fluorescent protein) analysis reveal that AmtR directly and negatively regulates the transcription and expression of crn A, cre T, csh A, and hyu B. A growth test shows that C. glutamicum ATCC 14067 can use creatine or creatinine as a sole nitrogen source. (frontiersin.org)

Scope includes mutations and abnormal protein expression. (cancerindex.org)

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

A single transcription factor may bind to many CREs, and hence control the expression of many genes (pleiotropy). (wikipedia.org)
Cis-regulatory modules are non-random clusters at their specified target site that contain transcription factor binding sites. (wikipedia.org)
Progression to aggressive stages is characterized by overexpression of the transcription factor E2F1 and activation of downstream prometastatic gene regulatory networks (GRNs). (bvsalud.org)
His MAPK/ERK pathway study integrates concerns from other disciplines, such as Cancer research, KRAS and Protein kinase A. In general Genetics study, his work on Transcription factor, Promoter and Codon usage bias often relates to the realm of Trichostatin A and Vorinostat, thereby connecting several areas of interest. (research.com)
This gene product is a bZIP protein, which was also identified as a cellular transcription factor that binds to an enhancer in the promoter of the T cell leukemia virus type 1 promoter. (cancerindex.org)
Finally, the results of ROC curves, immunohistochemical staining, immune cell infiltration and kinase / miRNA / transcription factor regulation showed that KCNK2, KCNK4, KCNK5 and KCNK15 levels could be used as biomarkers for PTC diagnosis. (jcancer.org)

Identifying Stages of Kidney Renal Cell Carcinoma by Combining Gene Expression and DNA Methylation Data. (paperexplained.cn)
Additionally, DNMT1, the DNA methyltransferase that maintains methylation patterns, is aberrantly upregulated in HCC cell lines, and its overexpression is responsible for hypermethylation of the miR-148a promoter. (spandidos-publications.com)
Epigenetic alternations in genomic DNA include cytosine methylation in CpG islands, which usually extend throughout the promoters and the first exons of genes. (spandidos-publications.com)
DNA methylation, which is associated with gene silencing ( 12 ), is carried out by DNA methyltransferases (DNMTs). (spandidos-publications.com)

Furthermore, nucleotide sequences related to the cluster vanHAX are present in this DNA, suggesting that the prolonged use of avoparcin in agriculture led to the uptake of glycopeptide resistance genes by animal commensal bacteria, which were subsequently transferred to humans. (cdc.gov)
The actual origins of acquired resistance genes are unknown, but environmental microbes, including the strains producing antimicrobial agents, are believed to be important sources ( 4 , 5 ). (cdc.gov)

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

Journal Article Genes (Basel) · December 16, 2021 Origins of DNA replication are specified by the ordered recruitment of replication factors in a cell-cycle-dependent manner. (duke.edu)

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)
In FlyBase (the Drosophila genetics database) we have therefore developed a pipeline to obtain such summaries from researchers who have worked extensively on each gene. (stanford.edu)

The most well characterized types of CREs are enhancers and promoters. (wikipedia.org)
The original definition presented cis-regulatory modules as enhancers of cis-acting DNA, which increased the rate of transcription from a linked promoter. (wikipedia.org)
We find 116 887 and 137 557 nucleosome-depleted regions (NDRs) in human and mouse FGCs, covering a large set of germline-specific and highly dynamic regulatory genomic elements, such as enhancers. (nature.com)

Small RNAs have proven to be essential regulatory molecules encoded within eukaryotic genomes. (biomedcentral.com)
These short RNAs participate in a diverse array of cellular processes including gene regulation, chromatin dynamics and genome defense. (biomedcentral.com)
Small RNAs play important roles in many aspects of pre- and post-transcriptional gene regulation, epigenetic modifications, chromosome segregation and genome structure. (biomedcentral.com)
Although the current generation of dCas9-based transcription activators is able to achieve up-regulation of some endogenous loci, the magnitude of transcriptional up-regulation achieved by individual single-guide RNAs (sgRNAs) 12 typically ranges from low to ineffective 8 - 11 . (cdc.gov)

The goal of this research is to identify targets for gene-based therapeutics. (ucsd.edu)
This study aimed to explore the molecular mechanism of osteoarthritis (OA) and provide information about new genes as potential targets for OA treatment. (biomedcentral.com)
A previous bioinformatics analysis indicates that lncRNAs (such as uc.343) and predicted target homeobox gene C8 ( HOXC8 ) are promising therapeutic targets for OA [ 10 ]. (biomedcentral.com)
This study implied that KCNK2, KCNK4, KCNK5 and KCNK15 are potential targets of precision therapy for patients with thyroid cancer and these genes are new biomarkers for the therapeutic target for thyroid cancer. (jcancer.org)
Expression levels of JAK-STAT signalling targets is increased with age, and STAT3 has been implicated in the regulation of self-renewal and stem cell fate in several tissues. (senescence.info)
E2a Is Required for Subsets of Smad2/3 Binding and for Global Patterns of Smad2/3 Target Gene Expression (A) Smad2/3 targets 1,027 distinct genomic regions in control stage 10.5 embryos (yellow) and 1,671 regions in E2a -depleted embryos (blue). (xenbase.org)
E and F) Significant overlap exists between genes that are Smad2/3 targets and genes that are downregulated in E2a -depleted embryos. (xenbase.org)

This gene encodes an ubiquitously expressed, cytosolic form of TrxR, which functions as a homodimer containing FAD, and selenocysteine (Sec) at the active site. (cancerindex.org)
The vanH gene encodes a D‑lactate dehydrogenase that provides the requisite D‑lactate. (cdc.gov)
The third gene, vanA , encodes an ATP-dependent D-Ala-D-Lac ligase. (cdc.gov)

Our goal is to efficiently integrate multi-omics data to study different regulatory aspects of multilayered processes that occur in organisms. (biomedcentral.com)

Explainable Artificial Intelligence as a reliable annotator of archaeal promoter regions. (openwetware.org)

Using this procedure, we evaluate 38 candidate regulatory networks in yeast and perform four high-priority gene knockout experiments. (biomedcentral.com)
First, we use the previously described modeling procedure to generate a library of models corresponding to different gene-regulatory systems in yeast. (biomedcentral.com)

Transcriptome and chromatin immunoprecipitation analysis revealed c-Myc as a new and direct downstream target of XBP1 for regulation of NK cell proliferation. (cancerindex.org)

Mapping all miRNAs to the tammar genome and comparing target genes among tammar, mouse and human, we identified 163 conserved target genes. (biomedcentral.com)
The characterization of new miRNA target genes and a unique profile for crasiRNAs has allowed for insight into multiple RNA mediated processes in the tammar, including gene regulation, species incompatibilities, centromere and chromosome function. (biomedcentral.com)
Intriguingly, the expression of DNMT1, which is a target of miR-148a, is inversely correlated with the expression of miR-148a in HCC cells. (spandidos-publications.com)
E7 from human papil omavirus type 16 cooperate to cancer: the European prospective investigation into doi:10.1093/carcin/bgp321 PMID:20047954 target the PDZ protein Na/H exchange regulatory cancer and nutrition study. (who.int)

De-shuang Huang, Ge Yunjian, Wen-Bo Zhao, 2002, Proceedings of the 2002 International Joint Conference on Neural Networks. (paperexplained.cn)

Transposable elements are emerging as an important source of cis-acting regulatory sequences and epigenetic marks that could influence gene expression. (nature.com)
We concluded that besides adding cis-regulatory sequences, Bari-Jheh influences gene expression by affecting the local chromatin state. (nature.com)
DNA structural and physical properties reveal peculiarities in promoter sequences of the bacterium Escherichia coli K-12. (openwetware.org)
We examined each of these small RNA classes with respect to the newly assembled tammar wallaby genome for gene and repeat features, salient features that define their canonical sequences, and the constitution of both highly conserved and species-specific members. (biomedcentral.com)
In the current report, a systematic approach is implemented to catalogue regulatory elements within HERVs, as a roadmap to potential functions of HERV sequences in gene networks. (mdpi.com)
I analyzed the presence of HERV sequences on consensus cis-regulatory elements (cCREs) from ENCODE data. (mdpi.com)
However, it is difficult to capture the complexity of transcript isoform variance using these libraries, and large cDNA sequences are often difficult to clone into size-limited viral expression vectors. (cdc.gov)

The Transcriptome study combines topics in areas such as Phenotype, Regulation of gene expression, Neuroepithelial cell and Gene expression profiling. (research.com)
2009. Gene Profiling of Human Adipose Tissue During Evoked Inflammation In Vivo . (umd.edu)
Projects focused on gene expression profiling of ageing and of dietary manipulations of ageing, such as caloric restriction. (senescence.info)

Characterization of promoters in archaeal genomes based on DNA structural parameters. (openwetware.org)
Plants respond to various stimuli under abiotic or biotic stress condition and express certain genes either structural or regulatory genes which maintain the plant integrity. (scielo.br)
In this disturbance the maintenance involve the gene expression under the stress either in the form of structural gene or regulatory. (scielo.br)

Construction and Analysis of Gene Co-Expression Network in the Pathogenic Fungus Ustilago maydis. (openwetware.org)

His studies in Regulation of gene expression integrate themes in fields like RNA, Protein biosynthesis, Three prime untranslated region, Messenger RNA and microRNA. (research.com)
The major challenge thus pertains to effectively integrate the variety of these relationships (layers) encoded in multiple networks. (biomedcentral.com)

Using logic-based in silico perturbation experiments of a core regulatory network, we identified that simultaneous perturbation of Protein kinase B (AKT1) and oncoprotein murine double minute 2 (MDM2) drastically reduces EMT in melanoma. (bvsalud.org)
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)

Using a combination of miRNA hairpin predictions and co-mapping with miRBase entries, we identified a highly conserved cluster of miRNA genes on the X chromosome in the tammar and a total of 94 other predicted miRNA producing genes. (biomedcentral.com)

The design of cis-regulatory modules is such that transcription factors and epigenetic modifications serve as inputs, and the output of the module is the command given to the transcription machinery, which in turn determines the rate of gene transcription or whether it is turned on or off. (wikipedia.org)

One popular approach to disease-gene association testing is a transcriptome-wide association study (TWAS). (ucsd.edu)
Plants show stress-specific regulation of transcription that affects their transcriptome under stress conditions. (intechopen.com)

Anatomy20

Organisms22

Diseases2

Chemicals and Drugs45

Analytical, Diagnostic and Therapeutic Techniques and Equipment40

Psychiatry and Psychology2

Phenomena and Processes104

Disciplines and Occupations7

Information Science32

Health Care10

Proteins10

Inference7

Transcriptional Regulation2

Pathways4

Genomics6

Modulate gene expression2

Nearby genes5

Mechanisms7

Datasets3

Tumor8

Functional8

Disease genes2

Ontology1

Genetic9

Systems biology4

20231

Class II genes1

Regulate10

Biology17

Identify disease-causi1

Approaches2

Infer3

MRNA6

Computational2

Sequence2

Regulators4

Human genes2

Interactions4

Regulates2

Protein expression1

Variants1

Transcription factor6

Methylation4

Resistance genes2

Reconstruction of regulatory networks1

20211

Drosophila2

Enhancers3

RNAs4

Targets7

Encodes3

Multi-omics data1

Regions1

Yeast2

Downstream1

Target4

Neural1

Sequences7

Profiling3

Structural3

Analysis of gene1

Integrate2

Experiments2

Chromosome1

Epigenetic modifications1

Transcriptome2