Gene regulation metabolic networks and pathways. Medical search. Frequent questions

Following this, the differentially expressed genes (DEGs) were included in Gene Ontology enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, protein‑protein interaction network and survival analyses. (cancerindex.org)
The pathways that are probably regulated by the identified plant phytoconstituents were analyzed using Kyoto encyclopedia of genes and genomes. (ijpsonline.com)
Kyoto encyclopedia of genes and genomes pathway identified eight pathways that are directly related to cognitive impairment. (ijpsonline.com)

In this study, differentially expressed genes (DEGs) under drought and flooding conditions were investigated using Illumina RNA-Seq transcriptome profiling. (frontiersin.org)
m6A Methylation Immunoprecipitation Sequencing (m6A MeRIP-Seq)-based comprehensive transcriptome-wide m6A profiling identified 102 differentially expressed genes that underwent m6A modification, of which 22 hypermethylated genes were downregulated and 49 hypomethylated genes were upregulated, suggesting a negative correlation between m6A methylation and gene expression. (bvsalud.org)
The transcriptomic data analysis revealed that 5198 genes were differentially expressed in response to the CFS exposure and among them 5169 were downregulated including most of the genes involved in biosynthetic gene clusters. (bvsalud.org)
By analyzing the methylomes and transcriptomes of 14 fetal and 181 adult livers, we identified 657 differentially methylated genes with adult-specific expression, these genes were enriched for transcription factor binding sites of HNF1A and HNF4A. (biomedcentral.com)
APEC infection resulted in more up-regulation than down-regulation of differentially expressed genes. (iastate.edu)
Immune response and metabolic processes were enriched with differentially expressed genes. (iastate.edu)
It is usually used to compare the content of metabolites in different groups of samples, identify differentially expressed metabolites, and explore the metabolic pathways between different metabolites. (uberant.com)
The GSE3467 , GSE3678 , GSE33630 and GSE53157 were obtained from the GEO database, including 100 thyroid tumors and 64 normal tissues to obtain the intersection of differentially expressed genes, and a protein-protein interaction network was constructed to obtain the HUB gene. (peerj.com)
With the development of RNA sequencing and microarray technology, the study of differentially expressed genes (DEGs) between cancer and normal tissues has improved our understanding of the molecular mechanism of PTC. (peerj.com)
Herein, we screened differentially expressed genes between hepatocytes and untreated BMSCs to identify the genes responsible for the differentiation of BMSCs into hepatocytes. (aging-us.com)

Our study contains an extensive sequencing and functional gene-annotation analysis of A. sativum L. The findings provide insights into the molecular basis of TFs, defensive genes, and a reference for future studies on the genetics and breeding of A. sativum L. (springeropen.com)

Metabolic plasticity enables cancer cells to switch their metabolism phenotypes between glycolysis and oxidative phosphorylation (OXPHOS) during tumorigenesis and metastasis. (nih.gov)
Previously, by modeling the gene regulation of cancer metabolism we have reported that cancer cells can acquire a stable hybrid metabolic state in which both glycolysis and OXPHOS can be used. (nih.gov)
Genes including the previously characterized NmsA, thought to encode an enzyme necessary for 2-methylnaphthalene metabolism, were not upregulated during growth of NaphS2 on naphthalene, nor were the corresponding protein products. (elsevierpure.com)
Transcript profiles involved in the starch and sugar metabolism pathways were also affected under both stress conditions. (frontiersin.org)
Metabolism underpins development and physiology, but little is known about how metabolic genes and pathways are regulated, especially in multicellular organisms. (biorxiv.org)
However, compared to developmental processes, knowledge about the epigenetic regulation of metabolism is limited in multicellular organisms. (biorxiv.org)
To determine how metabolism is regulated epigenetically, we first identified regulatory patterns of epigenetic modification across all metabolic domains. (biorxiv.org)
To map the epigenetic marks on metabolic enzymes, pathways, and domains, we used the genome-wide functional annotations of metabolism we generated previously ( 6 ). (biorxiv.org)
For example, genes associated with energy metabolism showed higher expression levels compared to those involved in specialized metabolism (Fig. S1B). (biorxiv.org)
With a minimalist model of metabolism, cell growth and transcriptional regulation in a microorganism, we explore how the interaction between environmental conditions and gene regulation set the growth rate of cells in the phase of exponential growth. (lu.se)
Given the substantial inter-individual variation seen in metabolism, regulation of nutrients, protein synthesis, and detoxification of xenobiotics. (biomedcentral.com)
Enterohepatic circulation of bile acids plays a central role within the regulation of bile acids synthesis, fatty acid, lipid, and lipoprotein synthesis, as well as glucose metabolism in the liver (KullakUblick et al. (5htreceptor.com)
The development of a second generation of constraints-based models by incorporating constraints associated with regulation of gene expression was described in a companion paper published in this journal, using flux-balance analysis to generate time courses of growth and by-product secretion using a skeleton representation of core metabolism. (ucsd.edu)
The CcpA regulon comprises genes involved in sugar uptake, fermentation and amino acids metabolism, confirming the role of CcpA as a link between carbon and nitrogen pathways. (studyres.com)
Some of the studied proteins were involved in glucose and iron metabolism, immune evasion, and chemotactic cytokine regulation. (lu.se)
Biochemical genetic testing and newborn screening are essential laboratory services for the screening, detection, diagnosis, and monitoring of inborn errors of metabolism or inherited metabolic disorders. (cdc.gov)

About 65,587 of 82,663 transcripts were translated into 99,307 peptides, and we were successful in assigning InterPro annotations to 45,209 peptides and gene ontology (GO) terms to 32,638 peptides. (oregonstate.edu)
In garlic, the next-generation sequencing analysis based on RNA from renewal buds resulted in de novo assembly of 128,000 unigenes that were annotated and analyzed with respect to Gene Ontology (GO) and metabolic pathways [ 28 ]. (springeropen.com)
The signature mechanism was studied by analyzing the gene ontology and the Kyoto Encyclopedia of Genes and Genome database. (peerj.com)
Gene ontology functional enrichment analysis was performed using search tool for the retrieval of interacting genes/proteins. (ijpsonline.com)
Gene ontology functional enrichment analysis revealed twenty eight biological processes and 10 molecular functions associated with cognitive impairment. (ijpsonline.com)

Database objects also describe molecular interactions, including metabolic pathways, transport events, and the regulation of gene expression. (wikipedia.org)
Mete Civelek uses big data analytics to understand the molecular pathways of disease and develops personalized medicine approaches to cardiovascular and metabolic disorders. (virginia.edu)
They use data science, systems biology, and traditional molecular biology approaches to discover novel disease pathways in human cells and in mice. (virginia.edu)
RNA sequencing has been used for the genome-wide quantification of absolute transcript levels, the identification of novel genes, the characterization of transcript structure (including 50 and 30 ends, introns, and exons), and the mining of molecular markers. (springeropen.com)
Life in a cell is carried out by many genes, proteins, and small molecular metabolites. (uberant.com)
We have gained crucial insights into molecular factors and pathways of the cells generating either the supporting gonadal cells or germ cells of both sexes. (lidsen.com)
This four-credit course will present a quantitative description of the molecular networks that underlie the myriad phenotypes of living cells, from yeast to human. (columbia.edu)

For example, â ¼25 genes responsible for the biosynthesis of carcinogenic aflatoxins by Aspergillus section Flavi species are grouped in a â ¼70 Kb cluster. (bvsalud.org)
Genes responsible for the biosynthesis of these compounds are wired into a complex network. (biorxiv.org)

We report a blood-induced microglia gene network and show that blood proteins elicit distinct receptor-mediated transcriptional changes and signaling programs in innate immune cells. (nature.com)
These variations can affect the liver's metabolic properties, leading to high levels of metabolites, either in the forms of lipids, proteins or xenobiotics, which can result in serious diseases or toxic side-effects. (biomedcentral.com)
The functional changes of upstream macromolecules (nucleic acids, proteins, etc.) will eventually be reflected in the metabolic level, such as changes in neurotransmitters, hormone regulation, receptor effects, cell signal release, energy transfer and communication between cells, etc. (uberant.com)
Epigenetic components (for example, Polycomb PRC1/2 and Trithorax group proteins) maintain the 'off' states of certain genes and the 'on' states of others, in a cell-type- and time-specific manner (the bottom panels show three genes, depicted schematically as chromatinized templates, in which transcription is triggered by specific transcription factors and silent or active states are maintained by PRC1/2 or Trithorax proteins, respectively). (nature.com)

Mazza A, Gat-Viks I, Farhan H, Sharan R. A minimum-labeling approach for reconstructing protein networks across multiple conditions. (tau.ac.il)
To further characterize pathways involved in naphthalene degradation in NaphS2, the draft genome was sequenced, and gene and protein expression examined. (elsevierpure.com)
What does this gene/protein do? (cancerindex.org)
We compared the ortholog gene family of the A. sativum transcriptome to A. thaliana , O. sativa , and Z. mays and found that 12,077 orthologous gene families are specific to A. sativum L. Furthermore, we identified genes involved in plant defense mechanisms, their protein-protein interaction network, and plant-pathogen interaction pathways. (springeropen.com)
Therefore, the metabolome is downstream of the network of gene regulation and protein action, providing the terminal information of biology. (uberant.com)
Although developed for use case of eQTLs regulatory genomic net-work community, study-results shown with our analysis with sample eQTL data-GraphBreak can be deployed for other studies if input data has been fed in requisite format, including but not limited to gene coexpression networks, protein-protein interaction network, signaling pathway and metabolic network. (longdom.org)
As a result, the function of the protein encoded by the gene changed so radically that it no longer performs its original function and instead acts as a toxin. (technologynetworks.com)
We further established a protein-protein interaction subnetwork for the Ccr6-correlated genes, which provides an insight on the interaction of G protein-coupled receptors, kallikrein-kinin system and neuroactive ligand-receptors. (cdc.gov)

The m6A sites of several key genes involved in the aflatoxin B1 biosynthesis pathway were significantly enriched in the coding sequence and around the stop codon, resulting in their downregulation. (bvsalud.org)
Furthermore, m6A methylation on genes related to the aflatoxin B1 biosynthesis pathway led to reduced mRNA stability. (bvsalud.org)
Additionally, we demonstrated that inhibition of aflatoxin was linked to N6-methyladenosine methylation of multiple genes in aflatoxin biosynthesis pathway. (bvsalud.org)
The best-performing hybrid models achieved over 95% accuracy on holdout test datasets, surpassing traditional ML and ANN models and also showed good accuracy on lignin biosynthesis pathway analysis. (mtu.edu)

Moreover, cIAPs are required for CD137 signaling toward the NF-?B and MAPK pathways and for costimulation of human and mouse T lymphocytes. (unav.edu)
Enriched expression of genes in LRECb was associated with stem cell attributes and identified WNT, TGF-β, and MAPK pathways of self renewal and proliferation. (frontiersin.org)

His laboratory studies the complex interactions among genes and environment that increase our risk for heart disease and type 2 diabetes. (virginia.edu)
To see if there are any interactions between epigenetic modifications across metabolic genes, we computed pairwise Pearson's correlation coefficients between the 16 epigenetic modifications based on their relative abundance at each metabolic gene region. (biorxiv.org)
In contrast, metabolic genes involved in specialized and hormone metabolic domains, which are generally involved in interactions with biotic and abiotic environmental stimuli, showed distinct patterns with the enrichment of a repression mark H3K27me3 and an activation mark H3K18ac ( Fig. 1B ). (biorxiv.org)
Garlic contains various bioactive compounds whose metabolic pathways, plant-pathogen interactions, defensive genes, identify interaction networks, and functional genomics were not previously predicted in the garlic at the genomic level. (springeropen.com)
Interactions among genes together with their expression level determine a phenotype in a given organism. (embnet.org)

EcoCyc provides several genome-scale visualization tools to aid in the analysis of omics data, such as by painting gene expression or metabolomics data onto the full regulatory network of E. coli. (wikipedia.org)
Chia () Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development. (oregonstate.edu)
and the regulation of the expression of enzyme-coding genes associated with important metabolic pathways. (oregonstate.edu)
We are testing the hypothesis that specific transcription factors form regulatory networks to execute gene expression programs important for SSC fate decisions (self-renewal and differentiation), and ultimately, spermatogenesis. (utsa.edu)
RESULTS: Draft genome sequencing, gene expression analysis, and proteomic analysis revealed that NaphS2 degrades naphthoyl-CoA in a manner analogous to benzoyl-CoA degradation. (elsevierpure.com)
therefore, it is imperative to assess the expression of genes involved in response to flood and drought stress. (frontiersin.org)
The expression of photosynthesis and chlorophyll synthesis related genes were significantly reduced under both types of stresses, which limit the metabolic processes and thus help prolong survival under extreme conditions. (frontiersin.org)
The changes in expression of genes involved in regulating the flux of cell wall precursors and starch/sugar content can serve as an adaptive mechanism for soybean survival under stress conditions. (frontiersin.org)
Surprisingly, specialized metabolic genes, often involved in defense, were predominantly regulated by two modifications that have opposite effects on gene expression, H3K27me3 (repression) and H3K18ac (activation). (biorxiv.org)
Our study suggests that this type of bivalent chromatin, which we name a kairostat, controls the precise timing of gene expression upon stimuli. (biorxiv.org)
Various levels of regulation, including epigenetic modifications and transcription factors, play important roles in coordinating the expression of genes. (biorxiv.org)
Groups I and II included mainly the epigenetic modifications that activate gene expression. (biorxiv.org)
The enrichment patterns of epigenetic modifications were consistent with expression levels of genes involved in each domain under healthy conditions (Fig. S1A). (biorxiv.org)
Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)
Expression profiles analysis identifies the values of carcinogenesis and the prognostic prediction of three genes in adrenocortical carcinoma. (cancerindex.org)
The analyzed gene datasets were downloaded from the Gene Expression Omnibus and The Cancer Genome Atlas (TCGA) database. (cancerindex.org)
However, there is substantial inter-individual variation in hepatic gene expression, and although numerous genetic factors have been identified, less is known about the epigenetic factors. (biomedcentral.com)
We observed that meQTL were more stable between tissues than eQTL and a very strong tissue-specificity for the identified associations between CpG methylation and gene expression. (biomedcentral.com)
Our analyses generated a comprehensive resource of factors involved in the regulation of hepatic gene expression, and allowed us to estimate the proportion of variation in gene expression that could be attributed to genetic and epigenetic variation, both crucial to understanding differences in drug response and the etiology of liver diseases. (biomedcentral.com)
It is essential to have a better understanding on inter-individual variation of gene expression, methylation and genetic effects specific to liver, and on different conditions, e.g. developmental stages. (biomedcentral.com)
In particular, such mechanisms can influence the expression of hepatic ADME genes. (biomedcentral.com)
Like diet program, nutrients, atmosphere, and management, quite a few elements can alter gene expression by epigenetic modulations (Tarallo et al. (5htreceptor.com)
Noncoding RNAs like miRNAs and lncRNAs had been one particular of the modification elements of gene expression regulation. (5htreceptor.com)
Red dashed represented differential expression genes in liver from grass-fed cattle.CONCLUSIONSOur final results indicated grass-fed induced the gene expression in glycolysis/gluconeogenesis, fatty acids degradation, and amino aci. (5htreceptor.com)
Gene expression patterns have previously been demonstrated to differ between chicken populations that are resistant vs. susceptible to bacterial infection, but little is currently known about gene expression response to APEC. (iastate.edu)
Increased understanding of gene expression patterns associated with resistance will facilitate genetic selection to increase resistance to APEC. (iastate.edu)
Although vaccination significantly reduced lesions in challenged bird, there was no detectable effect of vaccination on gene expression. (iastate.edu)
Also, expression verification and survival analysis of these candidate genes based on the TCGA database indicate the robustness of the above results. (peerj.com)
Finally, our hospital samples validated the expression levels of these genes. (peerj.com)
To support this metabolic phenotype, cancer cells adaptively regulate the expression of glycolytic enzymes and nutrient transporters. (northwestern.edu)
Cellular identity is now accepted to be the result of the expression of specific combinations of genes (Fig. 1 ). (nature.com)
Finally, higher-order 3D chromosome folding is also thought to modulate gene expression and might contribute to inheritance 15 . (nature.com)
GSE30419 gene microarray data of BMSCs and GSE72088 gene microarray data of primary hepatocytes were obtained from the Gene Expression Omnibus database. (aging-us.com)
The expression of the hub genes in the BMSCs and hepatocytes was verified by reverse transcription-quantitative PCR (RT-qPCR). (aging-us.com)
Constraints-based models: regulation of gene expression reduces the steady-state solution space. (ucsd.edu)
Because the environment encountered as well as methods that allow direct measurement of gene within a living host will be quite different from the external expression during interaction with a host. (cdc.gov)
Two of these environment, pathogens must be able to regulate the neces- methods, signature-tagged mutagenesis and in vivo sary genes in coordination as they move from the environ- expression technology, do not directly measure gene ment to the host and from one host niche to another. (cdc.gov)
expression and do not allow true genomic-scale analysis, The primary aim of investigating bacterial pathogenesis but they have been devised to identify genes necessary for is to understand the way that pathogens interact with the pathogens during real infections. (cdc.gov)
PERSPECTIVE their application to analysis of bacterial pathogens during terial gene expression during growth in vitro under condi- real infections is still in its infancy. (cdc.gov)
The Ccr6 gene is cis-regulated and its expression is significantly correlated with CORT+DFP treatment. (cdc.gov)
These effects are attributed not only to genetic changes but to epi genetic changes (ie, post-DNA modifications that occur throughout the lifespan) that modulate gene expression. (medscape.com)
These products have several anti-inflammatory properties of any/multiple islet autoantibodies (242 and 151 events, respec- such as regulation of immune-related gene expression and cy- tively) and T1D (71 events) by soluble fiber intake were calculated tokine release (8). (lu.se)

Innate immune cells integrate environmental signals to rapidly activate target genes and perform specialized cellular functions 5 . (nature.com)
Simple associations miRNA-disease through their target genes can be obtained querying a knowledge base such as miRò. (embnet.org)
Compared to other similar tools, with GraphBreak we can better detect communities with over representation of its member genes for statistical association with diseases, therefore target genes which can be prioritized for drug-positioning or drugrepositioning as the case be. (longdom.org)

Enrichment of modifications in each metabolic domain, relative to all the genes in the genome, revealed both shared and diverse patterns. (biorxiv.org)
Enrichment of these genes was seen in the immune, inflammation, cytokine, and neurological related categories. (cdc.gov)

The identified DEGs included 20 downregulated genes and 51 upregulated genes, which were highly associated with the cell cycle, organelle fission, chromosome segregation, cell division and spindle stability. (cancerindex.org)

The additional information gen- these responses will increase understanding of the molec- erated by whole genome studies goes far beyond that ular mechanisms of pathogenesis, identify new bacterial derived by characterizing in isolation more genes and gene virulence factors, and aid in the design of new vaccines. (cdc.gov)
Bacterial pathogens must be able to gain gene-at-a-time" approach. (cdc.gov)

The EcoCyc project performs literature-based curation of the E. coli genome, and of E. coli transcriptional regulation, transporters, and metabolic pathways. (wikipedia.org)
s transcriptional regulation of metabolic pathways an optimal strategy for fitness? (lu.se)
Transcriptional regulation of the genes in metabolic pathways is a highly successful strategy, which is virtually universal in microorganisms. (lu.se)

Here, to comprehensively characterize cancer metabolic activity, we establish a theoretical framework by coupling gene regulation with metabolic pathways. (nih.gov)
These constraints restrict the allowable behaviors of a network to a convex mathematical solution space whose edges are extreme pathways that can be used to characterize the optimal performance of a network under a stated performance criterion. (ucsd.edu)

Blood induced widespread microglial transcriptional changes, including changes involving oxidative stress and neurodegenerative genes. (nature.com)

It is responsible for various metabolic functions such as the immune response of cells and neural regulation. (technologynetworks.com)
Our current research goal is to define and characterise extreme immune response phenotypes which should resolve functional alleles, mechanisms of gene regulation and pathophysiology. (ox.ac.uk)

The experimental results confirm that TNBC cells can maintain a hybrid metabolic phenotype and targeting both glycolysis and OXPHOS is necessary to eliminate their metabolic plasticity. (nih.gov)
We propose a software tool that using gene-phenotypes association techniques in connection with gene network-based correlation algorithms allows the identification of statistically significant microRNA-phenotype-drug associations. (embnet.org)
An increased carbon flux and exploitation of metabolic pathways for the rapid generation of biosynthetic precursors is a common phenotype observed in breast cancer. (northwestern.edu)

Degradation of toluene and 2-methylnaphthalene, and the presence of at least one bss-like and bbs-like gene cluster in this organism, suggests that NaphS2 degrades both compounds via parallel mechanisms. (elsevierpure.com)
The imposition of environmental conditions and regulatory mechanisms sharply reduces the number of active extreme pathways. (ucsd.edu)
The method developed here provides a way to interpret how regulatory mechanisms are used to constrain network functions and produce a small range of physiologically meaningful behaviors from all allowable network functions. (ucsd.edu)
In this review, we highlighted some of the main gene networks and regulatory mechanisms involved in the plasticity of sex-determining pathways that help to establish a functional ovary that can nurture the follicles to generate a good ovarian reserve, both in quantity and quality. (lidsen.com)
The insulin-producing cells that we can make from these patients can then be used to understand the mechanisms by which these risk genes cause dysfunction of beta-cells. (lu.se)

1000) as substrates and products of various metabolic pathways. (uberant.com)

Our modeling results demonstrate a direct association between the activities of AMPK and HIF-1, master regulators of OXPHOS and glycolysis, respectively, with the activities of three major metabolic pathways: glucose oxidation, glycolysis, and fatty acid oxidation. (nih.gov)
Each species in the pathway is replaced by specie id ,like in glycolysis glucose can be represented as [S1]. (amrita.edu)
About 18% of all C. difficile genes are regulated by glucose, for which 50% depend on CcpA for regulation. (studyres.com)

Inside the metabolic processes and pathways networks, we located lots of genes have been regulated by one particular or several miRNAs and lncRNAs (Figure four). (5htreceptor.com)
The construction of gene regulatory networks (GRNs) is vital for understanding the regulation of metabolic pathways, biological processes, and complex traits during plant growth and responses to environmental cues and stresses. (mtu.edu)
The behavioural and biological responses of a child to the obesogenic environment can be shaped by processes even before birth, placing an even greater number of children on the pathway to becoming obese when faced with an unhealthy diet and low physical activity. (who.int)

Metabolomics focuses on the study of the metabolic pathways of endogenous metabolites in the whole organism, organs or tissues, and the influence of internal or external factors and the law of changes over time. (uberant.com)
This was made possible by a metabolomics approach, using NMR to map metabolic pathway activity in cells. (lu.se)

It is likely when a set of genes are regulated by a set of genetic variants, the genes set is recruited for a common or related functional purpose. (longdom.org)

This study investigated the transcriptomic differences in host responses associated with mild vs. severe pathology, in addition to the effects of vaccination and challenge, thus revealing genes and networks associated with response to APEC and providing a foundation for future studies on, and genetic selection for, genetic resistance to APEC. (iastate.edu)

A. Correlation analysis reveals four groups of epigenetic marks, activating (red) and repressing (blue), based on their relative abundance on metabolic genes. (biorxiv.org)
More examples on epigenetic regulation of ADME genes have been reviewed by Kacevska et al. (biomedcentral.com)
Although the number of samples was somewhat compact, our data supplied initial evaluation on epigenetic regulation mechanism. (5htreceptor.com)

However, we now have a number of methods that must also produce factors that result (directly or indirectly) allow identification of genes critical for survival in a host in host damage. (cdc.gov)

Whole-genome sequencing also revealed divergence in malic enzyme-encoding genes between the strains predicted to impact the activity of the malate metabolic pathway. (nih.gov)
Comparative growth assays in urine comparing wild-type ABSA and gene-deficient mutants that were functionally inactivated for the malic enzyme metabolic pathway by targeted disruption of the maeE or maeK gene in ABSA demonstrated attenuated growth of the mutants in normal human urine as well as synthetic human urine containing malic acid. (nih.gov)
This gene encodes a DNA topoisomerase, an enzyme that controls and alters the topologic states of DNA during transcription. (cancerindex.org)
Rhea can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analysis. (biokeanos.com)
The OCRL gene provides instructions for making an enzyme that helps modify fat (lipid) molecules called membrane phospholipids. (medlineplus.gov)
Some mutations in the OCRL gene prevent the production of any OCRL enzyme. (medlineplus.gov)

Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases. (biokeanos.com)

This study has revealed the involvement of TFs, transporters, and photosynthetic genes, and has also given a glimpse of hormonal cross talk under the extreme water regimes, which will aid as an important resource for soybean crop improvement. (frontiersin.org)

Identify and conduct absolute quantitative analysis of one or more specific components of the metabolites of interest, such as a class of compounds with related structure and properties (amino acids, organic acids, cisediols) or all intermediates of a metabolic pathway or signature components of multiple metabolic pathways. (uberant.com)
Given a list of genes, e.g. those composing a metabolic pathway, we lead a phenotypic and miRNAs-based analysis by calculating distances among gene pairs. (embnet.org)
In this research, we conducted a multi-step analysis through comprehensive bioinformatics analysis to identify hub genes in THCA. (peerj.com)
Han Y , He X , Lee S , Mao Y , Liu X , Sun H , Jin M , Kwon T , . Network analysis for the identification of hub genes and related molecules as potential biomarkers associated with the differentiation of bone marrow-derived stem cells into hepatocytes. (aging-us.com)
Transcriptome Analysis Console software showed that 1896 genes were upregulated and 2506 were downregulated in hepatocytes as compared with BMSCs. (aging-us.com)
Here, we examine the reduction of the solution space due to regulatory constraints using extreme pathway analysis. (ucsd.edu)
Using combination of chromatin immunoprecipitation and genome sequence analysis, we detected 55 CcpA binding sites corresponding to 140 genes directly controlled by CcpA. (studyres.com)

The main module page also shows the location of these motifs within the upstream sequences of the module member genes. (systemsbiology.net)
cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. (systemsbiology.net)

Using camalexin biosynthesis genes as an example, we confirmed that these two modifications were co-localized to form bivalent chromatin. (biorxiv.org)

Even the crudest transcriptional network is shown to substantially increase the fitness of the organism, and this effect persists even when the range of nutrient levels is kept very narrow. (lu.se)
Biologists have long sought to understand how a fertilized egg can form an organism composed of hundreds of specialized cell types, each expressing a defined set of genes. (nature.com)

When a second nutrient and its metabolic pathway are introduced, the system must further decide whether and how to activate both pathways. (lu.se)
The pluripotency of the initial cell and the establishment of cell types depend to a large extent on the coordinated deployment of hundreds of transcription factors that bind to specific DNA sequences to activate or repress the transcription of cell lineage genes 1 . (nature.com)

Second, networks of genes and hormones regulate the advancement of sex determination and gonad differentiation, known as the gonadal sex phase. (lidsen.com)
These hormones regulate the body's growth, and are involved in cell to cell communication, control metabolic activity, sleep-wake homeostasis, and altered regulation or dysregulation of adaptive response in various physiologic and pathophysiologic states. (medscape.com)

SVMRFE a modification of SVM ranks the genes based on their discriminatory power and eliminate the genes which are not involved in causing the disease. (researchgate.net)
Researchers at the Technical University of Munich (TUM) have investigated how the toxin emerged between 50 and 120 million years ago through the modification of a gene that also occurs in mammals and other reptiles. (technologynetworks.com)

In garlic, the major flavor precursor is sulfur-alk(en)yl cysteine sulfoxide (ACSO, alliin), which is degraded by alliinase enzymes upon tissue disruption to give pyruvate, ammonia, and thiosulfinate. (springeropen.com)
In particular, vitamin B1 (thiamine) is utilized as an essential cofactor for metabolic enzymes that intersect at critical junctions within the glycolytic network. (northwestern.edu)

Gat-Viks I, Meller R, Kupiec M, Shamir R: Understanding gene sequence variation in the context of transcription regulation in yeast. (tau.ac.il)
These genes comprise 289 Transcription Factors (TFs) representing Basic Helix-loop Helix (bHLH), Ethylene Response Factors (ERFs), myeloblastosis (MYB), No apical meristem (NAC), and WRKY amino acid motif (WRKY) type major families known to be involved in the mechanism of stress tolerance. (frontiersin.org)
The top 14 hub genes were subsequently confirmed by reverse transcription‑quantitative polymerase chain reaction in ACC and adrenocortical adenoma samples. (cancerindex.org)
The increasing availability of public databases has facilitated the development of numerous methods for inferring gene regulatory relationships between transcription factors and their targets. (mtu.edu)

We provide a transcriptomic and phosphoproteomic atlas of fibrin-, iC3b- and lipopolysaccharide (LPS)-selective activation of innate immunity and reveal ligand-selective pathways with differential functions in MS and AD mice. (nature.com)

Identifying key genes, networks and pathways for therapeutic intervention is particularly important given the high failure rate of drug trials, with genetic evidence enhancing predictions of drug efficacy. (ox.ac.uk)

In Arabidopsis, trimethylation of lysine 36 in histone 3 (H3K36me3) activates energy related pathways ( 3 ) and trimethylation of lysine 27 in histone 3 (H3K27me3) represses lipid biosynthesis pathways ( 4 ). (biorxiv.org)
We examined regulation of lipid partioning in beta-cells and its control of insulin secretion. (lu.se)

However, cell wall synthesis related genes were up-regulated under drought stress and down-regulated under flooding stress. (frontiersin.org)
SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others. (bioseek.eu)
whereas LREC in suprabasal epithelial layers are enriched for more committed progenitor cells, expressing some genes that are associated with stem cell attributes along with those indicative of cell differentiation. (frontiersin.org)
Similarly, up-regulation was also observed in breast cancer cell lines compared to human mammary epithelial cells. (northwestern.edu)
In males (who have only one X chromosome), one altered copy of the gene in each cell is sufficient to cause the condition. (medlineplus.gov)

Mutations in the OCRL gene cause Lowe syndrome. (medlineplus.gov)
Other cases result from new mutations in the gene and occur in males with no history of the disorder in their family. (medlineplus.gov)

However, it is still largely unknown how cancer cells orchestrate gene regulation to balance their glycolysis and OXPHOS activities. (nih.gov)
Our model further characterizes the hybrid metabolic state and a metabolically inactive state where cells have low activity of both glycolysis and OXPHOS. (nih.gov)

Part I covers key laboratory manipulations, including DNA cloning, gene characterization, association of genes with disease, and methods for studying gene regulation and activities of gene products. (columbia.edu)

The subject of the present study is the design of an environment in which microRNAs-drugs-phenotypes relationships can be deduced using more advanced network-based techniques. (embnet.org)
Starting from matrices of phenotypic and drugs similarities,the tool provides users an interface to establish those miRNAs, known to be responsible for the regulation of genes involved in a disease, associated with other diseases showing similar phenotypes. (embnet.org)
In the first step, we extract for each pairs of genes the phenotypes from OMIM. (embnet.org)
This allows the construction of a complete list of phenotypes associated to each genes pair. (embnet.org)
In the second step, we calculate the phenotypic distance matrix between any two genes according to the their common phenotypes. (embnet.org)

Topics covered include various high-throughput genomics technologies (genome sequencing, DNA microarrays, proteomics), quantitative modeling of transcriptional and post-transcriptional regulatory networks, synthetic biology, and the world of RNA structure, dynamics, and function. (columbia.edu)

Anatomy7

Organisms15

Chemicals and Drugs26

Analytical, Diagnostic and Therapeutic Techniques and Equipment25

Phenomena and Processes70

Disciplines and Occupations12

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture4

Humanities1

Information Science27

Health Care9

Kyoto Encyclo3

Differentially10

Genetics1

Metabolism16

Ontology5

Molecular7

Responsible for the biosynthesis2

Proteins4

Protein8

Biosynthesis pathway4

MAPK2

Interactions5

Expression42

Target genes3

Enrichment2

DEGs1

Bacterial2

Transcriptional regulation3

Characterize2

Oxidative stress1

Immune2

Phenotype3

Mechanisms5

Various metabolic1

Glucose3

Processes3

Metabolomics2

Variants1

Thus revea1

Epigenetic3

Survival1

Enzyme6

Biological1

Transporters1

Analysis7

Member genes2

Chromatin1

Organism2

Activate2

Regulate2

Modification2

Enzymes2

Transcription4

Differential1

Identifying1

Lipid2

Cell5

Mutations2

Glycolysis2

Characterization1

Phenotypes5

Regulatory networks1