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Results for “Pathway analysis”

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At least 721 records · Page 40Linked to original sources

PubMed2026

Integrative multi-omics analysis of metabolite-protein interaction networks across different stages of coronary heart disease.

To elucidate the molecular characteristics of synergistic interactions across the clinical stages of coronary heart disease (CHD)-specifically stable angina pectoris (SAP), unstable angina pectoris (UAP), and acute myocardial infarction (AMI)-through integrated metabolomic and proteomic analyses. Based on a cohort including SAP, UAP, AMI, and healthy controls, metabolomic and proteomic analyses were performed to identify differentially expressed molecules, followed by KEGG pathway enrichment analysis. Pathways co-enriched across both omics platforms were selected to construct metabolite-protein interaction networks. The number of pathways co-enriched in both metabolomic and proteomic analyses increased markedly with disease stage. Only two pathways (histidine metabolism and arginine and proline metabolism) were identified in the SAP stage; this number increased to five in the UAP stage (including ferroptosis and efferocytosis) and expanded to 25 in the AMI stage, encompassing three major functional modules: immune inflammation, metabolic reprogramming, and cell signaling. The core network exhibited a stepwise increase in connectivity, shifting from a sparse structure in the SAP stage to a highly interconnected architecture in the AMI stage, with L-glutamate and KNG1 identified as the central hubs in this cross-sectional network. In addition, CNDP1 exhibited a stage-dependent functional transition, shifting from downregulation in SAP to upregulation in AMI. In this cross-sectional analysis, metabolic dysregulation and immune activation exhibited stepwise increases in interconnectivity across the SAP, UAP, and AMI groups, with the most extensive crosstalk observed in the AMI stage-a network configuration consistent with a tightly coupled "molecular storm". These findings provide novel insights into stage-associated molecular signatures of CHD and identify candidate hub molecules for stage-oriented therapeutic investigation.

Humans↗

PubMed2000

A DFT theoretical analysis of aldehyde condensation pathways onto methyllithium, lithium dimethylamide, and their aggregates

A DFT analysis of the condensation of monomeric methyllithium and lithium dimethylamide (LMA), as well as their homo and hetero dimers, on formaldehyde and acetaldehyde is reported. A stable complex, exhibiting a directional interaction between a lone pair of the oxygen on the aldehyde and a lithium, is first found. At this stage, the aldehyde carbonyl and the Li-X (X = C or N) bonds lie in the same plane. To proceed, the condensation reaction has to go through a transition state that mainly consists of a rotation of the aldehyde plane, placing it perpendicular to the C-C or C-N forming bond. The reaction then leads, in a strongly exothermic final step, to the addition product that is a lithium alcoholate or alpha-amino alcoholate, associating into an hetero-aggregate with the remaining moiety of the initial dimer. From the relative heights of the activation barriers, it appears that, for the heterodimer MeLi-LMA, the formation of the C-N bond should be kinetically favored over the C-C one, while the lithium ethylate resulting from the C-C binding is the thermodynamic product. A decomposition of the activation energy barriers has been carried out in order to determine the physicochemical forces responsible for the variation of the condensation activation barriers with the structure of the final species formed. The results obtained are discussed in relation with corresponding experimental data.

Journal Article↗

PubMedDate not supplied

Linking outcomes analysis to critical clinical pathways.

Expert decision-support soft-ware systems, when integrated with outcomes analyses, provide the opportunity to develop behavioral healthcare delivery systems in which providers are equipped to act decisively in a socially responsible manner. Key benefits of such systems include: enhancing the consistency and quality of clinical decision making across providers with varying professional backgrounds; providing a mechanism to ensure the rapid dissemination and implementation of new clinical research findings; performing severity-adjusted profiling of providers and programs based on the outcomes their services produce; and linking the prospective focus of clinical pathways with the retrospective rigor of outcomes analysis to accelerate advances in behavioral health. Integrating expert systems with outcomes analyses has the potential to rectify the historical failure by the behavioral healthcare professions to systematically link patient assessment data and their analysis to actual clinical decision making. Such systems will help make behavioral healthcare practice more accountable, thereby strengthening the argument for psychiatric patients to gain parity in healthcare benefits.

Expert Systems↗

PubMed2005

Recurrence of symptomatic atrial fibrillation after successful catheter ablation of atrioventricular accessory pathways: a multivariate regression analysis.

The primary aim of this study is to investigate the factors related to the recurrence of atrial fibrillation (AF) after a successful ablation of atrioventricular accessory pathway. Thirty-seven patients with spontaneous AF (study group) were selected from 401 consecutive patients who underwent radiofrequency catheter ablation of atrioventricular accessory pathway. A multivariate regression analysis was used in order to evaluate the relationships between AF recurrence and patients' age, sex, atrial size, left ventricular function, location of accessory pathways, heart rate during atrioventricular re-entrant tachycardia and atrial vulnerability (induction of sustained AF) after a successful ablation. Atrioventricular accessory pathway was abolished in 36 of the study group patients and 351 of the control group patients. During the follow-up of 36 +/- 11 months, four patients (11.1%) from the study group experienced sustained AF. Multivariate regression analysis showed that, in patients with pre-ablation AF, older age and post-ablation atrial vulnerability were the only independent predictive factors for AF recurrence. We concluded that radiofrequency catheter ablation of atrioventricular accessory pathway greatly reduces the risk of AF in patients who had a history of symptomatic AF. Older patients and patients with inducible AF after accessory pathway ablation are at an increased risk of AF recurrence. These patients should be closely monitored after successful ablation of atrioventricular accessory pathways.

Adult↗

PubMed2006

Major carcinogenic pathways identified by gene expression analysis of peritoneal mesotheliomas following chemical treatment in F344 rats.

This study was performed to characterize the gene expression profile and to identify the major carcinogenic pathways involved in rat peritoneal mesothelioma (RPM) formation following treatment of Fischer 344 rats with o-nitrotoluene (o-NT) or bromochloracetic acid (BCA). Oligo arrays, with over 20,000 target genes, were used to evaluate o-NT- and BCA-induced RPMs, when compared to a non-transformed mesothelial cell line (Fred-PE). Analysis using Ingenuity Pathway Analysis software revealed 169 cancer-related genes that were categorized into binding activity, growth and proliferation, cell cycle progression, apoptosis, and invasion and metastasis. The microarray data were validated by positive correlation with quantitative real-time RT-PCR on 16 selected genes including igf1, tgfb3 and nov. Important carcinogenic pathways involved in RPM formation included insulin-like growth factor 1 (IGF-1), p38 MAPkinase, Wnt/beta-catenin and integrin signaling pathways. This study demonstrated that mesotheliomas in rats exposed to o-NT- and BCA were similar to mesotheliomas in humans, at least at the cellular and molecular level.

Acetates↗

PubMed2003

A genomics-guided approach for discovering and expressing cryptic metabolic pathways.

Genome analysis of actinomycetes has revealed the presence of numerous cryptic gene clusters encoding putative natural products. These loci remain dormant until appropriate chemical or physical signals induce their expression. Here we demonstrate the use of a high-throughput genome scanning method to detect and analyze gene clusters involved in natural-product biosynthesis. This method was applied to uncover biosynthetic pathways encoding enediyne antitumor antibiotics in a variety of actinomycetes. Comparative analysis of five biosynthetic loci representative of the major structural classes of enediynes reveals the presence of a conserved cassette of five genes that includes a novel family of polyketide synthase (PKS). The enediyne PKS (PKSE) is proposed to be involved in the formation of the highly reactive chromophore ring structure (or "warhead") found in all enediynes. Genome scanning analysis indicates that the enediyne warhead cassette is widely dispersed among actinomycetes. We show that selective growth conditions can induce the expression of these loci, suggesting that the range of enediyne natural products may be much greater than previously thought. This technology can be used to increase the scope and diversity of natural-product discovery.

Actinobacteria↗

PubMed2026

A CFH- and SPINT2-based prognostic signature for cholangiocarcinoma.

BACKGROUND: Cholangiocarcinoma (CCA) is a highly malignant tumor with a poor prognosis, and reliable biomarkers for postoperative risk stratification remain limited. This study aimed to develop and validate a CFH- and SPINT2-based prognostic signature to support postoperative risk stratification and inform adjuvant therapy selection in CCA through integrative machine learning and single-cell transcriptomics. METHODS: Differentially expressed genes were screened from GSE26566. Integrative machine learning (least absolute shrinkage and selection operator-Cox, random forest, and univariate Cox regression) was performed in the training cohort (GSE89749; n=115) to construct a risk model, which was externally validated in two independent cohorts: cohort 1 (E-MTAB-6389; n=75) and cohort 2 [The Cancer Genome Atlas Cholangiocarcinoma (TCGA-CHOL) data set; n=36]. Systematic analysis was conducted and included examinations of immune infiltration [via single-sample gene set enrichment analysis (ssGSEA)], pathway enrichment (via hallmark GSEA), cellular localization (via single-cell RNA sequencing), and drug sensitivity (via the Genomics of Drug Sensitivity in Cancer 2 database). RESULTS: Two genes, CFH and SPINT2, were identified and incorporated into a prognostic risk score. High-risk patients in the training cohort had a significantly worse overall survival (log-rank P=0.02). External validation was performed in two independent cohorts. In validation cohort 1, the risk group was an independent prognostic factor [hazard ratio =2.27, 95% confidence interval (CI): 1.18-4.37; P=0.01]. In validation cohort 2, the model demonstrated acceptable discriminative ability (concordance index =0.721; 3-year area under the curve =0.692). The high-risk group exhibited an immunosuppressive microenvironment characterized by increased infiltration of macrophages and myeloid-derived suppressor cells, along with the activation of epithelial-mesenchymal transition, inflammatory response, and NF-κB signaling pathways. Single-cell analysis revealed a cell-type-specific expression pattern: CFH was predominantly expressed in fibroblasts, while SPINT2 was mainly expressed in malignant cells. Drug sensitivity analysis demonstrated that the high-risk group was more sensitive to gemcitabine, cisplatin, poly(ADP-ribose) polymerase (PARP) inhibitors, and mammalian target of rapamycin (mTOR) inhibitors, whereas the low-risk group was more sensitive to lapatinib. CONCLUSIONS: The CFH- and SPINT2-based prognostic signature may serve as an independent biomarker for postoperative risk stratification in CCA. High-risk patients, characterized by fibroblast-derived CFH enrichment and malignant-cell SPINT2 loss, exhibit an immunosuppressive microenvironment and may be more suitable for gemcitabine-based chemotherapy or PARP/mTOR inhibitors, whereas low-risk patients may benefit from less intensive adjuvant strategies or HER2/EGFR-targeted lapatinib. Prospective validation is warranted before clinical implementation.

Cholangiocarcinoma (CCA)↗

PubMed1990

A budding and fusing journey through the secretory pathway. Genetic and In Vitro Analysis of Cell Compartmentalization: A UCLA symposium, Taos, NM, USA, February 3-9, 1990.

Reconstitution of vesicular transport events and the molecular and genetic analysis of the secretory pathway have taken the field of membrane traffic into a new era. Already, proteins have been discovered that facilitate multiple transport steps, and studies of the identities and modes of action of additional transport components, such as those that specify the targets of transport vesicles, will soon follow. Even after we understand how transport vesicles form, find their targets, and then fuse, other fundamental questions will still remain. How are proteins sorted into distinct transport vesicles? How is the directionality of protein transport achieved? How do organelles maintain their identities in the face of large volumes of membrane traffic? Finally, how is membrane traffic regulated? Answers to each of these fundamental questions are likely to be available in the not-too-distant future.

Animals↗

PubMed2003

FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps.

MOTIVATION: The analysis of structure, pathways and flux distributions in metabolic networks has become an important approach for understanding the functionality of metabolic systems. The need of a user-friendly platform for stoichiometric modeling of metabolic networks in silico is evident. RESULTS: The FluxAnalyzer is a package for MATLAB and facilitates integrated pathway and flux analysis for metabolic networks within a graphical user interface. Arbitrary metabolic network models can be composed by instances of four types of network elements. The abstract network model is linked with network graphics leading to interactive flux maps which allow for user input and display of calculation results within a network visualization. Therein, a large and powerful collection of tools and algorithms can be applied interactively including metabolic flux analysis, flux optimization, detection of topological features and pathway analysis by elementary flux modes or extreme pathways. The FluxAnalyzer has been applied and tested for complex networks with more than 500,000 elementary modes. Some aspects of the combinatorial complexity of pathway analysis in metabolic networks are discussed. AVAILABILITY: Upon request from the corresponding author. Free for academic users (license agreement). Special contracts are available for industrial corporations. SUPPLEMENTARY INFORMATION: http://www.mpi-magdeburg.mpg.de/projects/fluxanalyzer.

Combinatorial Chemistry Techniques↗

PubMed2026

Metabolism pathway-based subtyping in pancreatic adenocarcinoma: an integrated study by bulk RNA-sequence and machine learning algorithms.

BACKGROUND: Pancreatic adenocarcinoma (PAAD) is highly aggressive, and its tumor microenvironment has significant metabolic and immune microenvironment complexity and genomic instability. In this study, by integrating the metabolic pathway activity score and clinical data, we constructed a novel risk assessment model to reveal the unique biological behavior and clinical significance behind different PAAD subtypes. METHODS: In this study, the transcriptome and clinical data of TCGA and GSE57495 databases were integrated to explore the interaction between metabolic pathways. Based on unsupervised clustering analysis of pathway activity and survival prognosis, patients with PAAD were classified into metabolic subtypes with significant prognostic differences. Subsequently, we assessed the heterogeneity of these subtypes in terms of clinical outcomes, genomic characteristics, and immune microenvironment composition. Based on the differentially expressed genes (DEGs) among metabolic subtypes, a clinical prognostic risk model and nomogram were constructed, which were double-validated by GSE57495-independent cohort and GSE57495 + TCGA-PAAD combined cohort. Finally, the correlations between risk scores (RSs) and signaling pathway activity and tumor immune microenvironment characteristics were evaluated. RESULTS: Based on metabolic pathway correlation and prognostic information, 240 patients in the TCGA-PAAD and GSE57495 datasets were divided into three subgroups. There were significant differences between subgroups in gene expression, pathway activity, clinical prognosis, and immune infiltration characteristics among the subtypes. Using machine learning algorithms, an RS model was constructed from DEGs among the subgroups, with the random forest method showing the best performance. A nomogram integrating the RS and clinical indicators demonstrated excellent predictive accuracy for 1-, 3-, and 5-year survival rates, confirming the RS as an independent prognostic factor. High- and low-risk groups exhibited significant differences in immune infiltration, pathway activity, and gene mutations. Drug sensitivity analysis showed that the high-risk group was more sensitive to AZD6244, ABT737, and other drugs. CONCLUSION: This study stratified patients with PAAD into three subgroups based on metabolic pathways and prognostic information, revealing significant differences in clinical outcomes, immune characteristics, and genetic mutations. The robust RS model developed from these findings demonstrated strong predictive power for patient survival and identified promising therapeutic strategies, providing valuable insights for advancing precision medicine in PAAD.

immune microenvironment↗

PubMed1989

Operant conditioning of head-waving in Aplysia. III. Cellular analysis of possible reinforcement pathways.

Operant conditioning of the head-waving response in Aplysia, as well as conditioning of the electrical activity of identified neck muscles, can be induced readily when bright light is used as aversive reinforcement (Cook and Carew, 1986, 1989b). A cellular analysis of this type of operant conditioning requires an understanding of the neural circuitry that underlies the reinforcement pathways involved in the conditioning. In the present paper we describe a cellular analysis of possible reinforcement pathways that mediate the aversive effects of bright light in the CNS of Aplysia. Using a semi-intact "split-body" preparation, we explored the effects of bright light on the operant response pathway by recording intracellularly from identified pedal neck and body wall motor neurons, which contribute to the operant response. In these experiments we identified 2 light-sensitive pathways. One pathway, from the eyes and rhinophores, mediated functional inhibition of light-induced excitation of pedal motor neurons. The other pathway, from the oral veil (cerebral ganglion nerves C1-C3) mediated significant excitation of the same motor cells. Randomly occurring blank trials ruled out the possibility that the light-induced effects were due to sampling bias. Finally, surgical isolation of the CNS from the periphery showed that none of the effects of light were due to direct illumination of central neurons. This identification of candidate reinforcement pathways will facilitate a cellular analysis of operant conditioning of head-waving in Aplysia.

Animals↗

PubMed2002

Phi value analysis of heterogeneity in pathways of allosteric transitions: Evidence for parallel pathways of ATP-induced conformational changes in a GroEL ring.

What are the mechanisms of ligand-induced allosteric transitions in proteins? A powerful method to characterize pathways and transition states of reactions is phi value analysis. A phi value is the ratio between the changes on a perturbation (e.g., mutation) in the activation and equilibrium free energies of a reaction. Here, phi value analysis is used to characterize the ATP-induced allosteric transitions of GroEL by using changes in ATP concentration as perturbations. GroEL consists of two stacked back-to-back heptameric rings that bind ATP with positive cooperativity within rings and negative cooperativity between rings. Evidence is presented for the existence of parallel pathways for the allosteric transition of each ring. In both allosteric transitions, there is an abrupt ATP-dependent switch from a pathway with ATP-binding sites in the transition state that are very similar to those of the initial T state (phi = 0) to a pathway with a phi value of approximately 0.3. The phi value procedure outlined here should be useful in mapping the energy landscape of allosteric transitions of other proteins.

Adenosine Triphosphate↗

PubMed2000

Linkage analysis of candidate endothelin pathway genes in nonsyndromic familial orofacial cleft.

There is good evidence from linkage analysis and mouse model knockouts that the endothelin-1 gene (EDN1) is a good candidate for non-syndromic orofacial cleft (OFC) disease. EDN1 maps to the chromosomal region of the OFC1 locus in 6p23. Therefore we have examined three other candidate genes in the endothelin pathway (ECE1, EDNRA and EDNRB, which map to chromosomes 1, 4 and 13 respectively) in a linkage study of 9 families with OFC, where the disorder is not linked to chromosome 6p23. The total lod score for these 9 multiplex families never exceeded -2.00 and thus our data suggest that EDN1 and related genes are not involved in non-syndromic familial OFC.

Animals↗

PubMed1998

Usage of activating mutations in the analysis of cytokine signal transduction pathways.

Cytokine signal transduction pathways are highly redundant and complex. The analysis of the structure and function of signal transduction molecules was conventionally done by using mutated or truncated receptors, dominant negative molecules, and knockout mice. These methods are designed to look at the result of a subtraction of a part of the whole signal transduction pathway. In contrast, analysis using activating mutations of a signal transduction molecule is designed to look at the downstream result of one pathway which originated from the pertinent molecule. This method is less influenced by other signal transduction molecules which may have an overlapping effect on the downstream molecules. By combining both the subtraction and activating methods, we can gain more insight into the complex interactions between signal transduction molecules. An activating mutation of a signal transduction molecule is usually found as an oncogene. However, known oncogenes are not always the molecules of interest. In this review, several methods to create activating mutations of a target molecule are discussed.

Animals↗

PubMed1998

Provider overhauls pathway procedures to improve outcomes analysis, care efficiency.

Revamping your clinical pathways to make them even more efficient and effective. Anne Arundel Medical Center's successful total hip/total knee replacement pathway has already slashed length of stay 48%, but officials weren't satisfied. They've redesigned the pathway's documentation process to get consistent data for accurately measuring patient outcomes--and have improved efficiency and patient care and education as well. Find out how the new system works and why there's always room for improvement.

Arthroplasty, Replacement, Hip↗

PubMed1999

Role of a complex containing Rad17, Mec3, and Ddc1 in the yeast DNA damage checkpoint pathway.

Genetic analysis has suggested that RAD17, RAD24, MEC3, and DDC1 play similar roles in the DNA damage checkpoint control in budding yeast. These genes are required for DNA damage-induced Rad53 phosphorylation and considered to function upstream of RAD53 in the DNA damage checkpoint pathway. Here we identify Mec3 as a protein that associates with Rad17 in a two-hybrid screen and demonstrate that Rad17 and Mec3 interact physically in vivo. The amino terminus of Rad17 is required for its interaction with Mec3, and the protein encoded by the rad17-1 allele, containing a missense mutation at the amino terminus, is defective for its interaction with Mec3 in vivo. Ddc1 interacts physically and cosediments with both Rad17 and Mec3, indicating that these three proteins form a complex. On the other hand, Rad24 is not found to associate with Rad17, Mec3, and Ddc1. DDC1 overexpression can partially suppress the phenotypes of the rad24Delta mutation: sensitivity to DNA damage, defect in the DNA damage checkpoint and decrease in DNA damage-induced phosphorylation of Rad53. Taken together, our results suggest that Rad17, Mec3, and Ddc1 form a complex which functions downstream of Rad24 in the DNA damage checkpoint pathway.

Alleles↗

PubMedDate not supplied

Comprehensive analysis of blood coagulation pathways in teleostei: evolution of coagulation factor genes and identification of zebrafish factor VIIi.

It is not clear how the complex mammalian coagulation pathways evolved from an entirely dissimilar invertebrate coagulation cascade. Comprehensive analysis of pro-coagulant factors and their regulators is lacking in early vertebrates to discern the mechanism of evolution of these genes from the invertebrates. To elucidate the coagulation pathways found in early vertebrates, zebrafish cDNAs/gene orthologues for major coagulant, anticoagulant, and fibrinolytic proteins were identified and characterized by homology to mammalian sequences. We found that zebrafish carry all hemostatic genes present in mammals, providing evidence that the coagulation system of teleosts is nearly identical to mammals. Zebrafish factor VII and X genes were identified and analyzed to reveal a novel factor VII-like gene flanked by the factor VII and factor X genes. This gene encodes a protein homologous to factor VII, but lacks critical residues for factor VII activity. Expression of the factor VII-like protein (named factor VIIi) demonstrated that it functions as an inhibitor of blood coagulation in biochemical assays using zebrafish or human plasmas. Analysis of intergenic DNA between the zebrafish VII/VIIi/X gene cluster and a Drosophila trypsin gene cluster revealed significant homology, and based upon these data, we propose a model for a rapid evolution of coagulation factors from the invertebrates.

Amino Acid Sequence↗

PubMed2003

Dissection of floral induction pathways using global expression analysis.

Flowering of the reference plant Arabidopsis thaliana is controlled by several signaling pathways, which converge on a small set of genes that function as pathway integrators. We have analyzed the genomic response to one type of floral inductive signal, photoperiod, to dissect the function of several genes transducing this stimulus, including CONSTANS, thought to be the major output of the photoperiod pathway. Comparing the effects of CONSTANS with those of FLOWERING LOCUS T, which integrates inputs from CONSTANS and other floral inductive pathways, we find that expression profiles of shoot apices from plants with mutations in either gene are very similar. In contrast, a mutation in LEAFY, which also acts downstream of CONSTANS, has much more limited effects. Another pathway integrator, SUPPRESSOR OF OVEREXPRESSION OF CO 1, is responsive to acute induction by photoperiod even in the presence of the floral repressor encoded by FLOWERING LOCUS C. We have discovered a large group of potential floral repressors that are down-regulated upon photoperiodic induction. These include two AP2 domain-encoding genes that can repress flowering. The two paralogous genes, SCHLAFMUTZE and SCHNARCHZAPFEN, share a signature with partial complementarity to the miR172 microRNA, whose precursor we show to be induced upon flowering. These and related findings on SPL genes suggest that microRNAs play an important role in the regulation of flowering.

Animals↗