Log in

Relevant bibliographies by topics / Pathway analyses / Journal articles

To see the other types of publications on this topic, follow the link: Pathway analyses.

Journal articles on the topic 'Pathway analyses'

Author: Grafiati

Published: 5 June 2025

Last updated: 2 August 2025

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles

Select a source type:

Consult the top 50 journal articles for your research on the topic 'Pathway analyses.'

Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.

You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.

Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.

1

Ryan V, William G., Ali Sajid Imami, Hunter Eby, et al. "Interpreting and visualizing pathway analyses using embedding representations with PAVER." Bioinformation 20, no. 7 (2024): 700–704. http://dx.doi.org/10.6026/973206300200700.

Full text

Abstract:

Omics studies use large-scale high-throughput data to explain changes underlying different traits or conditions. However, omics analysis often results in long lists of pathways that are difficult to interpret. Therefore, it is of interest to describe a tool named PAVER (Pathway Analysis Visualization with Embedding Representations) for large scale genomic analysis. PAVER curates similar pathways into groups, identifies the pathway most representative of each group, and provides publication-ready intuitive visualizations. PAVER clusters pathways defined by their vector embedding representations

APA, Harvard, Vancouver, ISO, and other styles

2

Choi, Shing Wan, Judit García-González, Yunfeng Ruan, et al. "PRSet: Pathway-based polygenic risk score analyses and software." PLOS Genetics 19, no. 2 (2023): e1010624. http://dx.doi.org/10.1371/journal.pgen.1010624.

Full text

Abstract:

Polygenic risk scores (PRSs) have been among the leading advances in biomedicine in recent years. As a proxy of genetic liability, PRSs are utilised across multiple fields and applications. While numerous statistical and machine learning methods have been developed to optimise their predictive accuracy, these typically distil genetic liability to a single number based on aggregation of an individual’s genome-wide risk alleles. This results in a key loss of information about an individual’s genetic profile, which could be critical given the functional sub-structure of the genome and the heterog

APA, Harvard, Vancouver, ISO, and other styles

3

Tanabe, Shihori, Sabina Quader, Ryuichi Ono, et al. "Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway." Current Issues in Molecular Biology 47, no. 6 (2025): 466. https://doi.org/10.3390/cimb47060466.

Full text

Abstract:

The coronavirus pathogenesis pathway, which consists of severe acute respiratory syndrome (SARS) coronavirus infection and signaling pathways, including the interferon pathway, the transforming growth factor beta pathway, the mitogen-activated protein kinase pathway, the apoptosis pathway, and the inflammation pathway, is activated upon coronaviral infection. An artificial intelligence approach based on machine learning was utilized to develop models with images of the coronavirus pathogenesis pathway to predict the activation states. Data on coronaviral infection held in a database were analy

APA, Harvard, Vancouver, ISO, and other styles

4

Luo, Mengxian, Chuanmei Zhu, Yujie Xie, et al. "Network and Pathway Analyses of Exercise Therapy on Cerebral Infarction Related Genes." Journal of Physical Medicine and Rehabilitation 6, no. 1 (2024): 26–34. https://doi.org/10.33696/rehabilitation.6.043.

Full text

Abstract:

Background: Few efforts were made to conduct a comprehensive analysis of potential genes within the action of exercise therapy on cerebral infarction (CI). Methods: We used RNA sequencing (RNA-seq) and weighted gene co-expression network analysis (WGCNA) to provide more important insights information than the conventional single-gene analyses. We performed RNA-Seq on the macroscopically preserved and lesioned SD rat CI model (N=4 pairs). The WGCNA constructed a correlation network and identified the modules in the dataset by the dynamic tree-cutting algorithm. We defined the module membership

APA, Harvard, Vancouver, ISO, and other styles

5

Sahajpal, Nikhil Shri, Ashis Mondal, Meenakshi Ahluwalia, et al. "Clinical utility of comprehensive genomic pathway and integrated network analyses in personalized oncology." Journal of Clinical Oncology 38, no. 15_suppl (2020): e14051-e14051. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e14051.

Full text

Abstract:

e14051 Background: Adoption of next-generation sequencing (NGS) technology in routine clinical practice has enabled the detection of genetic aberrations such as single nucleotide variants, copy number alterations, and gene fusions. Pathway and network analyses (PNA) are key components for evaluation of NGS data in a clinical setting to explain findings involving thousands of altered genes and proteins with a smaller and more interpretable set of altered processes. Though PNA have been applied to identify driver genes and pathways in cohort-based analyses, its application in precision oncology

APA, Harvard, Vancouver, ISO, and other styles

6

Mok, Kim, Lee, et al. "HisCoM-PAGE: Hierarchical Structural Component Models for Pathway Analysis of Gene Expression Data." Genes 10, no. 11 (2019): 931. http://dx.doi.org/10.3390/genes10110931.

Full text

Abstract:

Although there have been several analyses for identifying cancer-associated pathways, based on gene expression data, most of these are based on single pathway analyses, and thus do not consider correlations between pathways. In this paper, we propose a hierarchical structural component model for pathway analysis of gene expression data (HisCoM-PAGE), which accounts for the hierarchical structure of genes and pathways, as well as the correlations among pathways. Specifically, HisCoM-PAGE focuses on the survival phenotype and identifies its associated pathways. Moreover, its application to real

APA, Harvard, Vancouver, ISO, and other styles

7

Chae, H., M. Kim, and E. Lee. "P014 Bioinformatic analysis of gene expression profiling data on shift work sleep disorder." Sleep Advances 5, Supplement_1 (2024): A34. https://doi.org/10.1093/sleepadvances/zpae070.096.

Full text

Abstract:

Abstract Introduction Shift work sleep disorder (SWSD) is a circadian rhythm sleep disorder affecting individuals who work nontraditional hours, such as night shifts. The complexity of SWSD arises from the altered interactions between thousands of genes, making it challenging to prioritize disease mechanism, biomarkers, and drug targets. This study aims to identify the patterns of pathways and upstream regulators involved in SWSD using a transcriptome from isolated peripheral blood mononuclear cells (PBMCs) of hospital nurses. Method We conducted bioinformatic analyses on the GSE122541 dataset

APA, Harvard, Vancouver, ISO, and other styles

8

Thibodeau, Asa, and Dong-Guk Shin. "TriPOINT: a software tool to prioritize important genes in pathways and their non-coding regulators." Bioinformatics 35, no. 15 (2018): 2686–89. http://dx.doi.org/10.1093/bioinformatics/bty998.

Full text

Abstract:

Abstract Summary Current approaches for pathway analyses focus on representing gene expression levels on graph representations of pathways and conducting pathway enrichment among differentially expressed genes. However, gene expression levels by themselves do not reflect the overall picture as non-coding factors play an important role to regulate gene expression. To incorporate these non-coding factors into pathway analyses and to systematically prioritize genes in a pathway we introduce a new software: Triangulation of Perturbation Origins and Identification of Non-Coding Targets. Triangulati

APA, Harvard, Vancouver, ISO, and other styles

9

Dessie, Eskezeia Y., Lili Ding, Latha Satish, and Tesfaye B. Mersha. "Co-Expression Network and Machine Learning Analysis of Transcriptomics Data Identifies Distinct Gene Signatures and Pathways in Lesional and Non-Lesional Atopic Dermatitis." Journal of Personalized Medicine 14, no. 9 (2024): 960. http://dx.doi.org/10.3390/jpm14090960.

Full text

Abstract:

Background: Atopic dermatitis (AD) is a common inflammatory skin condition with complex origins. Current treatments often yield suboptimal results due to an incomplete understanding of its underlying mechanisms. This study aimed to identify pathway and gene signatures that distinguish between lesional AD, non-lesional AD, and healthy skin. Method: We conducted differential gene expression and co-expression network analyses to identify differentially co-expressed genes (DCEGs) in lesional AD vs. healthy skin, lesional vs. non-lesional AD, and non-lesional AD vs. healthy skin. Modules associated

APA, Harvard, Vancouver, ISO, and other styles

10

Xuan, Huidong, Yanzhong Huang, Li Zhou, et al. "Key Soybean Seedlings Drought-Responsive Genes and Pathways Revealed by Comparative Transcriptome Analyses of Two Cultivars." International Journal of Molecular Sciences 23, no. 5 (2022): 2893. http://dx.doi.org/10.3390/ijms23052893.

Full text

Abstract:

Seedling drought stress is one of the most important constraints affecting soybean yield and quality. To unravel the molecular mechanisms under soybean drought tolerance, we conducted comprehensive comparative transcriptome analyses of drought-tolerant genotype Jindou 21 (JD) and drought-sensitive genotype Tianlong No.1 (N1) seedlings that had been exposed to drought treatment. A total of 6038 and 4112 differentially expressed genes (DEGs) were identified in drought-tolerant JD and drought-sensitive N1, respectively. Subsequent KEGG pathway analyses showed that numerous DEGs in JD are predomin

APA, Harvard, Vancouver, ISO, and other styles

11

Dai, Tingting, Jiyu Gong, and Shuying Liu. "Prediction of molecular mechanism of processed ginseng in the treatment of heart failure based on network pharmacology and molecular docking technology." Medicine 102, no. 49 (2023): e36576. http://dx.doi.org/10.1097/md.0000000000036576.

Full text

Abstract:

Background: Heart failure (HF) is the most common cardiovascular disease in clinics. Processed Panax ginseng C.A. Mey. Products have significant therapeutic effects on HF. Therefore, it is of great significance to explore the mechanism of action of Processed Panax ginseng C.A. Mey. Products in the treatment of HF. Methods: The saponin-like constituents of 3 different ginseng preparations were characterized by UPLC/QE-MS and the identified saponin constituents were subjected to network pharmacological analysis. Protein–protein interaction analyses of the targets of different ginseng preparation

APA, Harvard, Vancouver, ISO, and other styles

12

Zhang, Yin-Ping, Yao-Zhong Liu, Yan Guo, et al. "Pathway-Based Association Analyses Identified TRAIL Pathway for Osteoporotic Fractures." PLoS ONE 6, no. 7 (2011): e21835. http://dx.doi.org/10.1371/journal.pone.0021835.

Full text

APA, Harvard, Vancouver, ISO, and other styles

13

Zhang, Yin-Ping, Yao-Zhong Liu, Yan Guo, et al. "Pathway-based association analyses identified TRAIL pathway for osteoporotic fractures." Bone 47 (October 2010): S398. http://dx.doi.org/10.1016/j.bone.2010.09.177.

Full text

APA, Harvard, Vancouver, ISO, and other styles

14

German, Benjamin D., Jeffrey Allen Borgia, Ankur D. Naqib, et al. "RNA pathway enrichment in serum-based mass spectroscopy prognostic analyses." Journal of Clinical Oncology 38, no. 15_suppl (2020): e15197-e15197. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e15197.

Full text

Abstract:

e15197 Background: Veristrat(VS) good and poor labels were found to be prognostic in the front-line NSCLC setting with or without immune checkpoint inhibitors. Little is known about RNA expression data corresponding to these good and poor prognostic labels. Methods: Raw RNA seq expression data was obtained from TEMPUS XP RNA analysis. Sequences were filtered for allowing only genes that had an overall count of at least 20 across all samples. Samples were then processed through the EdgeR analysis in the R programming environment. Along with a Z-scored heatmap, PCA plot was also generated. Diffe

APA, Harvard, Vancouver, ISO, and other styles

15

Han, Junwei, Chunquan Li, Haixiu Yang, et al. "A novel dysregulated pathway-identification analysis based on global influence of within-pathway effects and crosstalk between pathways." Journal of The Royal Society Interface 12, no. 102 (2015): 20140937. http://dx.doi.org/10.1098/rsif.2014.0937.

Full text

Abstract:

Identifying dysregulated pathways from high-throughput experimental data in order to infer underlying biological insights is an important task. Current pathway-identification methods focus on single pathways in isolation; however, consideration of crosstalk between pathways could improve our understanding of alterations in biological states. We propose a novel method of pathway analysis based on global influence (PAGI) to identify dysregulated pathways, by considering both within-pathway effects and crosstalk between pathways. We constructed a global gene–gene network based on the relationship

APA, Harvard, Vancouver, ISO, and other styles

16

Jiang, Xiao-wen, Hong-yuan Lu, Ziru Xu, et al. "In Silico Analyses for Key Genes and Molecular Genetic Mechanism in Epilepsy and Alzheimer’s Disease." CNS & Neurological Disorders - Drug Targets 17, no. 8 (2018): 608–17. http://dx.doi.org/10.2174/1871527317666180724150839.

Full text

Abstract:

Background: Epilepsy and Alzheimer's disease are common neuropathies with a complex pathogenesis. Both of them have some correlations in etiology, pathogenesis, pathological changes, clinical manifestations and treatment. Objective: This study investigated the key genes and molecular genetic mechanism in epilepsy and Alzheimer’s disease by bioinformatics analysis. Method: Two gene expression profiles were used to screen differentially expressed genes by GEO2R tool. The Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway enrichment analysis was performed using the Databa

APA, Harvard, Vancouver, ISO, and other styles

17

Lilleberg, Stan L., Jeffrey Durocher, Jill Hempel, et al. "In-Depth Mutation Scanning of Signaling Pathway Genes Involved in the Development and Targeted Treatment of Hematopoietic Malignancies." Blood 106, no. 11 (2005): 4399. http://dx.doi.org/10.1182/blood.v106.11.4399.4399.

Full text

Abstract:

Abstract The Raf/MEK/ERK, Wnt/beta-catenin, JAK/STAT and PI3K/Akt signal transduction pathways have key roles in the regulation of cell cycle progression and apoptosis, and are current focal points of therapeutic development and intervention strategies for hematopoietic neoplasias. These pathways have several regulatory components that keep proliferative and anti-apoptotic mechanisms in check, but which can also drive neoplastic processes when their functions are altered by genetic and epigenetic events. Links between critical pathways are also being established and, although only partially un

APA, Harvard, Vancouver, ISO, and other styles

18

Pei, Lishan, Xia Shen, Yonggang Yan, et al. "Virtual Screening of the Multi-pathway and Multi-gene Regulatory Molecular Mechanism of Dachengqi Decoction in the Treatment of Stroke Based on Network Pharmacology." Combinatorial Chemistry & High Throughput Screening 23, no. 8 (2020): 775–87. http://dx.doi.org/10.2174/1386207323666200311113747.

Full text

Abstract:

Background: Stroke is ranked second among diseases that cause mortality worldwide. Owing to its complicated pathogenesis, no satisfactory treatment strategies for stroke are available. Dachengqi decoction (DCQD), a traditional Chinese herbal medicine, has been widely used in China for a long time, as it has a good effect on stroke. However, the molecular mechanism underlying this effect of DCQD is unclear. Objective: In the present study, we aimed to reveal and explore the multi-pathway and multi-gene regulatory molecular mechanism of Dachengqi decoction in the treatment of stroke. Methods: In

APA, Harvard, Vancouver, ISO, and other styles

19

Jiao, Xinyi, Haiying Liu, Qinan Lu, et al. "Study on the Mechanism of Prunella Vulgaris L on Diabetes Mellitus Complicated with Hypertension Based on Network Pharmacology and Molecular Docking Analyses." Journal of Diabetes Research 2021 (October 15, 2021): 1–14. http://dx.doi.org/10.1155/2021/9949302.

Full text

Abstract:

The role of traditional Chinese medicine Prunella vulagaris L in the treatment of tumors and inflammation has been widely confirmed. We found that some signaling pathways of Prunella vulgaris L action can also regulate diabetes and hypertension, so we decided to study the active ingredients, potential targets and signaling pathway of Prunrlla vulgaris L, and explore the “multi-target, multi-pathway” molecular mechanism of Prunella vulgaris L on diabetes mellitus complicated with hypertension(DH). Methods. Based on TCMSP(Traditional Chinese Medicine Systems Pharmacology Database and Analysis Pl

APA, Harvard, Vancouver, ISO, and other styles

20

Poretsky, Elly, and Alisa Huffaker. "MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information." PeerJ 8 (November 9, 2020): e10264. http://dx.doi.org/10.7717/peerj.10264.

Full text

Abstract:

The rapid assignment of genotypes to phenotypes has been a historically challenging process. The discovery of genes encoding biosynthetic pathway enzymes for defined plant specialized metabolites has been informed and accelerated by the detection of gene clusters. Unfortunately, biosynthetic pathway genes are commonly dispersed across chromosomes or reside in genes clusters that provide little predictive value. More reliably, transcript abundance of genes underlying biochemical pathways for plant specialized metabolites display significant coregulation. By rapidly identifying highly coexpresse

APA, Harvard, Vancouver, ISO, and other styles

21

Liu, Guiyou, Fang Zhang, Yongshuai Jiang, et al. "Integrating genome-wide association studies and gene expression data highlights dysregulated multiple sclerosis risk pathways." Multiple Sclerosis Journal 23, no. 2 (2016): 205–12. http://dx.doi.org/10.1177/1352458516649038.

Full text

Abstract:

Background: Much effort has been expended on identifying the genetic determinants of multiple sclerosis (MS). Existing large-scale genome-wide association study (GWAS) datasets provide strong support for using pathway and network-based analysis methods to investigate the mechanisms underlying MS. However, no shared genetic pathways have been identified to date. Objective: We hypothesize that shared genetic pathways may indeed exist in different MS-GWAS datasets. Methods: Here, we report results from a three-stage analysis of GWAS and expression datasets. In stage 1, we conducted multiple pathw

APA, Harvard, Vancouver, ISO, and other styles

22

Ruskovska, Tatjana, Irena Budić-Leto, Karla Fabiola Corral-Jara, et al. "Systematic Bioinformatic Analyses of Nutrigenomic Modifications by Polyphenols Associated with Cardiometabolic Health in Humans—Evidence from Targeted Nutrigenomic Studies." Nutrients 13, no. 7 (2021): 2326. http://dx.doi.org/10.3390/nu13072326.

Full text

Abstract:

Cardiometabolic disorders are among the leading causes of mortality in the human population. Dietary polyphenols exert beneficial effects on cardiometabolic health in humans. Molecular mechanisms, however, are not completely understood. Aiming to conduct in-depth integrative bioinformatic analyses to elucidate molecular mechanisms underlying the protective effects of polyphenols on cardiometabolic health, we first conducted a systematic literature search to identify human intervention studies with polyphenols that demonstrate improvement of cardiometabolic risk factors in parallel with signifi

APA, Harvard, Vancouver, ISO, and other styles

23

Cho-Baker, Sugene, Margarita Olivera-Aguilar, and Daniel Fishtein. "Using Latent Class Analysis to Link Career and Technical Education in Adolescence and Work and School Transitions in Young Adulthood." Career and Technical Education Research 46, no. 2 (2021): 59–79. http://dx.doi.org/10.5328/cter46.2.59.

Full text

Abstract:

Career and technical education (CTE) has recently gained national attention as a means of promoting college and career readiness. However, little is known about the joint trajectories of school and work during and following CTE participation in high school. Using the Educational Longitudinal Study of 2002, we conducted latent class analyses to examine latent pathways connecting high school CTE participation with employment during high school, as well as the subsequent educational and work transitions. Four latent pathways were identified, defined as: (a) CTE-to-work pathway, (b) BA-focused pat

APA, Harvard, Vancouver, ISO, and other styles

24

Andre, F., P. Dessen, B. Job, S. Delaloge, L. Pusztai, and V. Lazar. "Functional pathways analyses to identify candidate therapeutic targets in triple-negative breast cancer." Journal of Clinical Oncology 27, no. 15_suppl (2009): 569. http://dx.doi.org/10.1200/jco.2009.27.15_suppl.569.

Full text

Abstract:

569 Background: In the present study, we have analyzed dysregulated pathways in triple-negative breast cancers. Methods: Two datasets of cDNA arrays were used to identify differentially expressed genes between triple negative breast cancer and either normal/benign breast tissue or other molecular classes. The first dataset (I) was included 165 samples. The second data set (II) included 148 samples. Pathway analyses (gene set) were done based using BRB array tool and a software developed in house (SBIME). Results: Fifteen and 27 patients presented a triple negative breast cancer in the dataset

APA, Harvard, Vancouver, ISO, and other styles

25

Heft Neal, Molly E., Apurva D. Bhangale, Andrew C. Birkeland, et al. "Prognostic Significance of Oxidation Pathway Mutations in Recurrent Laryngeal Squamous Cell Carcinoma." Cancers 12, no. 11 (2020): 3081. http://dx.doi.org/10.3390/cancers12113081.

Full text

Abstract:

Organ preservation protocols are commonly used as first line therapy for advanced laryngeal cancer. Recurrence thereafter is associated with poor survival. The aim of this study is to identify genetic alterations associated with survival among patients with recurrent laryngeal cancer undergoing salvage laryngectomy. Sixty-two patients were sequenced using a targeted panel, of which twenty-two also underwent transcriptome sequencing. Alterations were grouped based on biologic pathways and survival outcomes were assessed using Kaplan-Meier analysis and multivariate cox regression. Select pathway

APA, Harvard, Vancouver, ISO, and other styles

26

Afsari, Bahman, Donald German, and Elana J. Fertig. "Learning Dysregulated Pathways in Cancers from Differential Variability Analysis." Cancer Informatics 13s5 (January 2014): CIN.S14066. http://dx.doi.org/10.4137/cin.s14066.

Full text

Abstract:

Analysis of gene sets can implicate activity in signaling pathways that is responsible for cancer initiation and progression, but is not discernible from the analysis of individual genes. Multiple methods and software packages have been developed to infer pathway activity from expression measurements for set of genes targeted by that pathway. Broadly, three major methodologies have been proposed: over-representation, enrichment, and differential variability. Both over-representation and enrichment analyses are effective techniques to infer differentially regulated pathways from gene sets with

APA, Harvard, Vancouver, ISO, and other styles

27

Liu, Yu, and Mark R. Chance. "Pathway Analyses and Understanding Disease Associations." Current Genetic Medicine Reports 1, no. 4 (2013): 230–38. http://dx.doi.org/10.1007/s40142-013-0025-3.

Full text

APA, Harvard, Vancouver, ISO, and other styles

28

Hu, Yaodong, Jiayu Su, Liyuan Cheng, Dan Lan, and Diyan Li. "Pectoral muscle transcriptome analyses reveal high-altitude adaptations in Tibetan chickens." Animal Biology 70, no. 4 (2020): 385–400. http://dx.doi.org/10.1163/15707563-bja10026.

Full text

Abstract:

Abstract The largest muscles in fowl are the pectorals, which provide the power required for birds to fly. Tibetan chickens show specific adaptations to high-altitude conditions, but changes in the muscle transcriptome associated with these adaptations have not been characterized yet. Therefore, in this study, we used next-generation sequencing technologies to generate eight libraries of mRNA sequences for four Tibetan chickens and four Beijing fatty chickens. A comprehensive transcriptome analysis was performed. In the eight samples, 12 333 annotated protein-coding genes were expressed. Among

APA, Harvard, Vancouver, ISO, and other styles

29

Chen, Yihong, Xiumei Zhao, Bei Gan, Leiyi Jin, Juanbing Wei, and Jianying Yan. "Metabolomics and proteomics analyses reveal the role of the glycerophospholipid metabolism pathway in unexplained recurrent spontaneous abortion." PeerJ 13 (April 30, 2025): e19317. https://doi.org/10.7717/peerj.19317.

Full text

Abstract:

Background Unexplained recurrent spontaneous abortion (URSA) is a complex pregnancy complication with a high miscarriage rate. Incomprehensive understanding of the molecular mechanism in URSA also leads to a lack of effective treatment methods. Hence, the current study aimed to explore the underlying pathogenesis of URSA applying metabonomic and bioinformatics analysis. Methods The decidual tissues of eight URSA samples and eight normal pregnancy (normal control, NC) samples were collected for liquid chromatography-mass spectrometry (LC-MS) analysis using the Progenesis QI metabolomics softwar

APA, Harvard, Vancouver, ISO, and other styles

30

Li, Zhaoyan, Lei Zhong, Zhenwu Du, et al. "Network Analyses of Differentially Expressed Genes in Osteoarthritis to Identify Hub Genes." BioMed Research International 2019 (April 16, 2019): 1–9. http://dx.doi.org/10.1155/2019/8340573.

Full text

Abstract:

Background. Osteoarthritis (OA) is the most common degenerative disease in orthopedics. However, the cause and underlying molecular mechanisms are not clear. This study aims to identify the hub genes and pathways involved in the occurrence of osteoarthritis. Methods. The raw data of GSE89408 were downloaded from the Gene Expression Omnibus (GEO) database, and the differentially expressed genes (DEGs) were identified by R software. The DAVID database was used for pathway and gene ontology analysis, and p<0.05 and gene count >2 were set as the cut-off point. Moreover, protein-protein inter

APA, Harvard, Vancouver, ISO, and other styles

31

Jahn, Ulrike, Harald Huber, Wolfgang Eisenreich, Michael Hügler, and Georg Fuchs. "Insights into the Autotrophic CO2 Fixation Pathway of the Archaeon Ignicoccus hospitalis: Comprehensive Analysis of the Central Carbon Metabolism." Journal of Bacteriology 189, no. 11 (2007): 4108–19. http://dx.doi.org/10.1128/jb.00047-07.

Full text

Abstract:

ABSTRACT Ignicoccus hospitalis is an autotrophic hyperthermophilic archaeon that serves as a host for another parasitic/symbiotic archaeon, Nanoarchaeum equitans. In this study, the biosynthetic pathways of I. hospitalis were investigated by in vitro enzymatic analyses, in vivo 13C-labeling experiments, and genomic analyses. Our results suggest the operation of a so far unknown pathway of autotrophic CO2 fixation that starts from acetyl-coenzyme A (CoA). The cyclic regeneration of acetyl-CoA, the primary CO2 acceptor molecule, has not been clarified yet. In essence, acetyl-CoA is converted int

APA, Harvard, Vancouver, ISO, and other styles

32

Baurley, James W., Anders Kjærsgaard, Michael E. Zwick, et al. "Bayesian Pathway Analysis for Complex Interactions." American Journal of Epidemiology 189, no. 12 (2020): 1610–22. http://dx.doi.org/10.1093/aje/kwaa130.

Full text

Abstract:

Abstract Modern epidemiologic studies permit investigation of the complex pathways that mediate effects of social, behavioral, and molecular factors on health outcomes. Conventional analytical approaches struggle with high-dimensional data, leading to high likelihoods of both false-positive and false-negative inferences. Herein, we describe a novel Bayesian pathway analysis approach, the algorithm for learning pathway structure (ALPS), which addresses key limitations in existing approaches to complex data analysis. ALPS uses prior information about pathways in concert with empirical data to id

APA, Harvard, Vancouver, ISO, and other styles

33

Li, Zhuo, Xiaomin Hou, Xuehua Liu, Linlin Ma, and Jiewen Tan. "Hyperbaric Oxygen Therapy-Induced Molecular and Pathway Changes in a Rat Model of Spinal Cord Injury: A Proteomic Analysis." Dose-Response 20, no. 4 (2022): 155932582211415. http://dx.doi.org/10.1177/15593258221141579.

Full text

Abstract:

Hyperbaric Oxygen Therapy (HBOT) has definitive therapeutic effects on spinal cord injury (SCI), but its mechanism of action is still unclear. Here, we’ve conducted a systemic proteomic analysis to identify differentially expressed proteins (DEPs) between SCI rats and HBOT + SCI rats. The function clustering analysis showed that the top enriched pathways of DEPs include oxygen transport activity, oxygen binding, and regulation of T cell proliferation. The results of functional and signal pathway analyses indicated that metabolic pathways, thermogenesis, LXR/RXR activation, acute phase response

APA, Harvard, Vancouver, ISO, and other styles

34

Chen, Biao, Yan Zheng, and Yanhua Liang. "Analysis of Potential Genes and Pathways Involved in the Pathogenesis of Acne by Bioinformatics." BioMed Research International 2019 (June 9, 2019): 1–8. http://dx.doi.org/10.1155/2019/3739086.

Full text

Abstract:

Acne is the eighth most frequent disease worldwide. Inflammatory response runs through all stages of acne. It is complicated and is involved in innate and adaptive immunity. This study aimed to explore the candidate genes and their relative signaling pathways in inflammatory acne using data mining analysis. Microarray data GSE6475 and GSE53795, including 18 acne lesion tissues and 18 matched normal skin tissues, were obtained. Differentially expressed genes (DEGs) were filtered and subjected to functional and pathway enrichment analyses. Protein–protein interaction (PPI) network and module ana

APA, Harvard, Vancouver, ISO, and other styles

35

Liu, Wenjun, Ville-Petteri Mäkinen, Wayne D. Tilley, and Stephen M. Pederson. "sSNAPPY: an R/Bioconductor package for single-sample directional pathway perturbation analysis." F1000Research 13 (June 13, 2024): 628. http://dx.doi.org/10.12688/f1000research.149494.1.

Full text

Abstract:

A common outcome of analysing RNA-Seq data is the detection of biological pathways with significantly altered activity between the conditions under investigation. Whilst many strategies test for over-representation of genes, showing changed expression within pre-defined gene-sets, these analyses typically do not account for gene-gene interactions encoded by pathway topologies, and are not able to directly predict the directional change of pathway activity. To address these issues we have developed sSNAPPY,now available as an R/Bioconductor package, which leverages pathway topology information

APA, Harvard, Vancouver, ISO, and other styles

36

Xin, Jingjing, Jiyong Tang, Ying Mao, Dongdong Ren, Ping Luo, and Yongyi Cui. "Comparative Transcriptome Profiling Reveals Differential Defense Responses of Resistant and Susceptible Phalaenopsis to Dickeya fangzhongdai." Horticulturae 11, no. 5 (2025): 534. https://doi.org/10.3390/horticulturae11050534.

Full text

Abstract:

Soft rot caused by Dickeya fangzhongdai is a destructive disease in Phalaenopsis production that seriously impacts the quality and yield of Phalaenopsis. To explore the molecular mechanisms underlying disease resistance, transcriptome analysis was conducted on resistant and susceptible Phalaenopsis varieties. By comparing the transcriptomes of the resistant variety ‘ES L20’ and the susceptible variety ‘Zishuijing’ after D. fangzhongdai infection, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed. The results revealed that the differentially expressed gen

APA, Harvard, Vancouver, ISO, and other styles

37

Begley, Máire, Peter A. Bron, Sinead Heuston, et al. "Analysis of the Isoprenoid Biosynthesis Pathways in Listeria monocytogenes Reveals a Role for the Alternative 2-C-Methyl-d-Erythritol 4-Phosphate Pathway in Murine Infection." Infection and Immunity 76, no. 11 (2008): 5392–401. http://dx.doi.org/10.1128/iai.01376-07.

Full text

Abstract:

ABSTRACT Most bacteria synthesize isoprenoids through one of two essential pathways which provide the basic building block, isopentyl diphosphate (IPP): either the classical mevalonate pathway or the alternative non-mevalonate 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway. However, postgenomic analyses of the Listeria monocytogenes genome revealed that this pathogen possesses the genetic capacity to produce the complete set of enzymes involved in both pathways. The nonpathogenic species Listeria innocua naturally lacks the last two genes (gcpE and lytB) of the MEP pathway, and bioinformati

APA, Harvard, Vancouver, ISO, and other styles

38

Lei, Yi, Yi Xu, Xu-feng Li, and Yan Chen. "Coexpression Network Analysis of lncRNA Associated with Overexpression of DNMT1 in Esophageal Epithelial Cells." BioMed Research International 2021 (October 8, 2021): 1–17. http://dx.doi.org/10.1155/2021/7162270.

Full text

Abstract:

Screening and preliminary identification of high DNMT1 expression-related lncRNA, which is involved in various interrelated signaling pathways, has led to the development of a theoretical basis for various types of disease mechanisms. Differential expression profiles of lncRNA and mRNA were identified in a microarray. Ten lncRNAs with high levels of variation were identified by qRT-PCR. KEGG and GO analyses were used to identify differentially expressed mRNAs. Six signaling pathways were selected based on the KEGG results of the lncRNA-mRNA expression network analysis. From the microarrays in

APA, Harvard, Vancouver, ISO, and other styles

39

Handong, Mei, Xu Xiao та Xu Sinan. "Sargent Gloryvine Extract Modulates Nuclear Factor κκB Signaling Pathway to Improve Severe Pancreatitis". Current Topics in Nutraceutical Research 22, № 2 (2024): 405–11. http://dx.doi.org/10.37290/ctnr2641-452x.22:405-411.

Full text

Abstract:

This study explored the mechanism of action of Sargent gloryvine extract in treating severe pancreatitis. We used the PubChem and SwissTargetPredicton databases to predict the potential targets. The database for Annotation, Visualization, and Integrated Discovery was used to perform Gene Ontology. The Kyoto Encyclopedia of Genes was used to perform Genomes enrichment analyses. These analyses, visualized via Cytoscape software followed by molecular docking validation, identified Salidroside, Lignans, Emodin, and Physcion as key active compounds in the extract. The protein-protein interaction ne

APA, Harvard, Vancouver, ISO, and other styles

40

Yang, Zimin, Wei Luo, Zhihong Huang, et al. "Genome-Wide Analysis of Differentially Expressed mRNAs and lncRNAs in Koi Carp Infected with Koi Herpesvirus." Viruses 14, no. 11 (2022): 2555. http://dx.doi.org/10.3390/v14112555.

Full text

Abstract:

Long noncoding RNAs (lncRNAs) constitute an emerging group of ncRNAs that modulate gene expression at the transcriptional or translational level. Koi herpesvirus (KHV), also known as Cyprinus herpesvirus type 3 (CyHV-3) and characterized by high pathogenicity and high mortality, has caused substantial economic losses in the common carp and koi carp fisheries industry. In this work, we sequenced the lncRNA and mRNA of host koi carp infected with KHV. A total of 20,178 DEmRNAs were obtained, of which 5021 mRNAs were upregulated and 15,157 mRNAs were downregulated. Both KEGG pathways and GO terms

APA, Harvard, Vancouver, ISO, and other styles

41

Yue, Li, Hui Wang, Qimike Shan, Zaituniguli Kuerban, Hongyan Mao, and Ming Yu. "Metabolomic and transcriptomic analyses of drought resistance mechanisms in sorghum varieties." PeerJ 13 (July 4, 2025): e19596. https://doi.org/10.7717/peerj.19596.

Full text

Abstract:

For a long time, sorghum breeding has focused on improving yield and quality traits, whereas little research has been conducted on drought resistance. To this end, this study evaluated the phenotypes of two sorghum varieties (GL98 and GL220) under drought stress and normal conditions, and sequenced their transcriptomes and metabolomes. After drought stress, the growth rates of the roots and shoots of GL220 exceeded those of GL98 at 72 h. A total of 6,344 differentially expressed genes (DEGs) were identified via RNA-seq differential expression analysis; these genes were significantly annotated

APA, Harvard, Vancouver, ISO, and other styles

42

Li, Heng, Nancy E. Ramia, Frédéric Borges, Anne-Marie Revol-Junelles, Finn Kvist Vogensen, and Jørgen J. Leisner. "Identification of Potential Citrate Metabolism Pathways in Carnobacterium maltaromaticum." Microorganisms 9, no. 10 (2021): 2169. http://dx.doi.org/10.3390/microorganisms9102169.

Full text

Abstract:

In the present study, we describe the identification of potential citrate metabolism pathways for the lactic acid bacterium (LAB) Carnobacterium maltaromaticum. A phenotypic assay indicated that four of six C. maltaromaticum strains showed weak (Cm 6-1 and ATCC 35586) or even delayed (Cm 3-1 and Cm 5-1) citrate utilization activity. The remaining two strains, Cm 4-1 and Cm 1-2 gave negative results. Additional analysis showed no or very limited utilization of citrate in media containing 1% glucose and 22 or 30 mM citrate and inoculated with Cm 6-1 or ATCC 35586. Two potential pathways of citra

APA, Harvard, Vancouver, ISO, and other styles

43

Zhao, Chengguo, Wenpei Ling, Chunyu Luo, Meifang Yin, and Shuzhi Qin. "Study on the Mechanism of Paeoniflorin Against Atherosclerosis Through Network Pharmacology and Molecular Docking." Journal of Biobased Materials and Bioenergy 14, no. 4 (2020): 467–75. http://dx.doi.org/10.1166/jbmb.2020.1993.

Full text

Abstract:

This study explored the mechanism of paeoniflorin (PF) against atherosclerosis (AS) at the molecular level using network pharmacology and molecular docking. The targets of PF and disease targets related to AS were obtained through literature mining and database search, the PPI network diagram was drawn, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed, and the PF structure was docked with core target. In the results, 130 common target proteins of PF and AS were obtained. GO enrichment analysis found 1071 items related to biologica

APA, Harvard, Vancouver, ISO, and other styles

44

She, Sha, Lingyu Jiang, Zhenfang Zhang, et al. "Identification of the C-Reactive Protein Interaction Network Using a Bioinformatics Approach Provides Insights into the Molecular Pathogenesis of Hepatocellular Carcinoma." Cellular Physiology and Biochemistry 48, no. 2 (2018): 741–52. http://dx.doi.org/10.1159/000491903.

Full text

Abstract:

Background/Aims: C reactive protein (CRP) levels are elevated in many diseases, including malignant tumors and cardiovascular disorders. In this study, the protein interaction network for CRP was evaluated to determine the importance of CRP and its interacting proteins in the molecular pathogenesis of hepatocellular carcinoma (HCC). Methods: Isobaric tags for relative and absolute quantitation (iTRAQ) and mass spectrometry were used to identify CRP interacting proteins in SMMC7721 cells. Moreover, Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to evaluate e

APA, Harvard, Vancouver, ISO, and other styles

45

Liu, Yanqing, Yueqiu Wang, Yanxia Zhang, et al. "Screening for Key Pathways Associated with the Development of Osteoporosis by Bioinformatics Analysis." BioMed Research International 2017 (2017): 1–8. http://dx.doi.org/10.1155/2017/8589347.

Full text

Abstract:

Objectives.We aimed to find the key pathways associated with the development of osteoporosis.Methods.We downloaded expression profile data of GSE35959 and analyzed the differentially expressed genes (DEGs) in 3 comparison groups (old_op versus middle, old_op versus old, and old_op versus senescent). KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses were carried out. Besides, Venn diagram analysis and gene functional interaction (FI) network analysis were performed.Results.Totally 520 DEGs, 966 DEGs, and 709 DEGs were obtained in old_op versus middle, old_op versus old,

APA, Harvard, Vancouver, ISO, and other styles

46

Zhu, Huijing, Xin Zhu, Yuhong Liu, et al. "Gene Expression Profiling of Type 2 Diabetes Mellitus by Bioinformatics Analysis." Computational and Mathematical Methods in Medicine 2020 (October 21, 2020): 1–10. http://dx.doi.org/10.1155/2020/9602016.

Full text

Abstract:

Objective. The aim of this study was to identify the candidate genes in type 2 diabetes mellitus (T2DM) and explore their potential mechanisms. Methods. The gene expression profile GSE26168 was downloaded from the Gene Expression Omnibus (GEO) database. The online tool GEO2R was used to obtain differentially expressed genes (DEGs). Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed by using Metascape for annotation, visualization, and comprehensive discovery. The protein-protein interaction (PPI) network of DEGs was co

APA, Harvard, Vancouver, ISO, and other styles

47

Wang, Shanyun, Huisi Hong, Yiming Yuan, Yinhao Yin, Jianfeng Zeng, and Jing Xiao. "Exploring the Mechanisms of Action of Quercetin for the Treatment of Cervical High-Risk-Human Papilloma Virus Using Network Pharmacology and Molecular Docking." Chinese medicine and natural products 04, no. 01 (2024): e35-e42. http://dx.doi.org/10.1055/s-0044-1782158.

Full text

Abstract:

Abstract Objective Our objective was to investigate the therapeutic mechanism of quercetin in the management of cervical HR-HPV through the integration of network pharmacology and molecular docking techniques. Methods The GeneCard database was utilized to analyze and identify potential therapeutic targets in HR-HPV. Subsequently, a protein–protein interaction (PPI) network was constructed by employing the String database. The visualization and construction of PPI networks were accomplished using Cytoscape. The R language was utilized to conduct Gene Ontology (GO) enrichment and Kyoto Encyclope

APA, Harvard, Vancouver, ISO, and other styles

48

Wang, Fengfei, Shuai Li, Le Ma, Yuefei Geng, Yongmei Shen, and Juanni Zeng. "Study on the Mechanism of Periplaneta americana Extract to Accelerate Wound Healing after Diabetic Anal Fistula Operation Based on Network Pharmacology." Evidence-Based Complementary and Alternative Medicine 2021 (March 9, 2021): 1–9. http://dx.doi.org/10.1155/2021/6659154.

Full text

Abstract:

Objective. Using network pharmacology research methods to explore the healing mechanism of American cockroach extract to accelerate wound healing after diabetic anal fistula surgery. Method. The main chemical constituents of extracts from Periplaneta americana were collected by literature retrieval. Chemical composition and targets related to diabetic anal fistula wound could be predicted based on PubChem, Swiss Target Prediction, OMIM, and GeneCards databases, and the putative targets of Periplaneta americana extraction (PAE) for diabetic anal fistula wound were obtained by Venn diagram. Thes

APA, Harvard, Vancouver, ISO, and other styles

49

Liu, Zhendong, Ruotian Zhang, Zhenying Sun, et al. "Identification of hub genes and small-molecule compounds in medulloblastoma by integrated bioinformatic analyses." PeerJ 8 (April 14, 2020): e8670. http://dx.doi.org/10.7717/peerj.8670.

Full text

Abstract:

Background Medulloblastoma (MB) is the most common intracranial malignant tumor in children. The genes and pathways involved in the pathogenesis of MB are relatively unknown. We aimed to identify potential biomarkers and small-molecule drugs for MB. Methods Gene expression profile data sets were obtained from the Gene Expression Omnibus (GEO) database and the differentially expressed genes (DEGs) were identified using the Limma package in R. Functional annotation, and cell signaling pathway analysis of DEGs was carried out using DAVID and Kobas. A protein-protein interaction network was genera

APA, Harvard, Vancouver, ISO, and other styles

50

Zhang, Lei, Yi-Ming Pan, Lu-Yao Wang, et al. "Therapeutic Targets of Bufalin on Renal Carcinoma and Mechanisms: Experimental Validation of Network Pharmacology Analysis." Evidence-Based Complementary and Alternative Medicine 2022 (January 28, 2022): 1–10. http://dx.doi.org/10.1155/2022/5469795.

Full text

Abstract:

The possible targets underlying the activity of bufalin on renal cell carcinoma (RCC) were investigated using network pharmacology and experimental approaches. PharmMapper and other databases were explored for predicting the bufalin targets and RCC-related targets. Finally, the enriched pathways and the targets were analyzed by the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathway enrichment analyses. Furthermore, in vitro cell experiments were used to verify bufalin activation of AKT and MAPK signaling pathways in human mesangial cells. The therapeutic targets rela

APA, Harvard, Vancouver, ISO, and other styles

We offer discounts on all premium plans for authors whose works are included in thematic literature selections. Contact us to get a unique promo code!