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- Signaling pathway analysis methods are commonly used to explain biological behaviors of disease cells. Effector genes typically decide functional attributes (associated with biological behaviors of disease cells) by abnormal signals they received.
pmc.ncbi.nlm.nih.gov/articles/PMC7430270/ KEGG PATHWAY Database - GenomeNet
Oct 1, 2024 · KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge of the molecular interaction, reaction and relation networks for: 1. Metabolism
Genes
KEGG GENES is a collection of genes and proteins in complete genomes of cellular …
Network
KEGG NETWORK represents a renewed attempt by KEGG to capture knowledge …
Kegg Compound Database
KEGG COMPOUND is one of the four original databases, together with KEGG …
Disease
The pathway maps and BRITE hierarchy files with mapping of disease genes and …
Orthology (Ko)
The KO (KEGG Orthology) database is a database of molecular functions …
Brite
1.4 Protein families: signaling and cellular processes (K numbers) 02000 …
Kegg Objects
The KEGG organism code is also used as a prefix to identify organism-specific …
Drug
KEGG DRUG is a comprehensive drug information resource for approved drugs …
Find Organism Code
Find organism code: ...
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Enter keywords to search pathway maps. This is a search against the relational …
Inference and analysis of cell-cell communication using CellChat
Feb 17, 2021 · Through manifold learning and quantitative contrasts, CellChat classifies signaling pathways and delineates conserved and context-specific pathways across different datasets. …
- Studies of Signaling Pathway Analysis
Pathway enrichment analysis and visualization of …
Jan 21, 2019 · We explain the procedures of pathway enrichment analysis and present a practical step-by-step guide to help interpret gene lists resulting from RNA-seq and genome-sequencing experiments.
Deciphering cell–cell interactions and communication from gene ...
Nov 9, 2020 · Cell–cell interactions orchestrate organismal development, homeostasis and single-cell functions. When cells do not properly interact or improperly decode molecular messages, …
Identifying significantly impacted pathways: a comprehensive …
Oct 9, 2019 · Pathway analysis approaches use available pathway databases and the given gene expression data to identify the pathways which are significantly impacted in a given condition. …
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A novel signaling pathway impact analysis - PMC - National …
Jan 1, 2009 · The impact analysis combines two types of evidence: (i) the over-representation of DE genes in a given pathway and (ii) the abnormal perturbation of that pathway, as measured …
Identification of active signaling pathways by …
Dec 31, 2018 · Here, we present a method to simultaneously predict the set of active signaling pathways, together with their pathway structure, by integrating protein-protein interaction network and gene expression data.
Identifying disease-associated signaling pathways through a …
In this study, we developed a novel signaling pathway analysis method called signaling pathway functional attributes analysis (SPFA) method. This method analyzes the signal variations that …
A Review of Pathway-Based Analysis Tools That Visualize …
Pathway analysis is a powerful method for data analysis in genomics, most often applied to gene expression analysis. It is also promising for single-nucleotide polymorphism (SNP) data …
Subpathway Analysis based on Signaling-Pathway …
Jul 24, 2015 · Pathway analysis is a common approach to gain insight from biological experiments. Signaling-pathway impact analysis (SPIA) is one such method and combines both the classical enrichment analysis and the actual …
PETAL: a Python tool for deep analysis of biological pathways
Dec 16, 2020 · Here, we developed PETAL, a Python tool that automatically explores and detects the most relevant nodes within a KEGG pathway, scanning and performing an in-depth …
Bioconductor - SPIA
This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with …
Ten Years of Pathway Analysis: Current Approaches and ... - PLOS
Feb 23, 2012 · We discuss the evolution of knowledge base–driven pathway analysis over its first decade, distinctly divided into three generations. We also discuss the limitations that are …
The Signaling Pathways Project, an integrated ‘omics ... - Nature
Oct 31, 2019 · Here, we designed a web knowledgebase, the Signaling Pathways Project (SPP), which incorporates community classifications of signaling pathway nodes (receptors, enzymes, …
Strategies for Pathway Analysis using GWAS and WGS Data
Single allele study designs, commonly used in genome-wide association studies (GWAS) as well as the more recently developed whole genome sequencing (WGS) studies, are a standard …
Signalling pathway impact analysis based on the strength of …
Aug 1, 2016 · In this study, the authors used newly developed signalling pathway impact analysis (SPIA) methods, SPIA based on Pearson correlation coefficient (PSPIA), and mutual …
Signaling pathway impact analysis by incorporating the …
Dec 1, 2017 · Signaling-pathway impact analysis (SPIA) provides a convenient framework which considers both the classical enrichment analysis and the actual perturbation on a given …
Dynamics and Sensitivity of Signaling Pathways
Jun 27, 2022 · In this review, we discuss how signaling pathway modeling can assist with identifying effective drugs for treating diseases, such as cancer.
Perturbation-response genes reveal signaling footprints in
Jan 2, 2018 · Aberrant cell signaling can cause cancer and other diseases and is a focal point of drug research. A common approach is to infer signaling activity of pathways from gene …
novel signaling pathway impact analysis - Oxford Academic
Nov 5, 2008 · Results: We describe a novel signaling pathway impact analysis (SPIA) that combines the evidence obtained from the classical enrichment analysis with a novel type of …
Inhibition of IRE1α/XBP1 axis alleviates LPS-induced acute lung …
5 days ago · Acute lung injury or acute respiratory distress syndrome (ALI/ARDS) is a devastating clinical syndrome with high incidence and mortality rates. IRE1α-XBP1 pathway is one of the …
Eubacterium siraeum suppresses fat deposition via decreasing …
Oct 30, 2024 · Functional enrichment analysis revealed that these metabolites were involved in 12 signaling pathways, with significant enrichment in the biosynthesis of unsaturated fatty acids …
GEFT inhibits the GSDM-mediated proptosis signalling pathway …
2 days ago · The metastasis or recurrence of rhabdomyosarcoma (RMS) is the primary cause of tumour-related deaths. Patients with high-risk RMS have poor prognosis with a 5-year overall …
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