Cargando…

Pathway Enrichment Analysis with Networks

Detecting associations between an input gene set and annotated gene sets (e.g., pathways) is an important problem in modern molecular biology. In this paper, we propose two algorithms, termed NetPEA and NetPEA’, for conducting network-based pathway enrichment analysis. Our algorithms consider not on...

Descripción completa

Detalles Bibliográficos
Autores principales:	Liu, Lu, Wei, Jinmao, Ruan, Jianhua
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	MDPI 2017
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5664096/ https://www.ncbi.nlm.nih.gov/pubmed/28956817 http://dx.doi.org/10.3390/genes8100246

Ejemplares similares

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks
por: Alexeyenko, Andrey, et al.
Publicado: (2012)

Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases
por: Liu, Yu, et al.
Publicado: (2012)

Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology
por: Aguirre-Plans, Joaquim, et al.
Publicado: (2018)

Network and pathway enrichment analysis of Attention Deficit/Hyperactivity Disorder candidate genes
por: Singh, Pratichi
Publicado: (2020)

EnrichNet: network-based gene set enrichment analysis
por: Glaab, Enrico, et al.
Publicado: (2012)

Pathway-targeting gene matrix for Drosophila gene set enrichment analysis
por: Cheng, Jack, et al.
Publicado: (2021)

NEAT: an efficient network enrichment analysis test
por: Signorelli, Mirko, et al.
Publicado: (2016)

Efficient pathway enrichment and network analysis of GWAS summary data using GSA-SNP2
por: Yoon, Sora, et al.
Publicado: (2018)

Weighted gene co-expression network analysis identifies modules and functionally enriched pathways in the lactation process
por: Farhadian, Mohammad, et al.
Publicado: (2021)

On the influence of several factors on pathway enrichment analysis
por: Mubeen, Sarah, et al.
Publicado: (2022)

Nine quick tips for pathway enrichment analysis
por: Chicco, Davide, et al.
Publicado: (2022)

KeyPathwayMinerWeb: online multi-omics network enrichment
por: List, Markus, et al.
Publicado: (2016)

aPEAR: an R package for autonomous visualization of pathway enrichment networks
por: Kerseviciute, Ieva, et al.
Publicado: (2023)

Gene Co-Expression Network Analysis for Identifying Modules and Functionally Enriched Pathways in Type 1 Diabetes
por: Riquelme Medina, Ignacio, et al.
Publicado: (2016)

IL6-mediated HCoV-host interactome regulatory network and GO/Pathway enrichment analysis
por: Politano, Gianfranco, et al.
Publicado: (2020)

CBNplot: Bayesian network plots for enrichment analysis
por: Sato, Noriaki, et al.
Publicado: (2022)

Integrative pathway enrichment analysis of multivariate omics data
por: Paczkowska, Marta, et al.
Publicado: (2020)

IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis
por: Zhang, Fan, et al.
Publicado: (2012)

Application of Differential Network Enrichment Analysis for Deciphering Metabolic Alterations
por: Iyer, Gayatri R., et al.
Publicado: (2020)

SEAS: A System for SEED-Based Pathway Enrichment Analysis
por: Mao, Xizeng, et al.
Publicado: (2011)

GAGE: generally applicable gene set enrichment for pathway analysis
por: Luo, Weijun, et al.
Publicado: (2009)

Identifying Key Genes and Functionally Enriched Pathways in Sjögren’s Syndrome by Weighted Gene Co-Expression Network Analysis
por: Yao, Qiuming, et al.
Publicado: (2019)

Network-based functional enrichment
por: Poirel, Christopher L, et al.
Publicado: (2011)

Neighbor Overlap Is Enriched in the Yeast Interaction Network: Analysis and Implications
por: Feiglin, Ariel, et al.
Publicado: (2012)

ceRNA Network and Functional Enrichment Analysis of Preeclampsia by Weighted Gene Coexpression Network Analysis
por: Wang, Chenxu, et al.
Publicado: (2022)

Identifying significant genes and functionally enriched pathways in familial hypercholesterolemia using integrated gene co-expression network analysis
por: Awan, Zuhier, et al.
Publicado: (2022)

On the performance of de novo pathway enrichment
por: Batra, Richa, et al.
Publicado: (2017)

Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis
por: Geistlinger, Ludwig, et al.
Publicado: (2016)

Long non-coding RNA NEAT1 promotes angiogenesis in hepatoma carcinoma via the miR-125a-5p/VEGF pathway
por: Guo, Jingyun, et al.
Publicado: (2022)

A Network of Conserved Damage Survival Pathways Revealed by a Genomic RNAi Screen
por: Ravi, Dashnamoorthy, et al.
Publicado: (2009)

Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics
por: Karp, Peter D., et al.
Publicado: (2021)

Polymer Networks for Enrichment of Calcium Ions
por: Heinze, Marcus, et al.
Publicado: (2021)

Comparing Bayesian-Based Reconstruction Strategies in Topology-Based Pathway Enrichment Analysis
por: Wang, Yajunzi, et al.
Publicado: (2022)

Colorectal cancer risk genes are functionally enriched in regulatory pathways
por: Lu, Xi, et al.
Publicado: (2016)

SMAC mimetic birinapant inhibits hepatocellular carcinoma growth by activating the cIAP1/TRAF3 signaling pathway
por: Ding, Jun, et al.
Publicado: (2020)

Using published pathway figures in enrichment analysis and machine learning
por: Shin, Min-Gyoung, et al.
Publicado: (2023)

Virtual pathway explorer (viPEr) and pathway enrichment analysis tool (PEANuT): creating and analyzing focus networks to identify cross-talk between molecules and pathways
por: Garmhausen, Marius, et al.
Publicado: (2015)

The Use of Gene Ontology Term and KEGG Pathway Enrichment for Analysis of Drug Half-Life
por: Zhang, Yu-Hang, et al.
Publicado: (2016)

A general co-expression network-based approach to gene expression analysis: comparison and applications
por: Ruan, Jianhua, et al.
Publicado: (2010)

ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis
por: Han, Junwei, et al.
Publicado: (2015)

Cannot write session to /tmp/vufind_sessions/sess_1hu280mttkudenegsbkv0484es