scholarly journals Advances in network-based metabolic pathway analysis and gene expression data integration

2014 ◽  
Vol 16 (2) ◽  
pp. 265-279 ◽  
Author(s):  
A. Rezola ◽  
J. Pey ◽  
L. Tobalina ◽  
A. Rubio ◽  
J. E. Beasley ◽  
...  
Keyword(s):  
Gene Expression ◽  
Data Integration ◽  
Gene Expression Data ◽  
Pathway Analysis ◽  
Metabolic Pathway ◽  
Expression Data ◽  
Metabolic Pathway Analysis

GENOME-WIDE PATHWAY ANALYSIS AND VISUALIZATION USING GENE EXPRESSION DATA

2001 ◽  
Author(s):  
M. P. KURHEKAR ◽  
S. ADAK ◽  
S. JHUNJHUNWALA ◽  
K. RAGHUPATHY
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Pathway Analysis ◽  
Expression Data ◽  
Genome Wide

scholarly journals HisCoM-PAGE: Hierarchical Structural Component Models for Pathway Analysis of Gene Expression Data

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 931 ◽  
Author(s):  
Mok ◽  
Kim ◽  
Lee ◽  
Choi ◽  
Lee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pancreatic Cancer ◽  
Gene Expression Data ◽  
Pathway Analysis ◽  
Structural Component ◽  
Biological Data ◽  
Gene Set Enrichment Analysis ◽  
Expression Data ◽  
Global Test ◽  
Causal Pathways

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 biological data analysis of pancreatic cancer data demonstrated that HisCoM-PAGE could successfully identify pathways associated with pancreatic cancer prognosis. Simulation studies comparing the performance of HisCoM-PAGE with other competing methods such as Gene Set Enrichment Analysis (GSEA), Global Test, and Wald-type Test showed HisCoM-PAGE to have the highest power to detect causal pathways in most simulation scenarios.

scholarly journals Genome-wide Pathway Analysis Using Gene Expression Data of Colonic Mucosa in Patients with Inflammatory Bowel Disease

2015 ◽  
pp. 1 ◽  
Author(s):  
Orazio Palmieri ◽  
Teresa M. Creanza ◽  
Fabrizio Bossa ◽  
Orazio Palumbo ◽  
Rosalia Maglietta ◽  
...  
Keyword(s):  
Gene Expression ◽  
Inflammatory Bowel Disease ◽  
Gene Expression Data ◽  
Pathway Analysis ◽  
Bowel Disease ◽  
Colonic Mucosa ◽  
Expression Data ◽  
Genome Wide ◽  
Inflammatory Bowel

Identification of perturbed signaling pathways from gene expression data using information divergence

2017 ◽  
Vol 13 (9) ◽  
pp. 1797-1804
Author(s):  
Xinying Hu ◽  
Hang Wei ◽  
Haoran Zheng
Keyword(s):  
Gene Expression ◽  
Probability Distribution ◽  
Signaling Pathways ◽  
Gene Expression Data ◽  
Pathway Analysis ◽  
Expression Data ◽  
Analysis Method ◽  
Information Divergence

We propose a pathway analysis method based on information divergence and the probability distribution of the regulation capacity.

scholarly journals Pathway analysis of transcriptomic data shows immunometabolic effects of vitamin D

2018 ◽  
Vol 60 (2) ◽  
pp. 95-108 ◽  
Author(s):  
Amadeo Muñoz Garcia ◽  
Martina Kutmon ◽  
Lars Eijssen ◽  
Martin Hewison ◽  
Chris T Evelo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Vitamin D ◽  
Cell Line ◽  
Gene Expression Data ◽  
Pathway Analysis ◽  
Immune Cell ◽  
Cell Model ◽  
Active Form ◽  
Expression Data ◽  
Regulatory Pathways

Unbiased genomic screening analyses have highlighted novel immunomodulatory properties of the active form of vitamin D, 1,25-dihydroxyvitamin D (1,25(OH)2D). However, clearer interpretation of the resulting gene expression data is limited by cell model specificity. The aim of the current study was to provide a broader perspective on common gene regulatory pathways associated with innate immune responses to 1,25(OH)2D, through systematic re-interrogation of existing gene expression databases from multiple related monocyte models (the THP-1 monocytic cell line (THP-1), monocyte-derived dendritic cells (DCs) and monocytes). Vitamin D receptor (VDR) expression is common to multiple immune cell types, and thus, pathway analysis of gene expression using data from multiple related models provides an inclusive perspective on the immunomodulatory impact of vitamin D. A bioinformatic workflow incorporating pathway analysis using PathVisio and WikiPathways was utilized to compare each set of gene expression data based on pathway-level context. Using this strategy, pathways related to the TCA cycle, oxidative phosphorylation and ATP synthesis and metabolism were shown to be significantly regulated by 1,25(OH)2D in each of the repository models (Z-scores 3.52–8.22). Common regulation by 1,25(OH)2D was also observed for pathways associated with apoptosis and the regulation of apoptosis (Z-scores 2.49–3.81). In contrast to the primary culture DC and monocyte models, the THP-1 myelomonocytic cell line showed strong regulation of pathways associated with cell proliferation and DNA replication (Z-scores 6.1–12.6). In short, data presented here support a fundamental role for active 1,25(OH)2D as a pivotal regulator of immunometabolism.

rPAC: Route based Pathway Analysis for Cohorts of Gene Expression Data Sets

Methods ◽  
2021 ◽  
Author(s):  
Pujan Joshi ◽  
Brent Basso ◽  
Honglin Wang ◽  
Seung-Hyun Hong ◽  
Charles Giardina ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Pathway Analysis ◽  
Data Sets ◽  
Expression Data
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