Journal ArticleDOI
Comparison of Methods for Differential Co-expression Analysis for Disease Biomarker Prediction.
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TLDR
A comparative study of four co-expression network module detection techniques, namely, THD-Module Extractor, DiffCoEx, MODA, and WGCNA, which can perform differential co- expression analysis on both gene and miRNA expression data are presented and the applications are discussed.About:
This article is published in Computers in Biology and Medicine.The article was published on 2019-10-01. It has received 54 citations till now.read more
Citations
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Journal ArticleDOI
Identification of key modules and genes associated with breast cancer prognosis using WGCNA and ceRNA network analysis.
TL;DR: This study provides a framework of the co-expression gene modules of breast cancer and identifies several important biomarkers in breast cancer development and prognosis.
Journal ArticleDOI
Construction and Analysis of the Tumor-Specific mRNA-miRNA-lncRNA Network in Gastric Cancer.
Xiao-Hao Zheng,Xiaohui Wang,Li Zheng,Hao Zhao,Wenbin Li,Bingzhi Wang,Liyan Xue,Yantao Tian,Yibin Xie +8 more
TL;DR: A 12-gene signature from both prognosis-related and tumor-specific genes was developed, and a ceRNA network was constructed based on the genes in this model, which may provide novel insights into the treatment of gastric cancer.
Journal ArticleDOI
Several miRNAs derived from serum extracellular vesicles are potential biomarkers for early diagnosis and progression of Parkinson's disease.
Shulei He,Lu Huang,Ci Shao,Tiejian Nie,Li Xia,Bozhou Cui,Fangfang Lu,Lin Zhu,Bolin Chen,Qian Yang +9 more
TL;DR: Wang et al. as mentioned in this paper used weighted gene co-expression network analysis (WGCNA) to identify the commonly expressed miRNAs in all stages of Parkinson's disease by constructing connections between modules, and specifically expressed miRNA in each stage of PD by functional enrichment analysis.
Journal ArticleDOI
Identifying potential gene biomarkers for Parkinson's disease through an information entropy based approach.
Alfonso Monaco,Ester Pantaleo,Nicola Amoroso,Loredana Bellantuono,Angela Lombardi,Andrea Tateo,Sabina Tangaro,Sabina Tangaro,Roberto Bellotti,Roberto Bellotti +9 more
TL;DR: This work used a publicly available substantia nigra microarray dataset, GSE20163, from NCBI GEO database, containing gene expression profiles for 10 PD patients and 18 normal controls to identify two gene communities that discriminated between the two groups with mean accuracy, and validated the results on an independent microarray experiment.
Journal ArticleDOI
Integrative network analysis identifies differential regulation of neuroimmune system in Schizophrenia and Bipolar disorder
Ankur Sahu,Hussain Ahmed Chowdhury,Mithil Gaikwad,Chen Chongtham,Uddip Talukdar,Jadab Kishor Phukan,Dhruba K. Bhattacharyya,Pankaj Barah +7 more
TL;DR: Differential activation of the immune system components and pathways may drive the common and unique pathogenesis of the BPD and SCZ.
References
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Journal ArticleDOI
WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder,Steve Horvath +1 more
TL;DR: The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis that includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software.
Journal ArticleDOI
Hierarchical Organization of Modularity in Metabolic Networks
TL;DR: It is shown that the metabolic networks of 43 distinct organisms are organized into many small, highly connected topologic modules that combine in a hierarchical manner into larger, less cohesive units, with their number and degree of clustering following a power law.
Journal ArticleDOI
A survey of best practices for RNA-seq data analysis
Ana Conesa,Pedro Madrigal,Pedro Madrigal,Sonia Tarazona,David Gomez-Cabrero,Alejandra Cervera,Andrew McPherson,Michał Wojciech Szcześniak,Daniel J. Gaffney,Laura L. Elo,Xuegong Zhang,Ali Mortazavi +11 more
TL;DR: All of the major steps in RNA-seq data analysis are reviewed, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping.
Journal ArticleDOI
Inferring Regulatory Networks from Expression Data Using Tree-Based Methods
TL;DR: This article presents GENIE3, a new algorithm for the inference of GRNs that was best performer in the DREAM4 In Silico Multifactorial challenge and compares favorably with existing algorithms to decipher the genetic regulatory network of Escherichia coli.
Journal ArticleDOI
The Role of Apolipoprotein E in Alzheimer's Disease
TL;DR: Therapeutic strategies based on APOE epsilon4 propose to reduce the toxic effects of apoE4 or to restore the physiological, protective functions of apiE, as well as its role in synaptic plasticity and neuro inflammation.
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