Parameterization of asymmetric sigmoid functions in weighted gene co-expression network analysis

ME Karabekmez, M Yarıcı - Computational Biology and Chemistry, 2024 - Elsevier
In most the biological contexts, examining gene expressions at the genomic level gives
more accurate results than examining genes individually. It can improve understanding of …

Comparative analysis of weighted gene co-expression networks in human and mouse

M Eidsaa, L Stubbs, E Almaas - Plos one, 2017 - journals.plos.org
The application of complex network modeling to analyze large co-expression data sets has
gained traction during the last decade. In particular, the use of the weighted gene co …

Optimizing weighted gene co-expression network analysis with a multi-threaded calculation of the topological overlap matrix

M Shuai, D He, X Chen - Statistical applications in genetics and …, 2021 - degruyter.com
Biomolecular networks are often assumed to be scale-free hierarchical networks. The
weighted gene co-expression network analysis (WGCNA) treats gene co-expression …

A general framework for weighted gene co-expression network analysis

Z Bin, H Steve - Statistical applications in genetics and …, 2005 - econpapers.repec.org
Gene co-expression networks are increasingly used to explore the system-level functionality
of genes. The network construction is conceptually straightforward: nodes represent genes …

A general framework for weighted gene co-expression network analysis

B Zhang, S Horvath - … applications in genetics and molecular biology, 2005 - degruyter.com
Gene co-expression networks are increasingly used to explore the system-level functionality
of genes. The network construction is conceptually straightforward: nodes represent genes …

PyWGCNA: a Python package for weighted gene co-expression network analysis

N Rezaie, F Reese, A Mortazavi - Bioinformatics, 2023 - academic.oup.com
Motivation Weighted gene co-expression network analysis (WGCNA) is frequently used to
identify modules of genes that are co-expressed across many RNA-seq samples. However …

Geometric interpretation of gene coexpression network analysis

S Horvath, J Dong - PLoS computational biology, 2008 - journals.plos.org
The merging of network theory and microarray data analysis techniques has spawned a new
field: gene coexpression network analysis. While network methods are increasingly used in …

Modeling multifunctionality of genes with secondary gene co-expression networks in human brain provides novel disease insights

JA Sánchez, AL Gil-Martinez, A Cisterna… - …, 2021 - academic.oup.com
Motivation Co-expression networks are a powerful gene expression analysis method to
study how genes co-express together in clusters with functional coherence that usually …

Correlation and gene co-expression networks

S Horvath, S Horvath - … Network Analysis: Applications in Genomics and …, 2011 - Springer
A correlation network is a network whose adjacency matrix is constructed on the basis of
pairwise correlations between numeric vectors. The numeric vectors may represent …

The prediction of local modular structures in a co-expression network based on gene expression datasets

Y Ogata, N Sakurai, H Suzuki, K Aoki… - … Informatics Series Vol …, 2009 - World Scientific
In scientific fields such as systems biology, evaluation of the relationship between network
members (vertices) is approached using a network structure. In a co-expression network …