Predicting candidate genes from phenotypes, functions and anatomical site of expression

J Chen, A Althagafi, R Hoehndorf - Bioinformatics, 2021 - academic.oup.com
… Consequently, even if a phenotype class is defined based on an anatomical location or a
function, this anatomical location or function class will not co-occur with a gene or disease that …

ESCO: single cell expression simulation incorporating gene co-expression

J Tian, J Wang, K Roeder - Bioinformatics, 2021 - academic.oup.com
… adopts the idea of the copula to impose gene co-expression, while preserving the highlights
of … We then assess the prediction accuracy (AUC scores) of connections for each imputation …

hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data

S Morabito, F Reese, N Rahimzadeh, E Miyoshi… - Cell reports …, 2023 - cell.com
… transcripts or genes. Here, we introduce hdWGCNA, a comprehensive methodological
framework for the inference, analysis, and interpretation of gene co-expression networks in high-…

Using weighted gene co-expression network analysis (WGCNA) to identify the hub genes related to hypoxic adaptation in yak (Bos grunniens)

Q Bao, X Zhang, P Bao, C Liang, X Guo, M Chu… - Genes & genomics, 2021 - Springer
… by constructing a weighted gene co-expression network. … of genes across all samples, and
the picks of threshold function … for GO and KEGG functional classification was both defined by …

High dimensional co-expression networks enable discovery of transcriptomic drivers in complex biological systems

S Morabito, F Reese, N Rahimzadeh, E Miyoshi… - Biorxiv, 2022 - biorxiv.org
… We projected gene co-expression modules from two bulk RNA-seq studies of AD (13, 49)
into a published snRNA-seq study of AD to assess their expression patterns within various cell …

CoCoCoNet: conserved and comparative co-expression across a diverse set of species

J Lee, M Shah, S Ballouz, M Crow… - Nucleic acids …, 2020 - academic.oup.com
… about its function, a fact that gene co-expression networks aim to … , which uses node degree
alone to predict module … fall into two major functional categories: those involved in gene

… of uterine leiomyosarcoma-associated hub genes and immune cell infiltration pattern using weighted co-expression network analysis and CIBERSORT algorithm

X Shen, Z Yang, S Feng, Y Li - World Journal of Surgical Oncology, 2021 - Springer
… by weighted gene co-expression network analysis (WGCNA). Subsequently, gene function
… to verify the hub gene, there is no further evidence to verify our prediction results. Our follow-…

Independent component analysis based gene co-expression network inference (ICAnet) to decipher functional modules for better single-cell clustering and batch …

W Wang, H Tan, M Sun, Y Han, W Chen… - Nucleic acids …, 2021 - academic.oup.com
… modules in single-cell transcriptome analysis has the … predicting gene co-expression
module(s) associated with rare cell type(s) owing to its ability to capture local gene co-expression

WGCNA identifies a comprehensive and dynamic gene co-expression network that associates with smut resistance in sugarcane

Q Wu, YB Pan, Y Su, W Zou, F Xu, T Sun… - International Journal of …, 2022 - mdpi.com
gene co-expression network analysis (WGCNA), which identified 5010 DEGs in 15 co-expressed
gene … The present study aimed to explore gene co-expression networks associated …

scLink: inferring sparse gene co-expression networks from single-cell expression data

WV Li, Y Li - Genomics, Proteomics and Bioinformatics, 2021 - academic.oup.com
… GENIE3 decomposes the prediction of a gene network between p genes into p different …
gene co-expression strength and use it to improve the inference of sparse gene co-expression