Gene co-expression analysis for functional classification and gene–disease predictions

S Van Dam, U Vosa, A van der Graaf… - Briefings in …, 2018 - academic.oup.com
Gene co-expression networks can be used to associate genes of unknown function with
biological processes, to prioritize candidate disease genes or to discern transcriptional …

[HTML][HTML] Dissection of regulatory networks that are altered in disease via differential co-expression

D Amar, H Safer, R Shamir - PLoS computational biology, 2013 - journals.plos.org
Comparing the gene-expression profiles of sick and healthy individuals can help in
understanding disease. Such differential expression analysis is a well-established way to …

(Differential) co-expression analysis of gene expression: a survey of best practices

HA Chowdhury, DK Bhattacharyya… - IEEE/ACM transactions …, 2019 - ieeexplore.ieee.org
Analysis of gene expression data is widely used in transcriptomic studies to understand
functions of molecules inside a cell and interactions among molecules. Differential co …

[HTML][HTML] Quantifying the relationship between co-expression, co-regulation and gene function

DJ Allocco, IS Kohane, AJ Butte - BMC bioinformatics, 2004 - Springer
Background It is thought that genes with similar patterns of mRNA expression and genes
with similar functions are likely to be regulated via the same mechanisms. It has been …

[HTML][HTML] Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer

DD Bhuva, J Cursons, GK Smyth, MJ Davis - Genome biology, 2019 - Springer
Background Elucidation of regulatory networks, including identification of regulatory
mechanisms specific to a given biological context, is a key aim in systems biology. This has …

GeneFriends: gene co-expression databases and tools for humans and model organisms

P Raina, R Guinea, K Chatsirisupachai… - Nucleic Acids …, 2023 - academic.oup.com
Gene co-expression analysis has emerged as a powerful method to provide insights into
gene function and regulation. The rapid growth of publicly available RNA-sequencing (RNA …

[HTML][HTML] Correlation AnalyzeR: functional predictions from gene co-expression correlations

HE Miller, AJR Bishop - BMC bioinformatics, 2021 - Springer
Background Co-expression correlations provide the ability to predict gene functionality
within specific biological contexts, such as different tissue and disease conditions. However …

GeneFriends: a human RNA-seq-based gene and transcript co-expression database

S van Dam, T Craig, JP de Magalhães - Nucleic acids research, 2015 - academic.oup.com
Co-expression networks have proven effective at assigning putative functions to genes
based on the functional annotation of their co-expressed partners, in candidate gene …

[HTML][HTML] Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles

C Prieto, A Risueño, C Fontanillo, J De Las Rivas - PloS one, 2008 - journals.plos.org
Background Analysis of gene expression data using genome-wide microarrays is a
technique often used in genomic studies to find coexpression patterns and locate groups of …

Canonical correlation analysis for RNA-seq co-expression networks

S Hong, X Chen, L Jin, M Xiong - Nucleic acids research, 2013 - academic.oup.com
Digital transcriptome analysis by next-generation sequencing discovers substantial mRNA
variants. Variation in gene expression underlies many biological processes and holds a key …