2021
DOI: 10.3389/fgene.2021.630187
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CoExp: A Web Tool for the Exploitation of Co-expression Networks

Abstract: Gene co-expression networks are a powerful type of analysis to construct gene groupings based on transcriptomic profiling. Co-expression networks make it possible to discover modules of genes whose mRNA levels are highly correlated across samples. Subsequent annotation of modules often reveals biological functions and/or evidence of cellular specificity for cell types implicated in the tissue being studied. There are multiple ways to perform such analyses with weighted gene co-expression network analysis (WGCN… Show more

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Cited by 20 publications
(17 citation statements)
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“…Majority of existing computational methodologies to construct gene co-expression networks in standard single-cell studies (Crow et al, 2016;Wang et al, 2016;García-Ruiz et al, 2021), intrinsically involve a dimension reduction step which achieves two goals: one is to avoid curse of dimensionality and aid computational feasibility; second is to preserve the intrinsic dimensionality while reducing the noise. The existing network methods, however, do not incorporate spatial information which are critical in spatial transcriptomics.…”
Section: Introductionmentioning
confidence: 99%
“…Majority of existing computational methodologies to construct gene co-expression networks in standard single-cell studies (Crow et al, 2016;Wang et al, 2016;García-Ruiz et al, 2021), intrinsically involve a dimension reduction step which achieves two goals: one is to avoid curse of dimensionality and aid computational feasibility; second is to preserve the intrinsic dimensionality while reducing the noise. The existing network methods, however, do not incorporate spatial information which are critical in spatial transcriptomics.…”
Section: Introductionmentioning
confidence: 99%
“…To functionally characterize the top associated interactions, we carried out loci connectivity analyses across gene-expression datasets from GTEX v.8 27 , gene-ontologies and molecular pathways using FUMA 28 , phenotype enrichment using PhenoExam 29 , functional gene interaction networks using STRING 30 , and gene co-expression network analysis using CoExp Web 31 . SNP lists from significant interactions were extracted for significant eQTL associations in PD-relevant tissues (caudate, putamen, nucleus accumbens and substantia nigra) in the GTEX v.8 data to obtain significant eQTL genes (eGenes).…”
Section: Functional Enrichment Analysis Methodsmentioning
confidence: 99%
“…CoExp is a resource developed to exploit gene co-expression networks (GCNs) to build gene groupings based on transcriptomic profiling 7 . The CoExp tool is an online web application consisting of a collection of 109 networks, powered by the CoExpNets suite of R packages.…”
Section: Co-expression Network Analysismentioning
confidence: 99%
“…7 . The CoExp tool is an online web application consisting of a collection of 109 networks, powered by the CoExpNets suite of R packages.…”
mentioning
confidence: 99%