ArticleGenome biology2018
Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers, 1 of them a synthesis that pooled it.
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Who cites it
114 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Enhancing the performance and interpretability of epigenetic clocks.Nucleic acids research · 2026Article
- Transcriptome profiling of intra-snail stages of the liver fluke Fasciola hepatica reveals key mediators underlying parasite development and interaction with the host.BMC genomics · 2026Article
- A proteome-wide biochemical screen defines binding determinants of the core autophagy protein LC3B.bioRxiv : the preprint server for biology · 2026Article
- A spatially informed matrix normal model for gene co-expression analysis in spatial transcriptomics studies.Nucleic acids research · 2025Article
- InCURA: integrative gene clustering based on transcription factor binding sites.Nucleic acids research · 2025Article
- Species-specific phylloplane responses to changes in external pH.Journal of experimental botany · 2025Article
- Proteomic characterization of the pseudocapsule of clear cell renal cell carcinoma in VHL disease reveals a distinct microenvironment at the tumor boundary zone.Neoplasia (New York, N.Y.) · 2025Article
- Environmentally relevant lead exposure impacts gene expression in SH-SY5Y cells throughout neuronal differentiation.Toxicological sciences : an official journal of the Society of Toxicology · 2025Article
- RCANE: a deep learning algorithm for whole-genome pan-cancer somatic copy number aberration prediction using RNA-seq data.Communications biology · 2025Article
- Parasitic-Plant Parasite Rewires Flowering Pathways to Induce Stem-Derived Galls.Plant direct · 2025Article
- Longitudinal transcriptomic and epigenetic analysis of the blood in two astronauts.Scientific reports · 2025Article
- miRNA centered regulatory networks identify FN1 and miR27b as metastatic drivers in HPV negative head and neck cancer.Scientific reports · 2025Article
- Epiallelic Variation of TILLER ANGLE CONTROL 5 (TAC5) Regulates Tiller Angle by Modulating Gravitropism in Rice.Rice (New York, N.Y.) · 2025Article
- The Dynamic Landscape of 3'-UTR Alternative Polyadenylation Across Mouse Fetal Development and Anatomy.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Temporal dynamics of gene expression during the development ofMicrobial genomics · 2025Article
54 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
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Abstract
Identifying co-expressed gene clusters can provide evidence for genetic or physical interactions. Thus, co-expression clustering is a routine step in large-scale analyses of gene expression data. We show that commonly used clustering methods produce results that substantially disagree and that do not match the biological expectations of co-expressed gene clusters. We present clust, a method that solves these problems by extracting clusters matching the biological expectations of co-expressed genes and outperforms widely used methods. Additionally, clust can simultaneously cluster multiple datasets, enabling users to leverage the large quantity of public expression data for novel comparative analysis. Clust is available at https://github.com/BaselAbujamous/clust .
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.