ArticleGenome biology2014
OrthoClust: an orthology-based network framework for clustering data across multiple species.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
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- MATTE: a pipeline of transcriptome module alignment for anti-noise phenotype-gene-related analysis.Briefings in bioinformatics · 2023Article
- Bipartite tight spectral clustering (BiTSC) algorithm for identifying conserved gene co-clusters in two species.Bioinformatics (Oxford, England) · 2021Article
- Article
- Juxtapose: a gene-embedding approach for comparing co-expression networks.BMC bioinformatics · 2021Article
- Evolutionary conservation and divergence of the human brain transcriptome.Genome biology · 2021Article
- Comparative Analyses of Gene Co-expression Networks: Implementations and Applications in the Study of Evolution.Frontiers in genetics · 2021Review
- ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks.BMC genomics · 2019Article
- Comparing time series transcriptome data between plants using a network module finding algorithm.Plant methods · 2019Article
- Cross-species systems analysis of evolutionary toolkits of neurogenomic response to social challenge.Genes, brain, and behavior · 2019Article
- Feature related multi-view nonnegative matrix factorization for identifying conserved functional modules in multiple biological networks.BMC bioinformatics · 2018Article
- Discovery of two-level modular organization from matched genomic data via joint matrix tri-factorization.Nucleic acids research · 2018Article
- Molecular ecological network analysis reveals the effects of probiotics and florfenicol on intestinal microbiota homeostasis: An example of sea cucumber.Scientific reports · 2017Article
- MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions.PLoS computational biology · 2017Article
- Meta-analysis of Liver and Heart Transcriptomic Data for Functional Annotation Transfer in Mammalian Orthologs.Computational and structural biotechnology journal · 2017Article
- Expression of immunoproteasome genes is regulated by cell-intrinsic and -extrinsic factors in human cancers.Scientific reports · 2016Article
- Cross-Disciplinary Network Comparison: Matchmaking Between Hairballs.Cell systems · 2016Article
- Enrichment of Triticum aestivum gene annotations using ortholog cliques and gene ontologies in other plants.BMC genomics · 2015Article
- Comparative Transcriptomes and EVO-DEVO Studies Depending on Next Generation Sequencing.Computational and mathematical methods in medicine · 2015Review
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Authors and funding
6 authors.
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Abstract
Increasingly, high-dimensional genomics data are becoming available for many organisms.Here, we develop OrthoClust for simultaneously clustering data across multiple species. OrthoClust is a computational framework that integrates the co-association networks of individual species by utilizing the orthology relationships of genes between species. It outputs optimized modules that are fundamentally cross-species, which can either be conserved or species-specific. We demonstrate the application of OrthoClust using the RNA-Seq expression profiles of Caenorhabditis elegans and Drosophila melanogaster from the modENCODE consortium. A potential application of cross-species modules is to infer putative analogous functions of uncharacterized elements like non-coding RNAs based on guilt-by-association.
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