ArticlePLoS computational biology2017
CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Variability of Clinical Phenotypes Caused by Isolated Defects of Mitochondrial ATP Synthase.Physiological research · 2024Pooled it
- Assembly of the catalytic module and the rotor of human ATP synthase.The EMBO journal · 2026Article
- Specific activation of the integrated stress response uncovers regulation of central carbon metabolism and lipid droplet biogenesis.Nature communications · 2024Article
- Installation of LYRM proteins in early eukaryotes to regulate the metabolic capacity of the emerging mitochondrion.Open biology · 2024Article
- COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations.Nucleic acids research · 2023Article
- A cross-species co-functional gene network underlying leaf senescence.Horticulture research · 2023Article
- Integrated network analyses identify MYB4R1 neofunctionalization in the UV-B adaptation of Tartary buckwheat.Plant communications · 2022Article
- Genetic Complementation of ATP Synthase Deficiency Due to Dysfunction of TMEM70 Assembly Factor in Rat.Biomedicines · 2022Article
- The ATPase Inhibitory Factor 1 is a Tissue-Specific Physiological Regulator of the Structure and Function of Mitochondrial ATP Synthase: A Closer Look Into Neuronal Function.Frontiers in physiology · 2022Review
- TMEM70 and TMEM242 help to assemble the rotor ring of human ATP synthase and interact with assembly factors for complex I.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Co-expression analysis identifies neuro-inflammation as a driver of sensory neuron aging in Aplysia californica.PloS one · 2021Article
- Assembly of the peripheral stalk of ATP synthase in human mitochondria.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Independent evolution of transcript abundance and gene regulatory dynamics.Genome research · 2020Article
- Learning complex subcellular distribution patterns of proteins via analysis of immunohistochemistry images.Bioinformatics (Oxford, England) · 2020Article
- Identifying gene function and module connections by the integration of multispecies expression compendia.Genome research · 2019Article
- Tubulin mRNA stability is sensitive to change in microtubule dynamics caused by multiple physiological and toxic cues.PLoS biology · 2019Article
- Genome-wide analysis of yeast expression data based on a priori generated co-regulation cliques.Microbial cell (Graz, Austria) · 2019Article
- eIF2B activator prevents neurological defects caused by a chronic integrated stress response.eLife · 2019Article
- Mitochondrial DNA degradation: A quality control measure for mitochondrial genome maintenance and stress response.The Enzymes · 2019Review
- Computational systems biology approaches for Parkinson's disease.Cell and tissue research · 2018Review
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5 authors.
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Abstract
In recent years, there has been a huge rise in the number of publicly available transcriptional profiling datasets. These massive compendia comprise billions of measurements and provide a special opportunity to predict the function of unstudied genes based on co-expression to well-studied pathways. Such analyses can be very challenging, however, since biological pathways are modular and may exhibit co-expression only in specific contexts. To overcome these challenges we introduce CLIC, CLustering by Inferred Co-expression. CLIC accepts as input a pathway consisting of two or more genes. It then uses a Bayesian partition model to simultaneously partition the input gene set into coherent co-expressed modules (CEMs), while assigning the posterior probability for each dataset in support of each CEM. CLIC then expands each CEM by scanning the transcriptome for additional co-expressed genes, quantified by an integrated log-likelihood ratio (LLR) score weighted for each dataset. As a byproduct, CLIC automatically learns the conditions (datasets) within which a CEM is operative. We implemented CLIC using a compendium of 1774 mouse microarray datasets (28628 microarrays) or 1887 human microarray datasets (45158 microarrays). CLIC analysis reveals that of 910 canonical biological pathways, 30% consist of strongly co-expressed gene modules for which new members are predicted. For example, CLIC predicts a functional connection between protein C7orf55 (FMC1) and the mitochondrial ATP synthase complex that we have experimentally validated. CLIC is freely available at www.gene-clic.org. We anticipate that CLIC will be valuable both for revealing new components of biological pathways as well as the conditions in which they are active.
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