ArticlePloS one2011
Gene network landscape of the ciliate Tetrahymena thermophila.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
18 citing papers in PubMed, 41 citations in OpenAlex.
- Bromodomain protein IBD1 bridges histone acetylation and H2A.Z deposition to fine-tune transcription.Nucleic acids research · 2026Article
- Inferring gene-pathway associations from consolidated transcriptome datasets: an interactive gene network explorer forNAR genomics and bioinformatics · 2025Article
- Bromodomain-containing proteins in the unicellular eukaryoteZoological research · 2025Review
- A practical reference for studying meiosis in the model ciliateMarine life science & technology · 2022Review
- Diversification of CORVET tethers facilitates transport complexity inJournal of cell science · 2020Article
- Exploring the Histone Acetylation Cycle in the Protozoan ModelFrontiers in cell and developmental biology · 2020Review
- A distinct class of eukaryotic MT-A70 methyltransferases maintain symmetric DNA N6-adenine methylation at the ApT dinucleotides as an epigenetic mark associated with transcription.Nucleic acids research · 2019Article
- Remodeling the Specificity of an Endosomal CORVET Tether Underlies Formation of Regulated Secretory Vesicles in the Ciliate Tetrahymena thermophila.Current biology : CB · 2018Article
- The Co-regulation Data Harvester: automating gene annotation starting from a transcriptome database.SoftwareX · 2017Article
- Developmental regulation of the Tetrahymena thermophila origin recognition complex.PLoS genetics · 2015Article
- An aspartyl cathepsin, CTH3, is essential for proprotein processing during secretory granule maturation in Tetrahymena thermophila.Molecular biology of the cell · 2014Article
- Phosphoproteomic analysis of protein phosphorylation networks in Tetrahymena thermophila, a model single-celled organism.Molecular & cellular proteomics : MCP · 2014Article
- Article
- DeGNServer: deciphering genome-scale gene networks through high performance reverse engineering analysis.BioMed research international · 2013Article
- Tetrahymena functional genomics database (TetraFGD): an integrated resource for Tetrahymena functional genomics.Database : the journal of biological databases and curation · 2013Article
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- Article
- Conservation and innovation in Tetrahymena membrane traffic: proteins, lipids, and compartments.Methods in cell biology · 2012Review
Corrections and comments
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Authors and funding
10 authors at 5 institutions in 3 countries.
Funding
Abstract
backgroundGenome-wide expression data of gene microarrays can be used to infer gene networks. At a cellular level, a gene network provides a picture of the modules in which genes are densely connected, and of the hub genes, which are highly connected with other genes. A gene network is useful to identify the genes involved in the same pathway, in a protein complex or that are co-regulated. In this study, we used different methods to find gene networks in the ciliate Tetrahymena thermophila, and describe some important properties of this network, such as modules and hubs. METHODOLOGY/PRINCIPAL
findingsUsing 67 single channel microarrays, we constructed the Tetrahymena gene network (TGN) using three methods: the Pearson correlation coefficient (PCC), the Spearman correlation coefficient (SCC) and the context likelihood of relatedness (CLR) algorithm. The accuracy and coverage of the three networks were evaluated using four conserved protein complexes in yeast. The CLR network with a Z-score threshold 3.49 was determined to be the most robust. The TGN was partitioned, and 55 modules were found. In addition, analysis of the arbitrarily determined 1200 hubs showed that these hubs could be sorted into six groups according to their expression profiles. We also investigated human disease orthologs in Tetrahymena that are missing in yeast and provide evidence indicating that some of these are involved in the same process in Tetrahymena as in human. CONCLUSIONS/SIGNIFICANCE: This study constructed a Tetrahymena gene network, provided new insights to the properties of this biological network, and presents an important resource to study Tetrahymena genes at the pathway level.
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Registered trials
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.