ArticleGenome research2007
Reliable prediction of regulator targets using 12 Drosophila genomes.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 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
104 citing papers in PubMed, 162 citations in OpenAlex.
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- Dichotomous cis-regulatory motifs mediate the maturation of the neuromuscular junction by retrograde BMP signaling.Nucleic acids research · 2022Article
- Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics.PLoS computational biology · 2022Article
- microRNA-252 and FoxO repress inflammaging by a dual inhibitory mechanism on Dawdle-mediated TGF-β pathway in Drosophila.Genetics · 2022Article
- Evolutionary rewiring of regulatory networks contributes to phenotypic differences between human and mouse orthologous genes.Nucleic acids research · 2022Article
- Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators.Nature plants · 2021Article
- Prediction methods for microRNA targets in bilaterian animals: Toward a better understanding by biologists.Computational and structural biotechnology journal · 2021Review
- Computational biology approaches for mapping transcriptional regulatory networks.Computational and structural biotechnology journal · 2021Review
- Evolutionary dynamics of microRNA target sites across vertebrate evolution.PLoS genetics · 2020Article
- A Comprehensive Drosophila melanogaster Transcription Factor Interactome.Cell reports · 2019Article
- Retrograde BMP signaling activates neuronal gene expression through widespread deployment of a conserved BMP-responsive cis-regulatory activation element.Nucleic acids research · 2019Article
- Predicting microRNA targeting efficacy in Drosophila.Genome biology · 2018Article
- Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development.PLoS biology · 2018Article
- Direct measurement of pervasive weak repression by microRNAs and their role at the network level.BMC genomics · 2018Article
- The mir-7 and bag of marbles genes regulate Hedgehog pathway signaling in blood cell progenitors in Drosophila larval lymph glands.Genesis (New York, N.Y. : 2000) · 2018Article
- Phylogeny of the GenusGenetics · 2018Review
- Stereotypical architecture of the stem cell niche is spatiotemporally established by miR-125-dependent coordination of Notch and steroid signaling.Development (Cambridge, England) · 2018Article
- Stress-dependent miR-980 regulation of Rbfox1/A2bp1 promotes ribonucleoprotein granule formation and cell survival.Nature communications · 2018Article
44 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
Gene expression is regulated pre- and post-transcriptionally via cis-regulatory DNA and RNA motifs. Identification of individual functional instances of such motifs in genome sequences is a major goal for inferring regulatory networks yet has been hampered due to the motifs' short lengths that lead to many chance matches and poor signal-to-noise ratios. In this paper, we develop a general methodology for the comparative identification of functional motif instances across many related species, using a phylogenetic framework that accounts for the evolutionary relationships between species, allows for motif movements, and is robust against missing data due to artifacts in sequencing, assembly, or alignment. We also provide a robust statistical framework for evaluating motif confidence, which enables us to translate evolutionary conservation into a confidence measure for each motif instance, correcting for varying motif length, composition, and background conservation of the target regions. We predict targets of fly transcription factors and miRNAs in alignments of 12 recently sequenced Drosophila species. When compared to extensive genome-wide experimental data, predicted targets are of high quality, matching and surpassing ChIP-chip microarrays and recovering miRNA targets with high sensitivity. The resulting regulatory network suggests significant redundancy between pre- and post-transcriptional regulation of gene expression.
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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.