ArticleNature communications2018
Reprogramming of regulatory network using expression uncovers sex-specific gene regulation in Drosophila.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed.
- Inferring Gene Regulatory Networks From Single-Cell RNA Sequencing Data by Dual-Role Graph Contrastive Learning.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Leveraging transcription factor physical proximity for enhancing gene regulation inference.Bioinformatics (Oxford, England) · 2025Article
- Perspective on recent developments and challenges in regulatory and systems genomics.Bioinformatics advances · 2025Review
- Integrated analysis reveals NLRC4 as a potential biomarker in sepsis pathogenesis.Genes and immunity · 2024Article
- Deciphering lineage-relevant gene regulatory networks during endoderm formation by InPheRNo-ChIP.Briefings in bioinformatics · 2024Article
- SAILoR: Structure-Aware Inference of Logic Rules.PloS one · 2024Article
- Deciphering driver regulators of cell fate decisions from single-cell transcriptomics data with CEFCON.Nature communications · 2023Article
- NetREX-CF integrates incomplete transcription factor data with gene expression to reconstruct gene regulatory networks.Communications biology · 2022Article
- Using bioinformatics and systems biology to discover common pathogenetic processes between sarcoidosis and COVID-19.Gene reports · 2022Article
- Gene regulatory network inference in long-livediScience · 2022Article
- ParsVNN: parsimony visible neural networks for uncovering cancer-specific and drug-sensitive genes and pathways.NAR genomics and bioinformatics · 2021Article
- Data integration for inferring context-specific gene regulatory networks.Current opinion in systems biology · 2020Article
- Article
- Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks.mSystems · 2020Article
- Network inference in systems biology: recent developments, challenges, and applications.Current opinion in biotechnology · 2020Review
- Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses.Genome research · 2020Article
- Sex biased expression and co-expression networks in development, using the hymenopteran Nasonia vitripennis.PLoS genetics · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
Abstract
Gene regulatory networks (GRNs) describe regulatory relationships between transcription factors (TFs) and their target genes. Computational methods to infer GRNs typically combine evidence across different conditions to infer context-agnostic networks. We develop a method, Network Reprogramming using EXpression (NetREX), that constructs a context-specific GRN given context-specific expression data and a context-agnostic prior network. NetREX remodels the prior network to obtain the topology that provides the best explanation for expression data. Because NetREX utilizes prior network topology, we also develop PriorBoost, a method that evaluates a prior network in terms of its consistency with the expression data. We validate NetREX and PriorBoost using the "gold standard" E. coli GRN from the DREAM5 network inference challenge and apply them to construct sex-specific Drosophila GRNs. NetREX constructed sex-specific Drosophila GRNs that, on all applied measures, outperform networks obtained from other methods indicating that NetREX is an important milestone toward building more accurate GRNs.
Indexed as
Identifiers
What OpenQuestion holds
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.