ArticlePLoS computational biology2008
Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics.
Article in PLoS computational biology, 2008. 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 114 papers, 1 of them a synthesis that pooled it.
What it found
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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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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.
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Who cites it
114 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- TransPilot: mining key transcription factors by correlating binding sites with differentially expressed genes.Bioinformatics advances · 2026Article
- GeTeSEPdb: A comprehensive database and online tool for the identification and analysis of gene profiles with temporal-specific expression patterns.Computational and structural biotechnology journal · 2024Article
- A female-biased gene expression signature of dominance in cooperatively breeding meerkats.Molecular ecology · 2024Article
- A Preliminary Study on Factors That Drive Patient Variability in Human Subcutaneous Adipose Tissues.Cells · 2024Article
- Comparative transcriptomic analysis of the nodulation-competent zone and inference of transcription regulatory network in silicon applied Glycine max [L.]-Merr. Roots.Plant cell reports · 2024Article
- Reprogramming of the LXRα Transcriptome Sustains Macrophage Secondary Inflammatory Responses.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Multi-country clustering-based forecasting of healthy life expectancy.Quality & quantity · 2023Article
- An Evidence Theory and Fuzzy Logic Combined Approach for the Prediction of Potential ARF-Regulated Genes in Quinoa.Plants (Basel, Switzerland) · 2022Article
- SRSF6 balances mitochondrial-driven innate immune outcomes through alternative splicing of BAX.eLife · 2022Article
- Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics.PLoS computational biology · 2022Article
- Connections for Matters of the Heart: Network Medicine in Cardiovascular Diseases.Frontiers in cardiovascular medicine · 2022Review
- A conserved long noncoding RNA, GAPLINC, modulates the immune response during endotoxic shock.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- A comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks inComputational and structural biotechnology journal · 2021Article
- Gene Regulatory Strategies that Decode the Duration of NFκB Dynamics Contribute to LPS- versus TNF-Specific Gene Expression.Cell systems · 2020Article
- A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV.Cell reports · 2020Article
- Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure.Frontiers in genetics · 2020Article
- FACS-Seq analysis of Pax3-derived cells identifies non-myogenic lineages in the embryonic forelimb.Scientific reports · 2018Article
- Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages.Scientific reports · 2018Article
- Systematic Investigation of Multi-TLR Sensing Identifies Regulators of Sustained Gene Activation in Macrophages.Cell systems · 2017Article
54 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
- Erratum issued
Authors and funding
17 authors.
Funding
Abstract
Macrophages are versatile immune cells that can detect a variety of pathogen-associated molecular patterns through their Toll-like receptors (TLRs). In response to microbial challenge, the TLR-stimulated macrophage undergoes an activation program controlled by a dynamically inducible transcriptional regulatory network. Mapping a complex mammalian transcriptional network poses significant challenges and requires the integration of multiple experimental data types. In this work, we inferred a transcriptional network underlying TLR-stimulated murine macrophage activation. Microarray-based expression profiling and transcription factor binding site motif scanning were used to infer a network of associations between transcription factor genes and clusters of co-expressed target genes. The time-lagged correlation was used to analyze temporal expression data in order to identify potential causal influences in the network. A novel statistical test was developed to assess the significance of the time-lagged correlation. Several associations in the resulting inferred network were validated using targeted ChIP-on-chip experiments. The network incorporates known regulators and gives insight into the transcriptional control of macrophage activation. Our analysis identified a novel regulator (TGIF1) that may have a role in macrophage activation.
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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.