ArticleThe Journal of biological chemistry2014
Modulation of gene expression regulated by the transcription factor NF-κB/RelA.
Article in The Journal of biological chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 31 citations in OpenAlex.
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- HYPOXIA induces lncRNA HOTAIR for recruiting RELA in papillary thyroid cancer cells to upregulate miR-181a and promote angiogenesis.Journal of endocrinological investigation · 2024Article
- Gene-to-gene coordinated regulation of transcription and alternative splicing by 3D chromatin remodeling upon NF-κB activation.Nucleic acids research · 2024Article
- Connectivity Mapping Identifies BI-2536 as a Potential Drug to Treat Diabetic Kidney Disease.Diabetes · 2021Article
- Redox Homeostasis in Poultry: Regulatory Roles of NF-κB.Antioxidants (Basel, Switzerland) · 2021Review
- An efficient computational method for predicting drug-target interactions using weighted extreme learning machine and speed up robot features.BioData mining · 2021Article
- RSV Reprograms the CDK9•BRD4 Chromatin Remodeling Complex to Couple Innate Inflammation to Airway Remodeling.Viruses · 2020Review
- NF-κB c-Rel Dictates the Inflammatory Threshold by Acting as a Transcriptional Repressor.iScience · 2020Article
- Selective Antagonists of the Bronchiolar Epithelial NF-κB-Bromodomain-Containing Protein 4 Pathway in Viral-Induced Airway Inflammation.Cell reports · 2018Article
- Single-cell analyses reveal an attenuated NF-κB response in the Salmonella-infected fibroblast.Virulence · 2017Article
- Quantitative Assessment of the Effects of Trypsin Digestion Methods on Affinity Purification-Mass Spectrometry-based Protein-Protein Interaction Analysis.Journal of proteome research · 2017Article
- Novel Serine 176 Phosphorylation of YBX1 Activates NF-κB in Colon Cancer.The Journal of biological chemistry · 2017Article
- Decreased Expression of SRSF2 Splicing Factor Inhibits Apoptotic Pathways in Renal Cancer.International journal of molecular sciences · 2016Article
- Mesenchymal stem cells promote colorectal cancer progression through AMPK/mTOR-mediated NF-κB activation.Scientific reports · 2016Article
- Article
- Systematic Determination of Human Cyclin Dependent Kinase (CDK)-9 Interactome Identifies Novel Functions in RNA Splicing Mediated by the DEAD Box (DDX)-5/17 RNA Helicases.Molecular & cellular proteomics : MCP · 2015Article
- Analysis of the TGFβ-induced program in primary airway epithelial cells shows essential role of NF-κB/RelA signaling network in type II epithelial mesenchymal transition.BMC genomics · 2015Article
- Inferring genome-wide functional modulatory network: a case study on NF-κB/RelA transcription factor.Journal of computational biology : a journal of computational molecular cell biology · 2015Article
- Article
- Correcting positional correlations in Affymetrix® genome chips.Scientific reports · 2015Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
Abstract
Modulators (Ms) are proteins that modify the activity of transcription factors (TFs) and influence expression of their target genes (TGs). To discover modulators of NF-κB/RelA, we first identified 365 NF-κB/RelA-binding proteins using liquid chromatography-tandem mass spectrometry (LC-MS/MS). We used a probabilistic model to infer 8349 (M, NF-κB/RelA, TG) triplets and their modes of modulatory action from our combined LC-MS/MS and ChIP-Seq (ChIP followed by next generation sequencing) data, published RelA modulators and TGs, and a compendium of gene expression profiles. Hierarchical clustering of the derived modulatory network revealed functional subnetworks and suggested new pathways modulating RelA transcriptional activity. The modulators with the highest number of TGs and most non-random distribution of action modes (measured by Shannon entropy) are consistent with published reports. Our results provide a repertoire of testable hypotheses for experimental validation. One of the NF-κB/RelA modulators we identified is STAT1. The inferred (STAT1, NF-κB/RelA, TG) triplets were validated by LC-selected reaction monitoring-MS and the results of STAT1 deletion in human fibrosarcoma cells. Overall, we have identified 562 NF-κB/RelA modulators, which are potential drug targets, and clarified mechanisms of achieving NF-κB/RelA multiple functions through modulators. Our approach can be readily applied to other TFs.
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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.