SynthesisPLoS computational biology2012
MC EMiNEM maps the interaction landscape of the Mediator.
Synthesis in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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.
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.
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Who cites it
10 citing papers in PubMed, 17 citations in OpenAlex.
- NEM-Tar: A Probabilistic Graphical Model for Cancer Regulatory Network Inference and Prioritization of Potential Therapeutic Targets From Multi-Omics Data.Frontiers in genetics · 2021Article
- Context-Specific Nested Effects Models.Journal of computational biology : a journal of computational molecular cell biology · 2020Article
- DRUG-NEM: Optimizing drug combinations using single-cell perturbation response to account for intratumoral heterogeneity.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Context-Specific Nested Effects Models.Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- ) · 2018Article
- Inferring modulators of genetic interactions with epistatic nested effects models.PLoS computational biology · 2017Article
- Toward understanding of the mechanisms of Mediator function in vivo: Focus on the preinitiation complex assembly.Transcription · 2017Review
- Analyzing synergistic and non-synergistic interactions in signalling pathways using Boolean Nested Effect Models.Bioinformatics (Oxford, England) · 2016Article
- Refining Pathways: A Model Comparison Approach.PloS one · 2016Article
- NEMix: single-cell nested effects models for probabilistic pathway stimulation.PLoS computational biology · 2015Article
- Considering unknown unknowns: reconstruction of nonconfoundable causal relations in biological networks.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Mediator is a highly conserved, large multiprotein complex that is involved essentially in the regulation of eukaryotic mRNA transcription. It acts as a general transcription factor by integrating regulatory signals from gene-specific activators or repressors to the RNA Polymerase II. The internal network of interactions between Mediator subunits that conveys these signals is largely unknown. Here, we introduce MC EMiNEM, a novel method for the retrieval of functional dependencies between proteins that have pleiotropic effects on mRNA transcription. MC EMiNEM is based on Nested Effects Models (NEMs), a class of probabilistic graphical models that extends the idea of hierarchical clustering. It combines mode-hopping Monte Carlo (MC) sampling with an Expectation-Maximization (EM) algorithm for NEMs to increase sensitivity compared to existing methods. A meta-analysis of four Mediator perturbation studies in Saccharomyces cerevisiae, three of which are unpublished, provides new insight into the Mediator signaling network. In addition to the known modular organization of the Mediator subunits, MC EMiNEM reveals a hierarchical ordering of its internal information flow, which is putatively transmitted through structural changes within the complex. We identify the N-terminus of Med7 as a peripheral entity, entailing only local structural changes upon perturbation, while the C-terminus of Med7 and Med19 appear to play a central role. MC EMiNEM associates Mediator subunits to most directly affected genes, which, in conjunction with gene set enrichment analysis, allows us to construct an interaction map of Mediator subunits and transcription factors.
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.