ArticlePloS one2014
Inferring protein modulation from gene expression data using conditional mutual information.
Article in PloS one, 2014. 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 18 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
18 citing papers in PubMed.
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- Mining higher-order triadic interactions.Nature communications · 2025Article
- Differential Transcriptional Programs Reveal Modular Network Rearrangements Associated with Late-Onset Alzheimer's Disease.International journal of molecular sciences · 2025Article
- Genome-wide studies define new genetic mechanisms of IgA vasculitis.medRxiv : the preprint server for health sciences · 2024Article
- Network-based approaches for modeling disease regulation and progression.Computational and structural biotechnology journal · 2023Review
- Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses.Nature biotechnology · 2021Article
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- Systematic elucidation of neuron-astrocyte interaction in models of amyotrophic lateral sclerosis using multi-modal integrated bioinformatics workflow.Nature communications · 2020Article
- Master Regulator Analysis of the SARS-CoV-2/Human Interactome.Journal of clinical medicine · 2020Article
- Network inference performance complexity: a consequence of topological, experimental and algorithmic determinants.Bioinformatics (Oxford, England) · 2019Article
- Differential gene regulatory networks in development and disease.Cellular and molecular life sciences : CMLS · 2018Review
- Accelerated parallel algorithm for gene network reverse engineering.BMC systems biology · 2017Article
- Cattle genome-wide analysis reveals genetic signatures in trypanotolerant N'Dama.BMC genomics · 2017Article
- Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers.Scientific reports · 2016Article
- Article
- MIrExpress: A Database for Gene Coexpression Correlation in Immune Cells Based on Mutual Information and Pearson Correlation.Journal of immunology research · 2015Article
- Article
- Integrating 3D structural information into systems biology.The Journal of biological chemistryReview
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
Abstract
Systematic, high-throughput dissection of causal post-translational regulatory dependencies, on a genome wide basis, is still one of the great challenges of biology. Due to its complexity, however, only a handful of computational algorithms have been developed for this task. Here we present CINDy (Conditional Inference of Network Dynamics), a novel algorithm for the genome-wide, context specific inference of regulatory dependencies between signaling protein and transcription factor activity, from gene expression data. The algorithm uses a novel adaptive partitioning methodology to accurately estimate the full Condition Mutual Information (CMI) between a transcription factor and its targets, given the expression of a signaling protein. We show that CMI analysis is optimally suited to dissecting post-translational dependencies. Indeed, when tested against a gold standard dataset of experimentally validated protein-protein interactions in signal transduction networks, CINDy significantly outperforms previous methods, both in terms of sensitivity and precision.
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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.