ArticlePLoS computational biology2015
Loregic: a method to characterize the cooperative logic of regulatory factors.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- CoTF-reg reveals cooperative transcription factors in oligodendrocyte gene regulation using single-cell multi-omics.Communications biology · 2025Article
- NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation.Bioinformatics advances · 2025Article
- Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanisms.Briefings in bioinformatics · 2024Article
- Revealing gene regulation-based neural network computing in bacteria.Biophysical reports · 2023Article
- Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease.PLoS computational biology · 2022Article
- An integrative ENCODE resource for cancer genomics.Nature communications · 2020Article
- LogicNet: probabilistic continuous logics in reconstructing gene regulatory networks.BMC bioinformatics · 2020Article
- Feed-forward regulation adaptively evolves via dynamics rather than topology when there is intrinsic noise.Nature communications · 2019Article
- Ambiguity in logic-based models of gene regulatory networks: An integrative multi-perturbation analysis.PloS one · 2018Article
- YGMD: a repository for yeast cooperative transcription factor sets and their target gene modules.Database : the journal of biological databases and curation · 2017Article
- CRISPR Genome Engineering for Human Pluripotent Stem Cell Research.Theranostics · 2017Review
- Handshakes and Fights: The Regulatory Interplay of RNA-Binding Proteins.Frontiers in molecular biosciences · 2017Review
- Cross-Disciplinary Network Comparison: Matchmaking Between Hairballs.Cell systems · 2016Article
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Authors and funding
7 authors.
Funding
Abstract
The topology of the gene-regulatory network has been extensively analyzed. Now, given the large amount of available functional genomic data, it is possible to go beyond this and systematically study regulatory circuits in terms of logic elements. To this end, we present Loregic, a computational method integrating gene expression and regulatory network data, to characterize the cooperativity of regulatory factors. Loregic uses all 16 possible two-input-one-output logic gates (e.g. AND or XOR) to describe triplets of two factors regulating a common target. We attempt to find the gate that best matches each triplet's observed gene expression pattern across many conditions. We make Loregic available as a general-purpose tool (github.com/gersteinlab/loregic). We validate it with known yeast transcription-factor knockout experiments. Next, using human ENCODE ChIP-Seq and TCGA RNA-Seq data, we are able to demonstrate how Loregic characterizes complex circuits involving both proximally and distally regulating transcription factors (TFs) and also miRNAs. Furthermore, we show that MYC, a well-known oncogenic driving TF, can be modeled as acting independently from other TFs (e.g., using OR gates) but antagonistically with repressing miRNAs. Finally, we inter-relate Loregic's gate logic with other aspects of regulation, such as indirect binding via protein-protein interactions, feed-forward loop motifs and global regulatory hierarchy.
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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.