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Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes

https://doi.org/10.1101/093807
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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ChIP-seq and RNA-seq Methods to Study Circadian Control of Transcription in Mammals
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Cellular Decision Making and Biological Noise: From Microbes to Mammals
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Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape
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Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana
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Sequential Feedback Induction Stabilizes the Phosphate Starvation Response in Budding Yeast
inferredcites →https://doi.org/10.1016/j.immuni.2012.03.013openalex-snapshot
The JAK-STAT Pathway at Twenty
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STAT proteins: Signal tranducers and activators of transcription
inferredcites →https://doi.org/10.1016/s0952-7915(98)80165-9openalex-snapshot
JAK/STAT signaling by cytokine receptors
inferredcites →https://doi.org/10.1016/s0968-0004(00)01624-8openalex-snapshot
STAT proteins and transcriptional responses to extracellular signals
inferredcites →https://doi.org/10.1021/bi00089a010openalex-snapshot
Novel zinc finger motif in the basal transcriptional machinery: Three-dimensional NMR studies of the nucleic acid binding domain of transcriptional elongation factor TFIIS
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Random Forests
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The map-based sequence of the rice genome
inferredcites →https://doi.org/10.1038/nature10182openalex-snapshot
The ELF4–ELF3–LUX complex links the circadian clock to diurnal control of hypocotyl growth
inferredcites →https://doi.org/10.1038/nmeth.2016openalex-snapshot
Wisdom of crowds for robust gene network inference
inferredcites →https://doi.org/10.1038/nmeth0610-419openalex-snapshot
Partitioning biological data with transitivity clustering
inferredcites →https://doi.org/10.1038/nplants.2017.87openalex-snapshot
The evening complex coordinates environmental and endogenous signals in Arabidopsis
inferredcites →https://doi.org/10.1038/nprot.2013.099openalex-snapshot
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
inferredcites →https://doi.org/10.1038/nrg2641openalex-snapshot
ChIP–seq: advantages and challenges of a maturing technology
inferredcites →https://doi.org/10.1038/nrg3244openalex-snapshot
Studying and modelling dynamic biological processes using time-series gene expression data
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Integrating circadian dynamics with physiological processes in plants
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On the trail of EHEC/EAEC—unraveling the gene regulatory networks of human pathogenicEscherichia colibacteria
inferredcites →https://doi.org/10.1073/pnas.1316064110openalex-snapshot
Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins
inferredcites →https://doi.org/10.1073/pnas.1513609112openalex-snapshot
Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis
inferredcites →https://doi.org/10.1073/pnas.95.25.14863openalex-snapshot
Cluster analysis and display of genome-wide expression patterns
inferredcites →https://doi.org/10.1093/bioinformatics/btg347openalex-snapshot
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data
inferredcites →https://doi.org/10.1093/bioinformatics/bti623openalex-snapshot
ROCR: visualizing classifier performance in R
inferredcites →https://doi.org/10.1093/bioinformatics/btr454openalex-snapshot
Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis
inferredcites →https://doi.org/10.1093/bioinformatics/bts157openalex-snapshot
CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human
inferredcites →https://doi.org/10.1093/bioinformatics/bts222openalex-snapshot
Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks
inferredcites →https://doi.org/10.1093/bioinformatics/btt099openalex-snapshot
Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks
inferredcites →https://doi.org/10.1093/molbev/msv058openalex-snapshot
AnArabidopsisTranscriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors
inferredcites →https://doi.org/10.1093/nar/gkq699openalex-snapshot
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inferredcites →https://doi.org/10.1093/nar/gkr883openalex-snapshot
CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands
inferredcites →https://doi.org/10.1093/nar/gkr965openalex-snapshot
AnimalTFDB: a comprehensive animal transcription factor database
inferredcites →https://doi.org/10.1093/nar/gks1161openalex-snapshot
CircaDB: a database of mammalian circadian gene expression profiles
inferredcites →https://doi.org/10.1093/nar/gkv1156openalex-snapshot
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
inferredcites →https://doi.org/10.1101/gr.090233.108openalex-snapshot
High-resolution DNA-binding specificity analysis of yeast transcription factors
inferredcites →https://doi.org/10.1104/pp.104.044347openalex-snapshot
Diurnal Changes in the Transcriptome Encoding Enzymes of Starch Metabolism Provide Evidence for Both Transcriptional and Posttranscriptional Regulation of Starch Metabolism in Arabidopsis Leaves
inferredcites →https://doi.org/10.1104/pp.16.00789openalex-snapshot
Genome-Wide Targets Regulated by the OsMADS1 Transcription Factor Reveals Its DNA Recognition Properties
inferredcites →https://doi.org/10.1105/tpc.105.035261openalex-snapshot
Sugars and Circadian Regulation Make Major Contributions to the Global Regulation of Diurnal Gene Expression in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.105.038315openalex-snapshot
FLOWERING LOCUS C Mediates Natural Variation in the High-Temperature Response of the Arabidopsis Circadian Clock
inferredcites →https://doi.org/10.1105/tpc.106.047688openalex-snapshot
Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development
inferredcites →https://doi.org/10.1105/tpc.110.075606openalex-snapshot
Orchestration of the Floral Transition and Floral Development in Arabidopsis by the Bifunctional Transcription Factor APETALA2
inferredcites →https://doi.org/10.1105/tpc.112.098061openalex-snapshot
Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.16.00158openalex-snapshot
EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments
inferredcites →https://doi.org/10.1111/tpj.12276openalex-snapshot
Direct regulation of abiotic responses by the A rabidopsis circadian clock component PRR 7
inferredcites →https://doi.org/10.1126/science.1226339openalex-snapshot
Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals
inferredcites →https://doi.org/10.1126/science.290.5499.2110openalex-snapshot
Orchestrated Transcription of Key Pathways in Arabidopsis by the Circadian Clock
inferredcites →https://doi.org/10.1126/science.8197455openalex-snapshot
Jak-STAT Pathways and Transcriptional Activation in Response to IFNs and Other Extracellular Signaling Proteins
inferredcites →https://doi.org/10.1128/jb.01468-12openalex-snapshot
Genome Sequence of the Biocontrol Agent Microbacterium barkeri Strain 2011-R4
inferredcites →https://doi.org/10.1146/annurev-cellbio-100913-012908openalex-snapshot
Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution
inferredcites →https://doi.org/10.1146/annurev-genet-102209-163432openalex-snapshot
Circadian Control of Global Gene Expression Patterns
inferredcites →https://doi.org/10.1177/154405910408300516openalex-snapshot
Indian Hedgehog: A Mechanotransduction Mediator in Condylar Cartilage
inferredcites →https://doi.org/10.1186/1471-2105-13-328openalex-snapshot
Comparison of co-expression measures: mutual information, correlation, and model based indices
inferredcites →https://doi.org/10.1186/1471-2105-7-1openalex-snapshot
Fast-Find: A novel computational approach to analyzing combinatorial motifs
inferredcites →https://doi.org/10.1186/1471-2105-7-389openalex-snapshot
Fast index based algorithms and software for matching position specific scoring matrices
inferredcites →https://doi.org/10.1186/1752-0509-3-8openalex-snapshot
Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms
inferredcites →https://doi.org/10.1186/gb-2006-7-5-r36openalex-snapshot
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
inferredcites →https://doi.org/10.1186/gb-2011-12-8-r83openalex-snapshot
Cistrome: an integrative platform for transcriptional regulation studies
inferredcites →https://doi.org/10.1186/gb-2013-14-4-r36openalex-snapshot
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
inferredcites →https://doi.org/10.1186/s12859-016-0889-9openalex-snapshot
An individualized predictor of health and disease using paired reference and target samples
inferredcites →https://doi.org/10.1371/journal.pbio.0050008openalex-snapshot
Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles
inferredcites →https://doi.org/10.1371/journal.pgen.0040014openalex-snapshot
Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules
inferredcites →https://doi.org/10.1371/journal.pone.0012776openalex-snapshot
Inferring Regulatory Networks from Expression Data Using Tree-Based Methods
inferredcites →https://doi.org/10.1515/sagmb-2014-0082openalex-snapshot
CSI: a nonparametric Bayesian approach to network inference from multiple perturbed time series gene expression data
inferredcites →https://doi.org/10.2390/biecoll-jib-2008-91openalex-snapshot
MoRAine - A web server for fast computational transcription factor binding motif re-annotation
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.7554/elife.00675openalex-snapshot
Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis
inferredcites →https://doi.org/10.7916/d8g15zbpopenalex-snapshot
ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

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inferred← citeshttps://doi.org/10.1101/702183openalex-snapshot
Warm nights disrupt global transcriptional rhythms in field-grown rice panicles
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