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Detection and interpretation of metabolite–transcript coresponses using combined profiling data

https://doi.org/10.1093/bioinformatics/btr231
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What this work says

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

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Rheostat Control of Gene Expression by Metabolites
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Expression dynamics of a cellular metabolic network
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Parallel analysis of transcript and metabolic profiles: a new approach in systems biology
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Global expression profiling of sulfur‐starved Arabidopsis by DNA macroarray reveals the role of O‐acetyl‐ l ‐serine as a general regulator of gene expression in response to sulfur nutrition
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Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana
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Elucidation of Gene-to-Gene and Metabolite-to-Gene Networks inArabidopsis by Integration of Metabolomics andTranscriptomics
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Timing of Gene Expression Responses to Environmental Changes
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Metabolic Pathway Relationships Revealed by an Integrative Analysis of the Transcriptional and Metabolic Temperature Stress-Response Dynamics in Yeast
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Dynamics of Time-Lagged Gene-to-Metabolite Networks of Escherichia coli Elucidated by Integrative Omics Approach
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Using hidden Markov models to analyze gene expression time course data
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Observing and interpreting correlations in metabolomic networks
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The Graphical Query Language: a tool for analysis of gene expression time-courses
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Constrained mixture estimation for analysis and robust classification of clinical time series
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Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions
inferredcites →https://doi.org/10.1093/nar/gkl783openalex-snapshot
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis
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Regulation of Sulfur-Responsive Gene Expression by Exogenously Applied Cytokinins in Arabidopsis thaliana
inferredcites →https://doi.org/10.1104/pp.104.052142openalex-snapshot
Exploring the Temperature-Stress Metabolome of Arabidopsis
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Integrated Analysis of Metabolite and Transcript Levels Reveals the Metabolic Shifts That Underlie Tomato Fruit Development and Highlight Regulatory Aspects of Metabolic Network Behavior
inferredcites →https://doi.org/10.1105/tpc.109.068791openalex-snapshot
Efficient Operation of NAD(P)H Dehydrogenase Requires Supercomplex Formation with Photosystem I via Minor LHCI in Arabidopsis
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A tutorial on hidden Markov models and selected applications in speech recognition
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Analyzing Gene Expression Time-Courses
inferredcites →https://doi.org/10.1111/j.1365-313x.2007.03100.xopenalex-snapshot
Transcript and metabolite profiling during cold acclimation of Arabidopsis reveals an intricate relationship of cold‐regulated gene expression with modifications in metabolite content
inferredcites →https://doi.org/10.1111/j.1365-313x.2007.03293.xopenalex-snapshot
Data integration in plant biology: the O2PLS method for combined modeling of transcript and metabolite data
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A Test Case of Correlation Metric Construction of a Reaction Pathway from Measurements
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Orchestrated Transcription of Key Pathways in Arabidopsis by the Circadian Clock
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AtPIN: Arabidopsis thaliana Protein Interaction Network
inferredcites →https://doi.org/10.1186/1471-2105-11-214openalex-snapshot
Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis
inferredcites →https://doi.org/10.1186/1471-2105-7-203openalex-snapshot
Integrative investigation of metabolic and transcriptomic data
inferredcites →https://doi.org/10.1186/1471-2105-8-454openalex-snapshot
Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana
inferredcites →https://doi.org/10.1186/1752-0509-4-177openalex-snapshot
Individual vs. combinatorial effect of elevated CO2 conditions and salinity stress on Arabidopsis thaliana liquid cultures: Comparing the early molecular response using time-series transcriptomic and metabolomic analyses
inferredcites →https://doi.org/10.1186/gb-2006-7-8-r76openalex-snapshot
Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsisrosettes
inferredcites →https://doi.org/10.1371/journal.pcbi.1000270openalex-snapshot
Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces cerevisiae

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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