ArticleNucleic acids research2004
Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data.Algorithms for molecular biology : AMB · 2016Article
- From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach.PloS one · 2015Article
- Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells.Nature · 2014Article
- Mapping the human toxome by systems toxicology.Basic & clinical pharmacology & toxicology · 2014Review
- Non-coding RNA regulation in pathogenic bacteria located inside eukaryotic cells.Frontiers in cellular and infection microbiology · 2014Review
- OncoCis: annotation of cis-regulatory mutations in cancer.Genome biology · 2014Article
- The stress response factors Yap6, Cin5, Phd1, and Skn7 direct targeting of the conserved co-repressor Tup1-Ssn6 in S. cerevisiae.PloS one · 2011Article
- Article
- Sequence features that drive human promoter function and tissue specificity.Genome research · 2010Article
- TaNF-YC11, one of the light-upregulated NF-YC members in Triticum aestivum, is co-regulated with photosynthesis-related genes.Functional & integrative genomics · 2010Article
- Comparative pathogenesis and systems biology for biodefense virus vaccine development.Journal of biomedicine & biotechnology · 2010Review
- Identifying significant genetic regulatory networks in the prostate cancer from microarray data based on transcription factor analysis and conditional independency.BMC medical genomics · 2009Article
- Inferring Transcriptional Interactions by the Optimal Integration of ChIP-chip and Knock-out Data.Bioinformatics and biology insights · 2009Article
- Statistical identification of gene association by CID in application of constructing ER regulatory network.BMC bioinformatics · 2009Article
- MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Transcription factor network reconstruction using the living cell array.Journal of theoretical biology · 2009Article
- Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics.PLoS computational biology · 2008Article
- One hub-one process: a tool based view on regulatory network topology.BMC systems biology · 2008Article
- Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia.Genome biology · 2008Article
- Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors.BMC genomics · 2007Article
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3 authors.
Funding
Abstract
We have developed a computational method for transcriptional regulatory network inference, CARRIE (Computational Ascertainment of Regu latory Relationships Inferred from Expression), which combines microarray and promoter sequence analysis. CARRIE uses sources of data to identify the transcription factors (TFs) that regulate gene expression changes in response to a stimulus and generates testable hypotheses about the regulatory network connecting these TFs to the genes they regulate. The promoter analysis component of CARRIE, ROVER (Relative OVER-abundance of cis-elements), is highly accurate at detecting the TFs that regulate the response to a stimulus. ROVER also predicts which genes are regulated by each of these TFs. CARRIE uses these transcriptional interactions to infer a regulatory network. To demonstrate our method, we applied CARRIE to six sets of publicly available DNA microarray experiments on Saccharomyces cerevisiae. The predicted networks were validated with comparisons to literature sources, experimental TF binding data, and gene ontology biological process information.
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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.