ArticleGenome biology2006
Inferring transcriptional modules from ChIP-chip, motif and microarray data.
Article in Genome biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes.Nucleic acids research · 2019Article
- Associating expression and genomic data using co-occurrence measures.Biology direct · 2019Article
- MICRAT: a novel algorithm for inferring gene regulatory networks using time series gene expression data.BMC systems biology · 2018Article
- Gene regulatory network construction identified NFYA as a diffuse subtype-specific prognostic factor in gastric cancer.International journal of oncology · 2018Article
- Gene regulatory pattern analysis reveals essential role of core transcriptional factors' activation in triple-negative breast cancer.Oncotarget · 2017Article
- PyPanda: a Python package for gene regulatory network reconstruction.Bioinformatics (Oxford, England) · 2016Article
- Functional redundancy of transcription factors explains why most binding targets of a transcription factor are not affected when the transcription factor is knocked out.BMC systems biology · 2015Article
- A graphical model method for integrating multiple sources of genome-scale data.Statistical applications in genetics and molecular biology · 2013Article
- Computational methodology for ChIP-seq analysis.Quantitative biology (Beijing, China) · 2013Article
- Article
- Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection.BMC bioinformatics · 2013Article
- RMaNI: Regulatory Module Network Inference framework.BMC bioinformatics · 2013Article
- Cell-type specificity of ChIP-predicted transcription factor binding sites.BMC genomics · 2012Article
- Regulatory Snapshots: integrative mining of regulatory modules from expression time series and regulatory networks.PloS one · 2012Article
- Hierarchical modularity in ERα transcriptional network is associated with distinct functions and implicates clinical outcomes.Scientific reports · 2012Article
- DISCO-SCA and properly applied GSVD as swinging methods to find common and distinctive processes.PloS one · 2012Article
- Inferring a transcriptional regulatory network from gene expression data using nonlinear manifold embedding.PloS one · 2011Article
- The reconstruction of condition-specific transcriptional modules provides new insights in the evolution of yeast AP-1 proteins.PloS one · 2011Article
- Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data.BMC systems biology · 2010Article
- TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information.BMC bioinformatics · 2010Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
'ReMoDiscovery' is an intuitive algorithm to correlate regulatory programs with regulators and corresponding motifs to a set of co-expressed genes. It exploits in a concurrent way three independent data sources: ChIP-chip data, motif information and gene expression profiles. When compared to published module discovery algorithms, ReMoDiscovery is fast and easily tunable. We evaluated our method on yeast data, where it was shown to generate biologically meaningful findings and allowed the prediction of potential novel roles of transcriptional regulators.
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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.