ArticleGenome research2005
Discovering functional transcription-factor combinations in the human cell cycle.
Article in Genome research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 89 citations in OpenAlex.
- Transcription factor interactions explain the context-dependent activity of CRX binding sites.PLoS computational biology · 2024Article
- DrivAER: Identification of driving transcriptional programs in single-cell RNA sequencing data.GigaScience · 2020Article
- Fluctuating-rate model with multiple gene states.Journal of mathematical biology · 2020Article
- Genome-wide pathogenesis interpretation using a heat diffusion-based systems genetics method and implications for gene function annotation.Molecular genetics & genomic medicine · 2020Article
- Evolutionary conservation of MLO gene promoter signatures.BMC plant biology · 2019Article
- coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers.PLoS computational biology · 2018Article
- TIGERi: modeling and visualizing the responses to perturbation of a transcription factor network.BMC bioinformatics · 2017Article
- SWIM: a computational tool to unveiling crucial nodes in complex biological networks.Scientific reports · 2017Article
- PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information.BMC bioinformatics · 2015Article
- Characterization and identification of cis-regulatory elements in Arabidopsis based on single-nucleotide polymorphism information.Plant physiology · 2014Article
- Statistical significance of combinatorial regulations.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Targeting the Y/CCAAT box in cancer: YB-1 (YBX1) or NF-Y?Cell death and differentiation · 2013Review
- Functional analysis of transcription factor binding sites in human promoters.Genome biology · 2012Article
- Transcriptional modulation induced by ionizing radiation: p53 remains a central player.Molecular oncology · 2011Review
- Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data.Genome research · 2011Article
- Simplified method to predict mutual interactions of human transcription factors based on their primary structure.PloS one · 2011Article
- Comparative analysis of MTF-1 binding sites between human and mouse.Mammalian genome : official journal of the International Mammalian Genome Society · 2010Article
- NF-YC complexity is generated by dual promoters and alternative splicing.The Journal of biological chemistry · 2009Article
- A protein-protein interaction guided method for competitive transcription factor binding improves target predictions.Nucleic acids research · 2009Article
- Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data.Nucleic acids research · 2009Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the completion of full genome sequences and advancement in high-throughput technologies, in silico methods have been successfully used to integrate diverse data sources toward unraveling the combinatorial nature of transcriptional regulation. So far, almost all of these studies are restricted to lower eukaryotes such as budding yeast. We describe here a computational search for functional transcription-factor (TF) combinations using phylogenetically conserved sequences and microarray-based expression data. Taking into account both orientational and positional constraints, we investigated the overrepresentation of binding sites in the vicinity of one another and whether these combinations result in more coherent expression profiles. Without any prior biological knowledge, the search led to the discovery of several experimentally established TF associations, as well as some novel ones. In particular, we identified a regulatory module controlling cell cycle-dependent transcription of G2-M genes and expanded its functional generality. We also detected many homotypic combinations, supporting the importance of binding-site density in transcriptional regulation of higher eukaryotes.
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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.