ArticleGenomics, proteomics & bioinformatics2008
Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoter.
Article in Genomics, proteomics & bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed, 13 citations in OpenAlex.
- Identification of Genes Crucial for Biological Processes in Breast Cancer Liver Metastasis Relapse.International journal of molecular sciences · 2024Article
- Non-canonical RNA-DNA differences and other human genomic features are enriched within very short tandem repeats.PLoS computational biology · 2020Article
- TransmiR v2.0: an updated transcription factor-microRNA regulation database.Nucleic acids research · 2019Article
- HOP expression is regulated by p53 and RAS and characteristic of a cancer gene signature.Cell stress & chaperones · 2017Article
- Identification of candidate transcription factor binding sites in the cattle genome.Genomics, proteomics & bioinformatics · 2013Article
- Article
- MIRTFnet: analysis of miRNA regulated transcription factors.PloS one · 2011Article
- A retrospective review of the roles of multifunctional glucose-6-phosphatase in blood glucose homeostasis: Genesis of the tuning/retuning hypothesis.Life sciences · 2010Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 3 institutions in 1 country.
Funding
Abstract
A systematic phylogenetic footprinting approach was performed to identify conserved transcription factor binding sites (TFBSs) in mammalian promoter regions using human, mouse and rat sequence alignments. We found that the score distributions of most binding site models did not follow the Gaussian distribution required by many statistical methods. Therefore, we performed an empirical test to establish the optimal threshold for each model. We gauged our computational predictions by comparing with previously known TFBSs in the PCK1 gene promoter of the cytosolic isoform of phosphoenolpyruvate carboxykinase, and achieved a sensitivity of 75% and a specificity of approximately 32%. Almost all known sites overlapped with predicted sites, and several new putative TFBSs were also identified. We validated a predicted SP1 binding site in the control of PCK1 transcription using gel shift and reporter assays. Finally, we applied our computational approach to the prediction of putative TFBSs within the promoter regions of all available RefSeq genes. Our full set of TFBS predictions is freely available at http://bfgl.anri.barc.usda.gov/tfbsConsSites.
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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.