ArticleBMC bioinformatics2007
Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 16 citations in OpenAlex.
- MicroSalmon: A Comprehensive, Searchable Resource of Predicted MicroRNA Targets and 3'UTR Cis-Regulatory Elements in the Full-Length Sequenced Atlantic Salmon Transcriptome.Non-coding RNA · 2021Article
- Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures.BMC bioinformatics · 2014Article
- Specific miRNA stabilization by Gld2-catalyzed monoadenylation.Cell reports · 2012Article
- CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse.BMC bioinformatics · 2010Article
- Identification of functional TFAP2A and SP1 binding sites in new TFAP2A-modulated genes.BMC genomics · 2010Article
- Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium.BMC evolutionary biology · 2010Article
- Sequence context outside the target region influences the effectiveness of miR-223 target sites in the RhoB 3'UTR.Nucleic acids research · 2010Article
- Genome-wide survey of microRNA-transcription factor feed-forward regulatory circuits in human.Molecular bioSystems · 2009Article
- Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells.DNA research : an international journal for rapid publication of reports on genes and genomes · 2009Article
- Prediction of human miRNAs using tissue-selective motifs in 3' UTRs.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- RNA landscape of evolution for optimal exon and intron discrimination.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Over-represented sequences located on 3' UTRs are potentially involved in regulatory functions.RNA biologyArticle
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4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
background3' untranslated regions (3' UTRs) contain binding sites for many regulatory elements, and in particular for microRNAs (miRNAs). The importance of miRNA-mediated post-transcriptional regulation has become increasingly clear in the last few years.
resultsWe propose two complementary approaches to the statistical analysis of oligonucleotide frequencies in mammalian 3' UTRs aimed at the identification of candidate binding sites for regulatory elements. The first method is based on the identification of sets of genes characterized by evolutionarily conserved overrepresentation of an oligonucleotide. The second method is based on the identification of oligonucleotides showing statistically significant strand asymmetry in their distribution in 3' UTRs.
conclusionBoth methods are able to identify many previously known binding sites located in 3'UTRs, and in particular seed regions of known miRNAs. Many new candidates are proposed for experimental verification.
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