ArticleGenome research2008
Ab initio identification of functionally interacting pairs of cis-regulatory elements.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed, 17 citations in OpenAlex.
- Loss of LUC7L2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS.Molecular cell · 2021Article
- The combinatorial control of alternative splicing in C. elegans.PLoS genetics · 2017Article
- CoSREM: a graph mining algorithm for the discovery of combinatorial splicing regulatory elements.BMC bioinformatics · 2015Article
- Pick one, but be quick: 5' splice sites and the problems of too many choices.Genes & development · 2013Review
- A biophysical model for identifying splicing regulatory elements and their interactions.PloS one · 2013Article
- Quantitative evaluation of all hexamers as exonic splicing elements.Genome research · 2011Article
- Networking in a global world: establishing functional connections between neural splicing regulators and their target transcripts.RNA (New York, N.Y.) · 2011Review
- A network of conserved co-occurring motifs for the regulation of alternative splicing.Nucleic acids research · 2010Article
- Intronic motif pairs cooperate across exons to promote pre-mRNA splicing.Genome biology · 2010Article
- Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts.Genome research · 2009Article
- Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Cooperatively acting pairs of cis-regulatory elements play important roles in many biological processes. Here, we describe a statistical approach, compositionally orthogonalized co-occurrence analysis (coCOA) that detects pairs of oligonucleotides that preferentially co-occur in pairs of sequence regions, controlling for correlations between the compositions of the analyzed regions. coCOA identified three clusters of oligonucleotide pairs that frequently co-occur at 5' and 3' ends of human and mouse introns. The largest cluster involved GC-rich sequences at the 5' ends of introns that co-occur and are co-conserved with specific AU-rich sequences near intron 3' ends. These motifs are preferentially conserved when they occur together, as measured by a new co-conservation measure, supporting common in vivo function. These motif pairs are also enriched in introns flanking alternative "cassette" exons, suggesting a role in silencing of intervening exons, and we showed that these motifs can cooperatively silence splicing of an intervening exon in a splicing reporter assay. This approach can be easily generalized to problems beyond RNA splicing.
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What OpenQuestion holds
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.