ArticleBMC bioinformatics2007
A comparative study of S/MAR prediction tools.
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 13 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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Who cites it
13 citing papers in PubMed.
- In Vivo Selection of S/MAR Sequences to Favour AAV Episomal Maintenance in Dividing Cells.International journal of molecular sciences · 2024Article
- Genome-wide mapping of matrix attachment regions in Drosophila melanogaster.BMC genomics · 2014Article
- Myc-induced anchorage of the rDNA IGS region to nucleolar matrix modulates growth-stimulated changes in higher-order rDNA architecture.Nucleic acids research · 2014Article
- In vivo mapping of arabidopsis scaffold/matrix attachment regions reveals link to nucleosome-disfavoring poly(dA:dT) tracts.The Plant cell · 2014Article
- Relationship between DNA replication and the nuclear matrix.Genes to cells : devoted to molecular & cellular mechanisms · 2013Review
- Transposable element 'roo' attaches to nuclear matrix of the Drosophila melanogaster.Journal of insect science (Online) · 2013Article
- Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites.Nucleic acids research · 2012Article
- High-level transgene expression by homologous recombination-mediated gene transfer.Nucleic acids research · 2011Article
- Identification of Scaffold/Matrix Attachment (S/MAR) like DNA element from the gastrointestinal protozoan parasite Giardia lamblia.BMC genomics · 2010Article
- Determination of the in vivo structural DNA loop organization in the genomic region of the rat albumin locus by means of a topological approach.DNA research : an international journal for rapid publication of reports on genes and genomes · 2010Article
- Strand bias structure in mouse DNA gives a glimpse of how chromatin structure affects gene expression.BMC genomics · 2008Article
- Association of the matrix attachment region recognition signature with coding regions in Caenorhabditis elegans.BMC genomics · 2007Article
- Regulatory Elements in Vectors for Efficient Generation of Cell Lines Producing Target Proteins.Acta naturaeArticle
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
backgroundS/MARs are regions of the DNA that are attached to the nuclear matrix. These regions are known to affect substantially the expression of genes. The computer prediction of S/MARs is a highly significant task which could contribute to our understanding of chromatin organisation in eukaryotic cells, the number and distribution of boundary elements, and the understanding of gene regulation in eukaryotic cells. However, while a number of S/MAR predictors have been proposed, their accuracy has so far not come under scrutiny.
resultsWe have selected S/MARs with sufficient experimental evidence and used these to evaluate existing methods of S/MAR prediction. Our main results are: 1.) all existing methods have little predictive power, 2.) a simple rule based on AT-percentage is generally competitive with other methods, 3.) in practice, the different methods will usually identify different sub-sequences as S/MARs, 4.) more research on the H-Rule would be valuable.
conclusionA new insight is needed to design a method which will predict S/MARs well. Our data, including the control data, has been deposited as additional material and this may help later researchers test new predictors.
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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.