ArticleBMC bioinformatics2013
MatrixCatch--a novel tool for the recognition of composite regulatory elements in promoters.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- BestCRM: An Exhaustive Search for Optimal Cis-Regulatory Modules in Promoters Accelerated by the Multidimensional Hash Function.International journal of molecular sciences · 2024Article
- Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks.International journal of molecular sciences · 2024Article
- Using Euf1 transcription factor as a titrator of erythritol-inducible promoters in Yarrowia lipolytica; insight into the structure, splicing, and regulation mechanism.FEMS yeast research · 2024Article
- Guidelines on the performance evaluation of motif recognition methods in bioinformatics.Frontiers in genetics · 2023Article
- Identification of functional tumor necrosis factor-alpha promoter variants associated withWorld journal of gastroenterology · 2022Observational
- First insights into the molecular basis association between promoter polymorphisms of the IL1B gene and Helicobacter pylori infection in the Sudanese population: computational approach.BMC microbiology · 2021Article
- An Intergenic rs9275596 Polymorphism on Chr. 6p21 Is Associated with Multiple Sclerosis in Latvians.Medicina (Kaunas, Lithuania) · 2020Article
- A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package.Nucleic acids research · 2019Article
- Removing Background Co-occurrences of Transcription Factor Binding Sites Greatly Improves the Prediction of Specific Transcription Factor Cooperations.Frontiers in genetics · 2018Article
- Structural and developmental expression of Ss-riok-2, an RIO protein kinase encoding gene of Strongyloides stercoralis.Scientific reports · 2017Article
- c-Jun Contributes to Transcriptional Control of GNA12 Expression in Prostate Cancer Cells.Molecules (Basel, Switzerland) · 2017Article
- Candidate SNP Markers of Gender-Biased Autoimmune Complications of Monogenic Diseases Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters.Frontiers in immunology · 2016Article
- Computational Detection of Stage-Specific Transcription Factor Clusters during Heart Development.Frontiers in genetics · 2016Article
- Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells.Frontiers in genetics · 2016Review
- PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information.BMC bioinformatics · 2015Article
- Obesity-related known and candidate SNP markers can significantly change affinity of TATA-binding protein for human gene promoters.BMC genomics · 2015Article
- Exploring features and function of Ss-riok-3, an enigmatic kinase gene from Strongyloides stercoralis.Parasites & vectors · 2014Article
- Practical aspects of genome-wide association interaction analysis.Human genetics · 2014Review
- Toward understanding the functional role of Ss-RIOK-1, a RIO protein kinase-encoding gene of Strongyloides stercoralis.PLoS neglected tropical diseases · 2014Article
- CisMiner: genome-wide in-silico cis-regulatory module prediction by fuzzy itemset mining.PloS one · 2014Article
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Authors and funding
6 authors.
Funding
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Abstract
backgroundAccurate recognition of regulatory elements in promoters is an essential prerequisite for understanding the mechanisms of gene regulation at the level of transcription. Composite regulatory elements represent a particular type of such transcriptional regulatory elements consisting of pairs of individual DNA motifs. In contrast to the present approach, most available recognition techniques are based purely on statistical evaluation of the occurrence of single motifs. Such methods are limited in application, since the accuracy of recognition is greatly dependent on the size and quality of the sequence dataset. Methods that exploit available knowledge and have broad applicability are evidently needed.
resultsWe developed a novel method to identify composite regulatory elements in promoters using a library of known examples. In depth investigation of regularities encoded in known composite elements allowed us to introduce a new characteristic measure and to improve the specificity compared with other methods. Tests on an established benchmark and real genomic data show that our method outperforms other available methods based either on known examples or statistical evaluations. In addition to better recognition, a practical advantage of this method is first the ability to detect a high number of different types of composite elements, and second direct biological interpretation of the identified results. The program is available at http://gnaweb.helmholtz-hzi.de/cgi-bin/MCatch/MatrixCatch.pl and includes an option to extend the provided library by user supplied data.
conclusionsThe novel algorithm for the identification of composite regulatory elements presented in this paper was proved to be superior to existing methods. Its application to tissue specific promoters identified several highly specific composite elements with relevance to their biological function. This approach together with other methods will further advance the understanding of transcriptional regulation of genes.
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