ArticleGenome research2013
P-value-based regulatory motif discovery using positional weight matrices.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers, 2 of them syntheses that pooled it.
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Who cites it
36 citing papers in PubMed, 2 syntheses or guidelines pooled it, 69 citations in OpenAlex.
- FH535, a β-catenin pathway inhibitor, represses pancreatic cancer xenograft growth and angiogenesis.Oncotarget · 2016Pooled it
- Gene regulatory mechanisms underpinning prostate cancer susceptibility.Nature genetics · 2016Pooled it
- A weighted two-stage sequence alignment framework to identify motifs from ChIP-exo data.Patterns (New York, N.Y.) · 2024Article
- Identification of DNA motif pairs on paired sequences based on composite heterogeneous graph.Frontiers in genetics · 2024Article
- CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq.Briefings in bioinformatics · 2023Article
- A survey on algorithms to characterize transcription factor binding sites.Briefings in bioinformatics · 2023Review
- Structural remodeling of AAA+ ATPase p97 by adaptor protein ASPL facilitates posttranslational methylation by METTL21D.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Large-scale analysis of Drosophila core promoter function using synthetic promoters.Molecular systems biology · 2022Article
- Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data.Briefings in bioinformatics · 2022Article
- Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins.Bioinformatics (Oxford, England) · 2021Article
- Accurate prediction ofNAR genomics and bioinformatics · 2021Article
- Perspectives of CRISPR/Cas-mediatedHorticulture research · 2020Review
- ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery.Bioinformatics (Oxford, England) · 2019Article
- FisherMP: fully parallel algorithm for detecting combinatorial motifs from large ChIP-seq datasets.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- The APT complex is involved in non-coding RNA transcription and is distinct from CPF.Nucleic acids research · 2018Article
- MODSIDE: a motif discovery pipeline and similarity detector.BMC genomics · 2018Article
- The BaMM web server for de-novo motif discovery and regulatory sequence analysis.Nucleic acids research · 2018Article
- SamSelect: a sample sequence selection algorithm for quorum planted motif search on large DNA datasets.BMC bioinformatics · 2018Article
- Systems and Synthetic Biology Approaches to Engineer Fungi for Fine Chemical Production.Frontiers in bioengineering and biotechnology · 2018Review
- Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network.The Plant cell · 2017Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To analyze gene regulatory networks, the sequence-dependent DNA/RNA binding affinities of proteins and noncoding RNAs are crucial. Often, these are deduced from sets of sequences enriched in factor binding sites. Two classes of computational approaches exist. The first describe binding motifs by sequence patterns and search the patterns with highest statistical significance for enrichment. The second class uses the more powerful position weight matrices (PWMs). Instead of maximizing the statistical significance of enrichment, they maximize a likelihood. Here we present XXmotif (eXhaustive evaluation of matriX motifs), the first PWM-based motif discovery method that can optimize PWMs by directly minimizing their P-values of enrichment. Optimization requires computing millions of enrichment P-values for thousands of PWMs. For a given PWM, the enrichment P-value is calculated efficiently from the match P-values of all possible motif placements in the input sequences using order statistics. The approach can naturally combine P-values for motif enrichment, conservation, and localization. On ChIP-chip/seq, miRNA knock-down, and coexpression data sets from yeast and metazoans, XXmotif outperformed state-of-the-art tools, both in numbers of correctly identified motifs and in the quality of PWMs. In segmentation modules of D. melanogaster, we detect the known key regulators and several new motifs. In human core promoters, XXmotif reports most previously described and eight novel motifs sharply peaked around the transcription start site, among them an Initiator motif similar to the fly and yeast versions. XXmotif's sensitivity, reliability, and usability will help to leverage the quickly accumulating wealth of functional genomics data.
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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.